plants
Review

Management and Utilization of Plant Genetic Resources for a
Sustainable Agriculture
Ranjith Pathirana 1,2, * and Francesco Carimi 3
1

2

3

*

Citation: Pathirana, R.; Carimi, F.
Management and Utilization of Plant
Genetic Resources for a Sustainable
Agriculture. Plants 2022, 11, 2038.
https://doi.org/10.3390/
plants11152038
Academic Editors: Milan S.

Plant & Food Research Australia Pty Ltd., Waite Campus Research Precinct—Plant Breeding WT46,
University of Adelaide, Waite Rd, Urrbrae, SA 5064, Australia
School of Agriculture, Food and Wine, Waite Campus Research Precinct—Plant Breeding WT46,
University of Adelaide, Waite Rd, Urrbrae, SA 5064, Australia
Istituto di Bioscienze e BioRisorse (IBBR), C.N.R., Corso Calatafimi 414, 90129 Palermo, Italy
Correspondence: ranjith.pathirana@adelaide.edu.au

Abstract: Despite the dramatic increase in food production thanks to the Green Revolution, hunger isincreasing among human populations around the world, affecting one in nine people. The negativeenvironmental and social consequences of industrial monocrop agriculture is becoming evident,
particularly in the contexts of greenhouse gas emissions and the increased frequency and impact of
zoonotic disease emergence, including the ongoing COVID-19 pandemic. Human activity has altered
70–75% of the ice-free Earth’s surface, squeezing nature and wildlife into a corner. To prevent, halt,
and reverse the degradation of ecosystems worldwide, the UN has launched a Decade of Ecosystem
Restoration. In this context, this review describes the origin and diversity of cultivated species, theimpact of modern agriculture and other human activities on plant genetic resources, and approaches
to conserve and use them to increase food diversity and production with specific examples of the useof crop wild relatives for breeding climate-resilient cultivars that require less chemical and mechanicalinput. The need to better coordinate in situ conservation efforts with increased funding has beenhighlighted. We emphasise the need to strengthen the genebank infrastructure, enabling the use ofmodern biotechnological tools to help in genotyping and characterising accessions plus advanced
ex situ conservation methods, identifying gaps in collections, developing core collections, and linking
data with international databases. Crop and variety diversification and minimising tillage and otherfield practices through the development and introduction of herbaceous perennial crops is proposed
as an alternative regenerative food system for higher carbon sequestration, sustaining economic
benefits for growers, whilst also providing social and environmental benefits.

Stankovic, Paula Baptista andPetronia Carillo
Received: 29 June 2022

Keywords: centres of origin; crop wild relatives; crop domestication; cryopreservation; genebank;conservation; in vitro storage; germplasm; ecosystem restoration; plant breeding; climate change

Accepted: 1 August 2022
Published: 4 August 2022
Publisher’s Note: MDPI stays neutral
with regard to jurisdictional claims inpublished maps and institutional affiliations.

Copyright: © 2022 by the authors.
Licensee MDPI, Basel, Switzerland.
This article is an open access article
distributed under the terms andconditions of the Creative Commons
Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

1. Introduction
With the global population expected to reach 9 billion by the middle of this century
and the land area available for food production stagnating, or even reducing, the challengeof global food security is ever increasing. Almost one out of every nine people in theworld suffers from hunger, and the number of hungry people is growing, albeit slowly [1].
The 2030 Agenda for Sustainable Development puts forward a transformational vision
recognizing that our world is changing, bringing with it new challenges that must be
overcome if we are to live in a world without hunger, food insecurity, and malnutritionin any of its forms. More than 820 million people in the world go hungry today, up from784 million in 2015, emphasising the immense challenge of achieving the United Nations
Zero Hunger target by 2030 [2]. Hunger is rising in almost all subregions of Africa and,to a lesser extent, in Latin America and Western Asia. It is heartening to see progress inSouthern Asia in the last 5 years, but the prevalence of undernourishment in this subregion

Plants 2022, 11, 2038. https://doi.org/10.3390/plants11152038

https://www.mdpi.com/journal/plants

Plants 2022, 11, 2038

2 of 36is still the highest in Asia. Another disturbing scenario is the fact that about 2 billion people
in the world experience moderate to severe food insecurity, thus experiencing greater risk ofmalnutrition and poor health. With the drop in economic growth, food access disruptions,increasing unemployment, rising food costs, and exacerbated poverty, food insecurity willaffect a further 83–132 million people [3].
Concurrently with some regions of the global population increasingly experiencing
hunger, around one million animal and plant species are threatened with extinction purely
because of human activity—many within decades [4]. Even though natural ecosystemservices are critical for our survival—providing oxygen, regulating weather patterns,
pollinating our crops, and providing us with food, fibre, and feed for livestock—humanactivity has altered 70–75% of the global ice-free Earth’s surface [5], squeezing natural
ecosystems into an ever-decreasing corner of the planet. The health of ecosystems on
which we and all other species depend is deteriorating more rapidly than ever, affecting
the very foundations of our economies, livelihoods, food security, health, and quality oflife worldwide.
Using a data harmonisation procedure to reduce uncertainties in satellite-based land
cover maps, Song [6] estimated the annual value of the world’s total terrestrial ecosystemservices at USD 49.4 trillion. Land and its biodiversity also represent essential, intangible
benefits to humans, such as cognitive and spiritual enrichment, a sense of belonging, andaesthetic and recreational values. Valuing ecosystem services with economic methods
often overlooks these intangible services that shape societies, cultures, and quality of life,
as well as the intrinsic value of biodiversity. The Earth’s land area is finite. Using land
resources sustainably is fundamental to human well-being. Despite commitments made in2010, biodiversity has further declined in the past decade [7]. To prevent, halt, and reverse
the degradation of ecosystems worldwide, the UN has launched a Decade of Ecosystem
Restoration (2021–2030). This action plan is globally coordinated through the governing
body of the Convention on Biological Diversity and is in response to a call from scientists,
as articulated in the Special Report on Climate Change and Land of the Intergovernmental
Panel on Climate Change, the Rio Conventions on Climate Change and Biodiversity, andthe UN Convention to Combat Desertification. This new draft for the post-2020 Global
Biodiversity Framework comprises 21 targets and 10 milestones [8].
The Green Revolution aimed to resolve the global food crisis through breeding cultivars for mechanized monocultures with high inputs of pesticides and fertilizers. Although
the increased yield helped to save the cultivation of an estimated 17.9–26.7 million hectaresof new land under crops [9], the resulting increase in food production during the past
five decades was accompanied by environmental degradation and deficiency in micronutrients in populations [10]. Furthermore, there is strong evidence that modern farming
practices and intensified systems may be linked to disease emergence and amplification.
There are many examples of zoonotic disease emerging at the wildlife–livestock–humaninterface which are associated with agricultural intensification and environmental change,such as habitat fragmentation and ecotones, reduced biodiversity, agricultural changes,
and increasing human density in ecosystems [11,12], including Ebola virus [13,14] andrecently, COVID-19 [15]. It is now clear that, as predicted by Borlaug in his acceptancespeech for the Nobel Peace Prize (1970), further actions are needed to resolve the worsening
environmental and social crises limiting food production and planetary health.
We have seen unprecedented levels of global warming since the beginning of theindustrial era. Modelling has shown that each degree in temperature rise would causea drop in crop production of 7.4% for corn, 6% for wheat, 3.2% for rice, and 3.1% forsoybean [16]. This is significant because these four crops provide two-thirds of the humancaloric intake. It is not only production, but also the quality of food that is at stake.
Increased temperature and, to a lesser extent, increased atmospheric CO2 , will affect soil
biogeochemical processes by altering microbial community dynamics and activity, andgeochemical reactions. This will result in alterations of ionic composition of the rhizosphere,
hence affecting their uptake by crop plants. For example, it has been shown that futurePlants 2022, 11, 2038

3 of 36

conditions will likely lead to a greater proportion of the more toxic form of arsenic, porewater arsenite, in the rhizosphere of Asian and Californian rice soils. Simulating these
conditions under controlled environmental conditions, Muehe et al. [17] showed thatelevated temperatures not only reduced rice yield by 39%, but also increased the amount of
inorganic arsenic twofold in rice grain. Arsenic accumulation in rice is already becoming
a problem in many South and Southeast Asian countries [18,19]. Therefore, agriculture
requires more resilient varieties that can address likely problems induced by climate change;
germplasm collections hold the key to developing such cultivars.
In broad terms, germplasm is the diversity of a cultivated species and its wild relatives
that can hybridise and produce fertile progeny. Germplasm is of great importance for plant
breeding because it carries genes that have potential value for improving crop yield, quality,
and adaptation to the environment, including biotic and abiotic stresses. Thus, recognising
the increasing frequency of natural disasters affecting the agricultural sector and theirimpact on food security, the introduction of longer-term measures to increase farmers’
and households’ resilience to natural disasters and climate change, such as the promotionof drought-tolerant crops and varieties, and livelihood diversification, is important. It
is in this context that this paper on genetic diversity of cultivated species is presented,
discussing the current situation and possible response options to contribute positively tosustainable development.
2. Origin of Cultivated Species and Geographic Distribution of Crop Diversity
Although the first land plants, the embryophytes, appeared some 515–470 million
years ago in the Middle Cambrian–Early Ordovician period [20], humans who domesticatedplants appeared much later, just 195,000–160,000 years ago and migrated from Africa about
130,000–120,000 years ago [21]. They were roaming the wild as hunter–gatherers, relying
on wild plants and hunting wild animals for their food for another ~110,000 years before
they settled to cultivate plants and rear animals in the Neolithic period—the start ofthe domestication of species (Table 1). Thanks to plant domestication and the resulting
availability of food, humans became the predominant, most successful species on Earth,with a subsequent population explosion (Table 1) that demanded for more and more food.
Table 1. Evolutionary timescale of life on land illustrating that crop domestication is a very recent
event compared with evolution of land plants. mya—million years ago, ya—years ago. Data frommultiple sources referred in text.
Time in History

Event515–470 mya

First land plants

350 mya

Emergence of angiosperms

160 mya

Monocots separated from dicots

6.5 mya

Hominids appear

2 mya

Homo habilis

1.75 mya

Homo erectus

195,000–160,000 ya

Homo sapiens

130,000–120,000 ya

Human migration out of Africa

13,000 ya

Settled agriculture and beginning of crop domestication

2.1. Vavilov’s Centres of Origin of Cultivated Plants and the Theory of Homologous Seriesof Variation
The domestication of crops took place independently in eight geographic regions,described by Nikolai Vavilov [22] as primary centres of origin of cultivated plants in
1926 (Figure 1, Table 2). The criteria for these centres were high varietal diversity of thecrop, presence of wild ancestors along with the domesticated ones, and a long history2.1. Vavilov’s Centres of Origin of Cultivated Plants and the Theory of Homologous Series of
Variation
Plants 2022, 11, 2038

The domestication of crops took place independently in eight geographic regions,
4 of 36
described by Nikolai Vavilov [22] as primary centres of origin of cultivated plants in 1926
(Figure 1, Table 2). The criteria for these centres were high varietal diversity of the crop,presence of wild ancestors along with the domesticated ones, and a long history of theof the crop in the region. Vavilov was the first to observe that diversity of cultivatedcrop in the region. Vavilov was the first to observe that diversity of cultivated plants wasplants was not distributed equally around the world, but was associated with ancient
not distributed equally around the world, but was associated with ancient civilisations. It
civilisations. It was in the 1920s that he recognised the existence of these centres andwas in the 1920s that he recognised the existence of these centres and started collecting
started collecting germplasm through numerous expeditions [23,24]. He established the
germplasm through numerous expeditions [23,24]. He established the world’s first geneworld’s first genebank in Petrograd (Saint Petersburg), with branches across the Sovietbank in Petrograd (Saint Petersburg), with branches across the Soviet Union where almost
Union where almost any crop could be grown because of the vastness and diverse climatic
any crop could be grown because of the vastness and diverse climatic zones in the country.
zones in the country. The current status of this genebank and its activities are described by
The current status of this genebank and its activities are described by Dzyubenko [25].
Dzyubenko [25].

FigureFigure 1.
1. Eight
Eight main
main centres
centres of thethe origin
origin of cultivated plants according to Nikolai Vavilov (inset).
1. Mexico–Guatemala,Mexico–Guatemala,2.2.Peru–Ecuador–Bolivia,
Peru–Ecuador–Bolivia,2A.
2A.Southern
SouthernChile,
Chile,
2B.
Southern
Brazil,3. Medi1.
2B.
Southern
Brazil,3. Mediterterranean,
4. Middle
East,
Ethiopia,
CentralAsia,
Asia,7.7.Indo-Burma,
Indo-Burma,7A.
7A.Siam–Malaya–Java,
Siam–Malaya–Java, andandranean,4. Middle
East,
5. 5.
Ethiopia,
6. 6.Central
8. China
China andand Korea.
Korea.
8.

During his
his study
study ofof cultivatedcultivated plants
plants andand wild species, Vavilov
Vavilov noted
noted regularities
regularities ofof
Duringgenotypical andand phenotypicalphenotypical variation
variation within
within thethe polymorphism
polymorphism between
between related
related species
species
genotypicalof thethe samesame genus,
genus, between
between species in related plant genera of the same family,family, oror evenevenofbetween close
close families
families [26].
[26]. The first law ofof homologous
homologous series
series ofof variation
variation statesstates that
that
between“closelyallied
alliedLinnean
Linneanspecies
speciesare
arecharacterized
characterizedbybysimilar
similarand
andparallel
parallelseries
seriesofofvariation;
variation;and,“closely
and,
asas
a
rule,
thethenearera rule,nearerthese
theseLinneons
Linneonsare
aregenetically,
genetically,thethemoremoreprecise
preciseisisthe
thesimilarity
similarityofofmorphologicalmorphologicalandand physiologicalphysiological variability.
variability. Genetically
Genetically nearly
nearly related
related Linneons
Linneons have
have consequently
consequently similar
similar series
seriesofof hereditary
hereditary variation”.
variation”. As a sequence to the first law,
law, thethe second
second law
law statesstates thatthat “not“not only
only
geneticallygenetically closely
closely related
related Linnean
Linnean species,
species, but
but also
also closely
closely allied
allied genera,
genera, display
display similarity
similarity inin theirtheirseriesvariability”.
Thanksto tothisdiscovery,
the thevariation
series ofofphenotypical,
phenotypical,asaswellwellasasgenotypical,
genotypical,
variability”.
Thanksthis
discovery,variawithinalessstudiedspeciescanbepredicted
ifthevariabilityofarelatedspeciesisknown.
tion within a less studied species can be predicted if the variability of a related speciesisVoigt [27] has illustrated practical examples of the use of such predictions by Vavilov inplant breeding.
Such parallelism has been observed in recent molecular analyses of related crop
species, for example, in resequenced Brassica rapa and B. oleracea [28]. Understanding of
the existence of such parallelism is important in plant breeding because if a variant is

Plants 2022, 11, 2038

5 of 36

predicted to be present, the required genotype can be found through hybridisation andselection in segregating populations or using mutagenic techniques [29,30]. Use of induced
mutations to produce semi-dwarf rice mutants in Japonica and Javonica backgrounds in
California [31,32] and phytophthora (Phytophthora nicotianae var. parasitica)-resistant sesame(Sesamum indicum) mutants in Sri Lanka [33,34] are some examples of such practical use.
Table 2. Some of the crop species domesticated in different centres of diversity according toZhukovsky [35].
RegionCrop

South Mexico–Central
America

Avocado, Maize, Sweet Potato, Tomato, Capsicum spp., Tobacco, Cucurbita pepo, C.
moschata, Phaseolus spp., Amarnthus cruentus, A. hypochondriacus, and Gossypium hirsutum

South American Andes (Peru, Bolivia,
and Ecuador)

Potato, Quinoa, Lima Bean, Common Bean, Tomato, Capsicum spp., Cucurbita maxima, C.
moschata, Grain amaranth (Amaranthus caudtus), Oca (Oxalis tuberosa), Ulluco (Ullucus
tuberosus), Añu (Tropaeolum tuberosum), Achira (Canna edulis), Coca, Gossypium barbadense

Tropical lowland South America(Chile, Paraguay, and Southern Brazil)

Cassava, Arrowroot, Cocoyam, Peanut, Pineapple, and Capsicum chinense

Mediterranean

Grapevine, Carrot, Cabbage, Olive, Sugar Beet, European Pear, Vicia faba, V. sativa,
Lathyrus ochrus, Cicer arietinum, and AlmondAsia Minor (Middle East)

Cicer arietinum (secondary centre), Lens culinaris, L. orientalis, Vicia ervilia, Pisum sativum,
Medicago sativa, Trifolium resupinatum, Trigonella foenum-graecum, Onobrychis spp., Lathyrus
cicera, Vicia spp., Date Palm, and Lettuce

Abyssinia (Ethiopian
Centre)Millets, Sorghum, Castor, Coffee (Coffea arabica L.), Peanut, Teff (Eragrostis abyssiniaca
Link.), Finger Millet, Sesame, and Niger (Guizotia abyssiniaca Cass.)

Inner Asia

Wheat, Barley, Apple, and Onion

India

Mung Bean, Rice, Black Gram, Pigeon Pea, Horsegram, Mango, Little Millet (Panicum
sumatrense), and Flax

Indo-Malaya

Rambuttan, Banana, Sugarcane, and Yam

China

Rice, Soybean, Peach, Foxtail Millet (Setaria italica), Proso Millet (Panicum miliaceum),Hemp, Tea, Chinese Cabbage, Mulberry, and Citrus spp.

Study of crop domestication is complex, and was especially so during Vavilov’stime because of difficulty in accessing the many areas of crop domestication spanning
different continents. Later studies have shown that high varietal diversity does not exist
for some crops in the centre of origin [36]. Archaeological findings in recent times haveadded further complexity to the theme of crop domestication. This has revealed smaller
independent areas of domestication within large centres. For example, Vavilov considered
India as one major centre. Archaeological evidence suggests that there are five independent
centres within India [37]. Other broad regions, such as Near Oceania, Amazonia, Eastern
North America, and the river deltas of Western Africa, have also been identified as aresult of new archaeological and molecular biological findings. Thus, for example, theNiger River basin in West Africa is now considered a major cradle of crop domesticationin Africa, with sequencing and microsatellite marker studies confirming the origin ofAfrican rice (Oryza glaberrima) [38], African yam (Diascorea rotundata) [39], and pearl millet(Pennisatum glaucum) [40] in this area. Li [41] discussed the complexity of Vavilov’s ChineseCentre and identified four belts of origin of cultivated plants in this region: I. Northern
China, II. Southern China, III. Southern Asia, and IV. Southern Islands, according to theirlatitude. Archaeological evidence also suggests that in the early period, the focus ondomestication was on a few crop species, mainly cereals. Plant domestication resulted
in a lifestyle change for humans, from foraging to a more sedentary lifestyle. Increased
agricultural productivity supported larger populations, and the first civilisations arose as aresult. Purugganan and Fuller [42] describe 24 regions of domestication, most of them inand around Vavilov’s main centres.

Plants 2022, 11, 2038

6 of 36

2.2. Landrace and Modern Cultivars; Their Genetic Structure in Relation to Diversity Management
In later periods, large-scale breeding programmes or natural adaptation of crops
outside the main centres after introduction by humans resulted in the diversity of particularspecies that Vavilov called secondary centres of diversity. The main difference in thesesecondary centres is the poor representation of wild relatives. In primary centres where
the crop was domesticated, one sees wild relatives including the progenitors. Genetic
diversity studies of domesticated crops and their wild ancestors can provide insight into
the history and timing of domestication, shedding light on the food habits of our ancestors.
Additionally, we can understand the genes that underlie the main phenotypic and genetic
shifts in populations leading to domestication events, giving clues for the better use ofunderutilised crops for breeding. Most importantly, from crop genetic diversity studies,
we can identify genetic groups within populations that need to be retained as germplasm
for conservation and utilisation. The value of wild populations is in the large genomic
variation and novel genes and alleles they carry that can be introgressed into cultivatedspecies where there is typically lower genetic diversity due to domestication and selective
breeding [43–45]. Therefore, once candidate genes associated with adaptation to emerging
biotic and abiotic stresses in wild populations are identified, they can be introgressed
into new cultivars. This approach can contribute to increased resilience of the cultivatedspecies in new crop varieties destined to keep feeding the increasing population underclimate change.
Soybean (Glycine max) is a well-studied domesticated crop, arising in an area coveringparts of present-day China (Manchuria), Korea, and Southern Russia, where its progenitor
G. soja exists [46]. The genetic diversity measured using different genetic markers, such as
simple sequence repeat (SSR) [47], single-nucleotide polymorphism (SNP), 5S ribosomal
RNA polymorphism [48] markers, and a de novo assembly of sequence data [44] all point to
the larger variation and presence of novel alleles in G. soja compared with the domesticatedG. max, including rare alleles [43]. Furthermore, the genetic diversity of the cultivatedspecies in the centre of origin is far greater than in secondary centres. For example, North
America is a secondary centre of diversity of soybean, with more than 30 million ha and2242 cultivars registered in the USA alone within the period 1970–2008 [49]. However, only
a limited number of ancestral introductions have contributed to the germplasm developed
there, with only five introductions being the cytoplasm source for 121 of the 136 cultivars
studied by Specht and Williams [50]. The ancestry of nuclear material also was narrow,with only 12 introductions contributing to 88% of the germplasm [50]. This indicates thevalue and need for conservation of genetic resources at the source of origin, with special
attention to wild progenitors and other wild relatives because of the presence of a wider
diversity of alleles.
Despite the narrow genetic variability, secondary centres of diversity offer valuable
agronomic traits in their germplasm; hence, some countries can directly adopt some ofthese cultivars until national breeding efforts commence. A good example was the adoptionof U.S. soybean cultivars such as ‘Hardy’, ‘Lee’, ‘Improved Pelican’, ‘Davis’, and ‘Bragg’ innorth-central India in the 1960s [51,52] and in Sri Lanka in 1974 [53] until local breeding
programmes were initiated resulting in superior cultivars suitable for release [52,54].
Few cultivated species have been domesticated outside their region of origin. For
example, sunflower from South America was developed into oilseed sunflower in Russia [55–57]; grapefruit, a hybrid of Citrus sinensis from Southeast Asia and Citrus maxima
from Indonesia, was domesticated in Barbados in the 1820s [58]; and Chinese gooseberry(Actinidia spp.) from East Asia was domesticated and commercialised in New Zealand as
kiwifruit [59,60]. Again, the diversity of wild species is richer in the source region, withmany wild species of sunflower in South America, and 57 species of Actinidia in China [61]against 19 in New Zealand introduced before China embargoed further export of kiwifruit
genetic resources [62].

Plants 2022, 11, 2038

7 of 36

3. Crop Domestication and Domestication Traits
3.1. Primary Domestication Traits
Humans who had traditionally foraged (Table 1) started cultivating limited plant
species as food sources in the early Neolithic period (13,000 to 11,000 years ago). The
morphological, physiological, and biochemical changes in species during evolution cantake different directions under domestication depending on the part of the plant used. For
example, in cereals and pulses, there is evidence for an increase in grain size and nonshattering at maturity [22,42]. As a result of acquiring the non-shattering grain character,cereal crops lost their ability for dispersal and became dependant on humans for reproduction by sowing. Many tuber and root crops, on the other hand, lost the ability to sexually
reproduce as a result of selection for larger tuber or root, associated with selection for
polyploid types resulting in sterility. In Diascorea alata, a dioecious tuber crop, all 73 malegenotypes studied by Abraham and Gopinathan Nair [63] were tetraploid, whereas mostof the 30 female germplasm accessions were of higher ploidy (hexa and octaploids) andcompletely sterile.
Meyer and Purugganan [64] describe domestication traits as those selected during
the initial transformation and establishment of a new domesticated species from its wild
ancestor. Changes in resource allocation to the part of the plant commonly used for foodare typical in many crop categories, whereas loss of dormancy, determinate growth habit,
increase in seed size with thinner seed coat, and changes in inflorescence architecture arehallmark domestication traits in seed crops. These traits arose either through conscious
human selection or ability of the particular genotype to survive under deforested or disturbed habitats. Traits to facilitate harvest (e.g., non-shattering in cereals) represent theformer, and larger seed size the latter because of the ability of larger seeds to emerge after
burial during planting (competitive advantage) [37,42,65].
Archaeological evidence from wheat, barley, and rice suggests that the seed size
increase was one of the first traits selected under cultivation followed by the non-shatteringof grains, the latter taking a much longer time for fixation. Seed size increases in barley andrye were achieved within 500–1000 years, whereas in rice it happened at a much slower
pace, over the period 9000–5500 years ago [42,66,67]. On the other hand, pearl millet seedsize enlargement occurred only 2000 years after domestication [42] and occurred at several
locations [66]. Similarly, a 1500–2000-year period for seed size enlargement in mung bean
is evident from recent archaeological findings from Indian sites [65,66].
For the first time, Li et al. [68] cloned and characterised a gene, sh4, for the loss ofshattering in a grain crop (in rice), a hallmark trait of domestication, which, interestingly, isexpressed at a slower rate during grain maturation in cultivated O. sativa than in the seedshattering progenitor O. nivara. This was probably the result of selection in the regulatory
region of the gene for finer adjustment of the shattering/threshing balance in cultivated rice.
Another trait of domestication is tillering and branching. Generally, in most seed crops,
apical dominance has increased, with the suppression of lateral branching or tillering during
domestication. Doebley et al. [69] cloned teosinte branched I (tb1), the key gene contributing
to the increased apical dominance in maize (Zea mays ssp. mays) compared with its ancestor
teosinte (Z. mays ssp. parviglumis) (Figure 2). Their research led to the discovery that tb1
acts both to repress the growth of axillary organs and to enable the development of female
inflorescences. The gene is not expressed in the primary axillary meristems of teosinte,enabling them to develop into long branches with a tassel at the tip (Figure 2). During
domestication, the selection of forms that have high expression of tb1 in primary axillary
meristems led to the development of ear shoots rather than elongated tassel-tipped branches.
Thus, during maize domestication for less branching, an alteration of the gene regulationof tb1 has occurred rather than loss/gain or change in function. The most critical step inmaize domestication was the liberation of the kernel from the hardened, protective casingthat envelops the kernel in teosinte. This evolutionary step exposed the kernel on thesurface of the ear, such that it could readily be used by humans as a food source (Figure 2).
Wang et al. [70] mapped the factor controlling the phenotypic difference between maizePlants 2022, 11, 2038

a food source (Figure 2). Wang et al. [70] mapped the factor controlling the phenotypic
difference between maize and teosinte for this trait to a 1 kilobase region, within whichmaize and teosinte show only seven fixed differences in their DNA sequences. They
demonstrated that this key event in maize domestication is thus controlled by a single
gene (teosinte glume architecture I or tga1), belonging to the SBP-domain family 2 of tran8 of 36
scriptional regulators [70].
Plant size can be reduced either as in the case of wheat and rice during the Green
Revolution or from indeterminate growth habits to determinate growth, such as in beans
andforPlant
this architecture
trait to a 1 kilobase
region,withinwhichmaize andteosintee.g.,
show
only
andteosinte
soybean.
has been
selected
to suitharvesting
practices,
singleseven
fixed
differences intheir DNA
sequences.
demonstrated
this key
event
in
ear corn
or single-headsunflower.
Plantsare alsoThey
selectedfor ease of that
handling,
thus
losingmaize
domesticationisthus
controlledbyasinglegene(teosinteglume
architectureIortga1),
their natural protective features such as thorns and spines in the case of some Citrus spp.
belongingto theSBP-domain
family 2 of transcriptional regulators [70].
and Solanum
spp.,
respectively.

Figure2.
2. Domestication
Domestication promotes
promotes rapid
rapid phenotypic
phenotypicevolution
evolutionthroughthroughartificial
artificialselection.
selection. Pictured
Pictured
Figure
here
is
wild
grass
teosinte
(Zea
mays
ssp.
parviglumis)thatwasdomesticatedintomodernmaize(Z.
here is wild grass teosinte (Zea mays ssp. parviglumis) that was domesticated into modern maize
mays
ssp.
mays).
The
main
traitsselected
duringdomestication
included
the
ear
and
seed
size
(com(Z. mays ssp. mays). The main traits selected during domestication included the ear and seed size
pared in relation to a USD coin in the inset) and the suppression of axillary branching. Figure cour(compared in relation to a USD coin in the inset) and the suppression of axillary branching. Figure
tesy National Science Foundation, USA.
courtesy National Science Foundation, USA.

3.2. Diversification
Plant size canEvents
be reduced either as in the case of wheat and rice during the Green
After initial
domestication,
crops
underwent
diversification
as a secondaryFor
Revolution
or fromindeterminate
growthhabits todeterminate growth,such asevent.
in beans
example,stickyandarchitecturearomatic rice
popcornwereselectedfrom thecommonlygrown
andsoybean.
Plant
hasandbeen
selected
to suitharvesting
practices,e.g., singlericecorn
and ormaize
types, anda whole Plants
range ofoleraceae(kohlrabi,
cabbage,earsingle-headsunflower.
areBrassica
also selected
forvegetables
ease of handling,thus
losingBrussels
sprout,kale,
broccoli,
andcauliflower)
were
selectedfrommustard(Figureastheir natural protective features such as thorns and spines in the case of some Citrus 3)
spp.
a resultof diversification
events. Most of the diversification traits evolve under targetedandSolanumspp., respectively.
3.2. Diversification Events
After initial domestication, crops underwent diversification as a secondary event. For
example, sticky and aromatic rice and popcorn were selected from the commonly grown
rice and maize types, and a whole range of Brassica oleraceae vegetables (kohlrabi, cabbage,
Brussels sprout, kale, broccoli, and cauliflower) were selected from mustard (Figure 3) asa result of diversification events. Most of the diversification traits evolve under targeted
selection. Another interesting vegetable that has experienced through much diversificationis lettuce (Lactuca sativa L.). Grown and used in ancient Egypt and depicted in Egyptian
ancient art circa 2500 BC, it was a plant with narrow, erect leaves with prickles [71]. It has
been used as an oil-yielding crop, and de Vries [72] considers that it was domesticated even
earlier in the Kurdistan–Mesopotamia area. The fact remains that conscious selection has
produced the many forms of lettuce in production today: cos, stalk, butterhead, crispbread(iceberg), and Latin. The oil type of lettuce is still used in Greece as a soporific [71].
Purugganan and Fuller [42] reviewed the genes directly involved in crop domestication that have been isolated and characterised to date. Of the nine domestication lociidentified, eight encode transcriptional activators, including rice shattering genes sh4 andqSH1, maize architecture gene tb1 (suppresses axillary branch formation), and wheat inflorescence structure-determining AP2-like wheat gene Q. In contrast, more than half ofPlants 2022, 11, 2038

head, crispbread (iceberg), and Latin. The oil type of lettuce is still used in Greece as asoporific [71].
Purugganan and Fuller [42] reviewed the genes directly involved in crop domestication that have been isolated and characterised to date. Of the nine domestication loci identified, eight encode transcriptional activators, including rice shattering genes sh4 and
9 of36
qSH1, maize architecture gene tb1 (suppresses axillary branch formation), and wheat
inflorescence structure-determining AP2-like wheat gene Q. In contrast, more than half ofthe 26 genes involved in diversification where molecular function has been characterised
encodeenzymes.
Thus,indomestication
eventsareassociatedwith transcription
regulatory
the 26 genes
involved
diversification
wheremolecularfunctionhas been characterised
networks,
whereascrop
diversification
involvesalarger
proportionofenzyme-coding
encode enzymes. Thus, domestication events are associated with transcription regulatoryloci.
networks, whereas crop diversification involves a larger proportion of enzyme-coding loci.

Figurehave been
beenselected
selectedduring
duringthe
thediversification
diversification
BrasFigure3.3.AAwhole
wholerange
rangeofofBrassica
Brassica vegetables
vegetables have
ofof
Brassica
sica
oleracea(mustard),
first domesticatedas an oil-yieldingin the Kurdistan/Mesopotamiaarea.
oleracea(mustard),
first domesticatedas an oil-yielding
crop incrop
the Kurdistan/Mesopotamia
area. Brussels
Brussels
sproutsaretheyoungestinthefamilyofthesevegetables,
selectedinBelgiuminthemidsprouts are the youngest in the family of these vegetables, selected in Belgium in the mid-18th century.
18th century.

3.3. Physiological and Biochemical Changes
3.3. Physiologicaland Biochemical
ChangesDuring domestication,changesin morphological features as well as physiological andDuring features,
domestication,
in morphologicalfeaturesas welland
as seedphysiologicalbiochemicalsuch as changes
photoperiodism,
vernalisation
requirements,
and tuber
andbiochemicalsuch asChanges
photoperiodism,
vernalisation
requirements,
seeddormancy,
were features,very common.
in life cycle
to suit different
seasons inand
different
andtuberhavedormancy,
wereSome
very common.
Changesin life cycle
to suit different
seasonsinclimates
occurred.
crops havebeen turned
into annuals
from their
originaldifferent
haveoccurred.
Somecropspeahaveturnedintohaveannuals
fromnatural
theirperennialclimates
habit, suchas cotton,
castor,pigeonandbeencassava;otherslost theirprotective
toxins, e.g.,
many
crops
of the Solanaceae
family,humansselectedagainstoriginal
perennial
habit,
such
as cotton,
castor, pigeon
peaasandcassava;othershavethose
lost
Plants 2022, 11, x FOR PEER REVIEW
10 of 38
features.
Anotherexampleof majorfollowing selectionis theevolution
theirnaturalprotective
toxins,e.g.,physiologicalmany crops changeof the Solanaceae
family, as
humanssefromwild
Ananasbracteatus
todomesticatedpineapple
A.
comosus(Figure4).
lected against those features. Another example of major physiological change following
selection is the evolution from wild Ananas bracteatus to domesticated pineapple A. comosus (Figure 4).

Figure 4.
wild
Ananasbracteatus(left)(left)and domesticatedpineapples
A. comosus(right).
4. TheThedifference
differenceinin
wild
Ananasbracteatus
and domesticatedpineapples
A. comosus(right).

3.4. Genetic and Cytogenetic Changes
Polyploidy, the increase in genome copy number, is a central feature of plant diver-Plants 2022, 11, 2038

Figure 4. The difference in wild Ananas bracteatus (left) and domesticated pineapples A. comosus(right).

10 of 36

3.4. Genetic and Cytogenetic Changes
Polyploidy, the increase in genome copy number, is a central feature of plant diver3.4. Genetic and Cytogenetic Changes
sification. This could be autopolyploidy, where the same genome is represented multiple
Polyploidy,
the duplication)
increase in genome
copyofnumber,a central featureviaof plant
diversifitimes (wholegenomeas a result
sexual ispolyploidisation
unreduced
cation.
This
could
be
autopolyploidy,
where
the
same
genomeisrepresented
multipletimes
gametes, or somatic polyploidisation followed by sexual reproduction [30]. A classic ex(wholegenomeduplication)asaresultofsexualpolyploidisation
via
unreduced
gametes,
ample is cultivated potato (Solanum tuberosum) (2n = 4× = 48), which has tetrasomic inheror somatic polyploidisation followed by sexual reproduction [30]. A classic example isitance.
cultivated(Solanumtuberosum)(2nin=domesticated
4× = 48), which
has tetrasomic
inheritance.
The otherpotato
commonform ofpolyploidy
speciesis allopolyploidy(amThe other common form of polyploidy in domesticated species is allopolyploidy
phidiploidy), where genomes of two or more species are represented in the new species.
(amphidiploidy), where genomes of two or more species are represented in the new
Durum wheat (T. durum) (2n = 4× = 28; tetraploid) and bread wheat (T. aestivum) (2n = 6×
species. Durum wheat (T. durum) (2n = 4× = 28; tetraploid) and bread wheat (T. aestivum)= 42 hexaploid) are well-known examples. Canola (B. napus) provides an example of how(2n = 6× = 42 hexaploid) are well-known examples. Canola (B. napus) provides an examheterozygosity at polyploid level can increase selection advantage. It carries genomes ofple of how heterozygosity at polyploid level can increase selection advantage. It carries
B. oleraceae (2n = 18, CC genome) and B. rapa (2n = 20, AA genome). Using quantitative
genomes of B. oleraceae (2n = 18, CC genome) and B. rapa (2n = 20, AA genome). Using
trait loci analysis for yield, it was shown that canola yields were lower when it had allelicquantitative trait loci analysis for yield, it was shown that canola yields were lower when it
arrangements similar to the parental types, but when the arrangement differed from those
had allelic arrangements similar to the parental types, but when the arrangement differedof the parents, the yield was higher [73].
from those of the parents, the yield was higher [73].
The majority of cultivated bananas are derived from inter- and intra-specific crosses
The majority of cultivated bananas are derived from inter- and intra-specific crosses
between two diploids (2n = 2× = 22): Musa acuminata (AA genome) and M. balbisiana (BBbetween two diploids (2n = 2× = 22): Musa acuminata (AA genome) and M. balbisiana (BBgenome).
TheTheparentspecieshave
seededfruitfruit
withwith
littlelittle
starchand andare ofas a asgenome).
parentspecieshave
seededstarcharenoofvalue
no valuecrop(Figure
5).
Most
of
the
cultivatedbananasareparthenocarpic
seedless
triploids(2n=a crop (Figure 5). Most of the cultivated bananas are parthenocarpic seedless triploids
3× (2n= 33)= withAAA
(dessert
bananas),
AAB,
or
ABB
(mostly
cookingbananas)genomes.
3× = 33) with AAA (dessert bananas), AAB, or ABB (mostly cooking bananas)
These
variations
havevariations
been collectedsourcesin the wild;
thus, ingenomes.
These
have frombeen multiple
collectedindependent
from multiple
independentsourcesthethehybridisation
eventsandmutationsgivingrise
totheseedlessandparthenocarpic
wild; thus, the hybridisation events and mutations giving rise to the seedless andcharactershave occurredmanyhundredsof times
meaningthat bananas
were doparthenocarpic
charactershaveoccurredmany [74],hundredsof times[74], meaningthat
mesticatedinseveral
areas
of
the
Malayancentreofdiversity.
bananas were domesticated in several areas of the Malayan centre of diversity.

Figure5. Wild
bananais diploid
produces
seeds(left),
whereascultivatedbananais sterile
Figure5. Wild
bananais diploidandandproduces
seeds(left),
whereascultivatedbananais sterile
andandseedlessbecausea triploid(right).
seedlessbecauseit isitaistriploid(right).

4. Current Status of Plant Genetic Resources in the Centres of Diversity
As already described, along the path of domestication, humans have selected for only
a few traits in our crops over time, resulting in the narrowing of the gene pool available
for breeding. Landrace cultivars, although not as productive under high-input conditionsof modern agriculture, carry alleles that are useful in many other ways, including pest
and disease resistance, and tolerance to adverse soils, drought, salinity, and other abiotic
stresses, while also carrying valuable quality traits such as a better nutritional value thanmany modern cultivars. For example, using whole-genome shotgun data from seeds ofancient and modern common bean, Trucchi et al. [75] showed that selection strategies
during the past few centuries, as compared with historically, more intensively reduced
genetic variation within cultivars and produced further improvements by focusing on a few
plants carrying the traits of interest, at the cost of marked genetic erosion within Andean
landraces. Using data from collecting missions and survey data since 1927, Hammer andLaghetti [76] found higher historical rates of genetic erosion of wheat in Italy (13.2%)
compared with the period after 1950 (0.48–4%). Similar trends in genetic erosion have beenfound to occur in rice in India and China, T. durum and T. dicoccum in Ethiopia, and in
traditional wheat varieties in Greece [77]. Crop wild relatives (CWRs) evolving in theirnatural habitat can also have many useful traits. Contemporary plant breeders are awareof the need to broaden the genetic structure of the crops they breed, although it is noteasy to incorporate this aspect into breeding schemes because hybridisation with landracePlants 2022, 11, 2038

11 of 36

cultivars, more so with wild species, requires time-consuming back-crossing to achieve thehigh yields and other traits expected under modern cultural practices. As a result, the genepool of our crops often continues to narrow in breeders’ hands; at the same time, because ofurbanisation, deforestation, monocropping, etc., the genetic diversity of crops is reducing
at the centres of diversity.
Some of the centres of origin of cultivated species have recently become areas forlarge-scale irrigation and hydroelectric projects. By 2000, there were over 45,000 large
dams in more than 150 countries, and each year 160 to 320 new schemes are being built
worldwide [78], at the expense of habitat loss for terrestrial ecosystems. For example, theworld’s largest dam, the Three Gorges Dam in central China, was inserted in the middle ofa biodiversity hotspot. Located in the upper reaches of the Yangtze River, little affected by
the quaternary glaciations, the Three Gorges Reservation Area is one of the richest areas inbiodiversity in China and was considered to have had the highest diversity of genera andfamilies globally. It is the home of 6388 species of higher plants, belonging to 238 families
and 1508 genera, and accounting for 20% of all seed plant species in China, with 57 of them
being endangered [79].
In addition to industrial development, in some centres of crop diversity, protracted
wars have induced the displacement of farming communities, in some cases with thecomplete abandonment of farmland along with the crop genetic resources they contained.
Good examples are in the Middle East—Syria, Iraq, Yemen, and Palestine. The depletionof crop genetic resources is thus happening both at the centres of diversity, in what is leftof the natural environment, and on farmers’ lands. This is part of the larger problem ofenvironmental degradation, and the COVID-19 pandemic could be viewed as a symptomof a bigger problem of deforestation and biodiversity loss that needs addressing urgently.
Without continued genetic enhancement using diverse germplasm from both CWRs
and landrace cultivars, gains in crop yields obtained over the past seven decades are notsustainable, and yields might eventually grow more slowly or even decline, as already discussed [16]. Hence, comprehensive integrated programmes are needed for the conservationof plant genetic resources.
5. Role of Perennial Species in Sustainable Agriculture
Plants show a wide variability in the distribution of the limited resources available,
allocating them to growth, defence, and reproduction, with two contrasting strategies:
annual species, which complete their life cycle and die within a year; and perennial
species, which usually delay their flowering to a later year, sometimes interrupted byperiods of quiescence. Ensuring the need for agricultural products by a growing andmore demanding world population through the intensification of conventional agriculture
without causing significant damage to the environment is unrealistic. In recent decades, theenvironmental costs of intensifying conventional agriculture have begun to cause serious
concern. Ecological intensification has been proposed as a nature-based alternative thatcomplements or partially replaces external inputs [80]. Perennial plants are key componentsthat offer previously unattainable levels of ecological intensification in agriculture, reducing
the impact on the environment [81].
Although annual crops are the main source of our diet, several perennial crops could
also be important players in the coming decades. Approximately one-eighth of the total areaof global food production is composed of perennials, which are therefore a fundamental
source of nutrition worldwide [82]. Perennial crops have several advantages from the pointof view of environmental impact. One benefit is that they do not have to be reseeded or
replanted every year, so they do not require annual ploughing to establish. Moreover,to successfully grow annuals, farmers must chemically or mechanically control weeds to
avoid competition with crops for light, nutrients, and water, especially in the early stagesof seedling development. The resulting soil disturbance has caused significant amountsof carbon loss in the soil (which ends up in the atmosphere as CO2 ), soil erosion, nutrient
loss, and an impact on soil organisms [83]. From a study on the dynamics of soil organic

Plants 2022, 11, 2038

12 of 36

carbon, it was estimated that over a 20-year period, encompassing a change from annual toperennial crops led to an average 20% increase in organic carbon at 0–30 cm soil profile [84].
Compared with organic and conventional cultivation systems of annual wheat, recently
commercialised perennial intermediate wheatgrass (IWG) cultivation increased the soilorganic carbon in 30–60 cm soil depth, including the amount of carbon in the particulateorganic matter, implying reduced carbon losses and high carbon use efficiency [83]. Anotherstudy found that carbon flux, as well as carbon and nitrogen storage in soil were greatest in
IWG systems compared with both restored native vegetation and the annual monocropping
rotation of wheat, sorghum, and soybean [85].
In general, compared with annual crops, perennial crops are more robust, protect thesoil from erosion and improve its structure, increase the retention of nutrients, organiccarbon, water [83–85], and therefore can contribute to the adaptation and mitigation ofclimate change. Overall, they help ensure long-term food and water security. Anotheradvantage of perennial crops is that they can free farmers from economic instability bysignificantly reducing tillage and planting costs and their time in the field. In recent
years, research has contributed to improving agricultural techniques and practices tosupport environmentally friendly agricultural systems based on perennial crops. All these
ecological benefits were recently proven in 14 woody perennial polyculture farmlands whencompared with annual monocultures in the U.S. Midwest, one of the most industrialised
food-producing regions in the world [86]. A similar beneficial effect was found in semiarid West Africa when the correct woody perennials and shrubs were chosen for growing
along with annual cereals or legumes, particularly in farmer-managed natural regeneration
systems as an agroforestry strategy [87]. However, perennial species are particularly
recalcitrant to conventional breeding programs, because there are many obstacles to theirimprovement when compared with annual crops [82]. Many perennial species have long
juvenile phases and thus require up to several years before the yield and quality can beevaluated. Not only are the time, space, and infrastructure required for breeding perennials
often far greater than for breeding annuals, but the evaluation of commercially relevant
traits is also often more complex, time-consuming, and expensive [82].
Herbaceous Perennial Crops
Agroecosystems are in constant evolution, in order to adapt to the needs of a growing
population in a sustainable manner. Debates on the ecological impacts of agriculturalintensification, including soil degradation and erosion, have concentrated attention on
crops that provide both agricultural products and ecological services. Annual crops sown
every year deplete the soil and expose it to erosion, requiring weed control with herbicides.
Moreover, during the first phases of growth, shallow root systems are not efficient inabsorbing water and nutrients, resulting in ground and surface water pollution by nitrateleaching [88]. Perennial herbaceous crops, which can be harvested mechanically, areperceived as a sustainable alternative to annual crops used as a source of human and animal
food. They can grow for several years, produce a large root system that helps to reduce
soil erosion and increases the soil organic matter, and can support several below-groundmicrobial communities that make plants more competitive, with better performance and,at the same time, with a lower impact on the environment. However, these species, which
provide an opportunity to explore potential alternatives to annual crops, have been almost
absent from agriculture, and were rarely domesticated for seed or fruit production [81,84].
Different possible biological mechanisms have been proposed to explain the rarenessof herbaceous perennial crops. Among these, compromises between vegetative and reproductive tissues stand out, and it is now possible to develop these through phenotypicand genotypic selection [89]. The presence of genome sequences in wheat relatives suchas Thinopyrum intermedium that may be orthologous to domestication genes identified inannual grain crops gives optimism [88]. Plants must devote limited resources towards avariety of processes, including growth, defence, and reproduction. In wild species, allocation strategies must reflect trade-offs between these processes and are therefore central

Plants 2022, 11, 2038

13 of 36

to a species’ ecology. During the domestication process, artificial selection on allocation
was carried out, which generated high-yielding crops that often invest reduced resourcesin defence or longevity, thus limiting the number of herbaceous perennial crops [89,90].
Need in developing new perennial crops and better understanding domesticatedperennials has led to an increase in interest in the physiology, genetics, and evolutionof these species. Our ability to understand or predict evolutionary transitions between
strategies and their adaptive significance is limited by the lack of integration between the
different fields. The evolutionary transition between perenniality and annuality in plants
is exceptionally common among angiosperms. Reconstructions of the ancestral statususing phylogenetic approaches have generally found that annuals derive from perennial
ancestors; however, the evolution of perenniality was also observed. Empirical data support
the hypothesis that evolutionary changes to annual life histories are associated with arid,
disturbed/unstable environments in which adult survival is low or unpredictable [91].
The interest in developing new perennial crops through wide hybridization led tothe crossing of annual crops with perennial relatives and the de novo domestication ofwild, perennial, herbaceous species [92]. However, the idea of developing new perennial
crops to replace annual grains is controversial [89,93]. The opportunity costs associatedwith the low grain yield compared with the high yield index of annual crops are one of
the most persistent criticisms of perennial crops [94]. In his review, Smaje [94] raises threearguments against developing perennial grain agriculture: (a) ecological theory suggeststhat perennial grains may yield less than annual grains; (b) strong criticisms of annual
agriculture are unfounded, both socially and ecologically; and (c) focus on perennial grains
detracts from more important strategies for achieving agricultural sustainability. Crews
and DeHaan [95] counter these three arguments, concluding that perennial herbaceous
crops constitute a valid solution for enhancing sustainability in agriculture.
Many researchers have suggested that a more sustainable agricultural system willneed to consist of mostly perennial species, and will need to be more diverse than is thecase with present agroecosystems [96,97]. In the early 1980s, Wes Jackson [98] proposed
the idea of growing perennial grain crops, including cereals, pulses, and oilseeds, and byplanting them in complementary arrangements in prairie. This idea, which was considered
utopian by many researchers in the past, seems to be achievable today thanks to new plantbiotechnologies. In fact, the rapid deployment of technologies, such as CRISPR-Cas systems
and other genome editing processes, provides new opportunities for crop breeding. The denovo domestication strategy can be adopted to improve the elite foundation materials fromwild or semi-wild plant species in nature to achieve the main goals of genetic improvement,
followed by the introduction of desired traits through the application of new genetic engineering technologies while retaining their desired features, resulting in plants harbouring
new traits of interest [99]. If the new technologies that have been developed in recent years
are applied to perennial proto-crops, it would enable the development of new genotypes ofinterest, probably in decades as opposed to the centuries that were required to create ourcurrent annual food crops [96].
The idea of rapid neodomestication was propagated as a promising strategy for futuresustainable agriculture [100]. Despite accelerating the process, neodomestication throughcrosses would still suffer from the accumulation of deleterious mutations linked withdomestication traits alleles, the so-called domestication cost [101]. Although the scientificcommunity is not completely unanimous on the potential impact of crop neodomestication,
there are several successful studies rendering this concept of potential interest to agriculture [102]. Neodomestication was first utilized for a rapid sunflower breeding programthat introduced domestication traits into wild relatives through crosses [103]. In this regard,
the high phenotypic gains, approaching 320% in breeding sunflower as a perennial oil
crop [104], are encouraging. Subsequently, species of the genus Vigna were nominated as
candidates for neodomestication due to their stress resilience and common use as edible
wild plants [105].

Plants 2022, 11, 2038

14 of 36

Identifying the right herbaceous perennial species and germplasm for domestication
can be challenging. The construction of an online resource of wild, perennial, herbaceous
species—the Perennial Agriculture Project Global Inventory (PAPGI), comprising details of
perennial members of the three of the largest known plant families, Asteraceae, Fabaceae,
and Poacea, containing details of taxonomy, growth descriptors, ecology, reproductive
biology, genetics, economic uses, and toxicity [106] in this regard is invaluable. As the firstcomponent of the PAPGI project, focus has been on wild, perennial, herbaceous Fabaceae
species, with records of 6644 species and over 60 agriculturally important traits. Foodand forage uses of 314 legume species and toxicological data for 278 species have been
incorporated into searchable online resources [81].
6. Approaches to Germplasm Conservation
There are two main approaches to conserving crop germplasm: in situ and ex situ.
Article 2 of the Convention on Biological Diversity defines ex situ conservation as theconservation of components of biological diversity outside their natural habitat. In situ
conservation relates to the conservation of ecosystems and natural habitats, and the maintenance and recovery of viable populations of species and, in the case of domesticatedor cultivated species, in the surroundings where they have developed their distinctive
properties. Thus, in situ conservation has two major facets: (a) the conservation of ecosystems and natural habitats, mainly facilitating the conservation of CWR in the natural
ecosystems; and (b) the conservation of domesticated species in the habitats where they
were developed [107]. The latter is called on-farm conservation and is part of wider in situ
conservation.
6.1. In Situ Conservation
In situ conservation is important for conserving CWRs and landrace varieties of thecultivated species. In 1989, the Commission on Genetic Resources for Food and Agriculture(CGRFA) called for the establishment of networks of in situ conservation areas for plant
genetic resources for agriculture, for both crops and CWR.
6.1.1. Identity of Crop Wild Relatives
CWRs are commonly defined as wild species that are relatively closely related toagricultural and horticultural crops. Therefore, any taxon belonging to the same genus asa crop would fall into the CWR category. However, this definition covers large numbersof taxa and can result in the inclusion of species that are too remotely related to the cropor a large proportion of the species, e.g., in the Mediterranean Region and Europe almost
80% of flowering species are CWRs [108]. Considering the limited resources available
for ex situ conservation efforts, a more rational approach would be to use the gene poolconcept [109], where the close relatives are categorised as the primary gene pool, the more
remote relatives as the secondary gene pool, and the most distant relatives as the tertiary
gene pool. For many tropical species, where the relatedness in terms of crossing ability
and genetic diversity is not well understood, the taxonomic hierarchy may be used to
identify the relatedness of CWR to the cultivated species [110]. Even if relatedness is not
yet established, new-found taxa can become high priority for conservation, such as the casewith Oryza rhizomatis Vaughan, discovered in the late 1980s, mainly occurring in the driest
areas of Sri Lanka (Figure 6). It is rhizomatous [111] and has drought-avoidance traits. It
is in the near-threatened category in the IUCN Red List [112] and is a high priority ricetaxon in terms of in situ conservation with another three species (O. longiglumis, O. minuta,
and O. schlechteri).

Plants 2022, 11, 2038

identify the relatedness of CWR to the cultivated species [110]. Even if relatedness is not
yet established, new-found taxa can become high priority for conservation, such as thecase with Oryza rhizomatis Vaughan, discovered in the late 1980s, mainly occurring in thedriest areas of Sri Lanka (Figure 6). It is rhizomatous [111] and has drought-avoidancetraits. It is in the near-threatened category in the IUCN Red List [112] and is a high priority
15 of 36
rice taxon in terms of in situ conservation with another three species (O. longiglumis, O.
minuta, and O. schlechteri).

Figure6.6.Distribution
Distribution ofofOryza
Oryzarhizomatis
rhizomatis discovered
discovered inin thethe late
late 1980s
1980s ininthe
theperiphery
periphery ofof YalaYalaandandFigureWilpattu
National
Parks
in
the
driest
areas
of
Sri
Lanka
[113].
Reproduced
withpermission
fromWilpattu National Parks in the driest areas of Sri Lanka [113]. Reproduced with permission from thethe Food
and Agriculture
Organization
the United
Nations.
Food
and Agriculture
Organizationof theofUnited
Nations.

6.1.2.
6.1.2. Why
WhyIn
InSituSituConservation?
Conservation?
The
Theevolution
evolutionof
ofcropcropspecies
speciesisiscontinuing
continuing inin thethe centres
centres ofof diversity
diversity ofof cropcrop plants,
plants,with
newlandraces
emerging
andgenetic
frequencieschanging,
asshown,
forexample,with new landraces emerging and genetic frequencies changing, as shown, for example,
in the evolution of cultivated rice [114]. Thus, the main difference in maintaining thediversity in situ as against ex situ conservation in field genebanks or seed banks is that
we have a continually evolving population responding to the changing environment.
Allele frequencies vary over time in response to the changes in environment, thus making
available genotypes of particular interest for contemporary plant breeding problems. Older
ex situ collections, if not updated, remain frozen snapshots of a particular epoch of evolution
and will subsequently have genotypes that are not adapted to the changed environment of
the original collection site.
In addition to the conservation of genetic resources in the wild, on-farm conservation
also helps to protect the conditions that allow the emergence of new germplasm. This idea ofdynamic conservation extends to the whole farming system. This type of conservation enables
the maintenance of genetic resources at all levels—ecosystem, species, and intraspecific—
supporting and contributing to the overall agroecosystem health in locally tested farming
systems. This includes minimising the use of pesticides, restricting emissions, conserving soil,
and preventing pest and disease outbreaks as multiple crops and heterogeneous varieties
within a farming community provide less than ideal conditions for such outbreaks.
CWRs and landrace varieties provide new sources of variation for crop improvement
programmes. There are many examples of novel cultivars produced using these genetic
resources from the past and present. For example, when late blight (Phytophthora infestans)decimated the potato industry in Europe as a result of the import of infested seed potatoes

Plants 2022, 11, 2038

16 of 36

from the United States in 1845, the introgression of phytophthora disease resistance fromwild relatives, such as Solanum demissum from South America [115], helped to revive theindustry; most modern potato cultivars carry resistance genes from this wild species. Potato
blight caused one million deaths and the displacement of another one million people from
Ireland, a country that was totally dependent on potato at the time [115]; a historical lessonof the importance of diversification of food sources.
In recent times, rice improvement has greatly benefitted from wild relatives. Brown
plant hopper (BPH—Nilaparvata lugens Stål.) is one of the most destructive pests of ricethroughout Asia, causing severe yield reduction by directly sucking the plant sap andacting as a vector of virus diseases such as rice grassy stunt and ragged stunt. O. glaberrima
and O. minuta have durable resistance to this pest. Using embryo rescue techniques, thistrait was transferred to cultivated rice [116]. The resulting lines are being used worldwide
in rice breeding programmes. For example, screening of the introgression lines from thecrosses IR 64 x O. glaberrima and IR 31917-45-3-2 x O. minuta showed that the two wild
rice parents and the introgression lines had greater resistance to BPH than any of thelocal tolerant genotypes or IR 64, which has a Bph1 gene which imparts some tolerance to
BPH [117]. Examples of different wild rice species used in the improvement of targeted
traits in cultivated rice are given in Table 3. Considering the value of such germplasm,
both the Convention on Biological Diversity and the International Treaty on Plant Genetic
Resources for Food and Agriculture (ITPGRFA—termed Plant Treaty) highly recommend
the implementation of in situ conservation strategies.
Table 3. Some examples of traits of wild rice used in improving Oryza sativa—the cultivated speciesof rice.
Oryza Species

GenomeTrait of Interest

Line Number

ReferenceO. glaberrima

AA

Brown planthopper(Nilaparvata lugens Stål.)resistanceIR 75870-5-8-5-B-1-B),
IR 75870-5-8-5-B-2-B)[117]

O. nivaraAA

Brown planthopper
tolerance

IR28, IR29, IR30, IR34,
IR36, IR38, IR40, IR48,
IR50, IR56, IR58,[118]

O. minuta

BBCC

Brown plant hopper
resistanceIR 71033-6215, IR 71033-121-15[117]

O. nivaraAA

Sheath blight(Rhizoctonia solani)
tolerance

RPBio4918-10-3[119]

O. nivara

AA

Salinity tolerance

14S, 75S, 166S, IL 3-1K

[120]

O. rufipogon

AA

Salinity tolerance

Chinsurah Nona 2[118]

O. nivaraAA

Heat tolerance

166-2, 175-2, 3-1K

[121]

O. rufipogon

AA

Heat tolerance

377-13, 50[121]

O. nivaraAA

Heat tolerance

24S, 70S, 14-3S[122]

O. nivara

AA

High yield

220S, 10-2S[123]

O. nivaraAA

100 grain weight, early
flowering

NSL-15, NSL-22[124]

O. sativa f.
spontanea

AA

Cytoplasmic malesterility

O. rufipogon

AA

Rice tungro bacilliform
virus resistanceMatatag 9[118]

O. longistaminata

AA

Bacterial blight(Xanthomonas oryzae pv.
oryzae)Shanyou63-Xa21[125]

Mondal andHenry [118]Plants 2022, 11, 2038

17 of 36

Table 3. Cont.
Oryza Species

GenomeTrait of Interest

Line Number

Reference

O. rufipogon

AA

Acid sulphate tolerance

AS 996[118]

O. minuta

BBCC

Bacterial blight

41 Lines[126]

O. minuta

BBCC

Brown planthopper

11 Lines[126]

O. minuta

BBCC

Whitebacked
planthopper (Sogatella
furcifera)

7 Lines[126]

O.grandiglumis

CCDD

Grain weight and otheryield traits

HG 101[127]

O. meridionalis

AA

Iron tolerance

CM 23, CM 24[128]

Oryza rufipogon‘DXWR’

AA

Drought tolerance

Restorer line BIL627[129]

6.1.3. Implementation of In Situ Conservation
In general, implementing in situ conservation has been more challenging than ex situ
conservation for several reasons. The in situ conservation of traditional cultivars is not wellfunded, unlike traditional genebank activities. Management and coordination activities
of in situ collections have logistical problems because on-farm programmes have a poorconnection with mainstream genebanking activities at both national and international
level. In many environments, in situ conservation is still in an experimental stage and notsupported through mainstream funding which is available for genebanking.
About forty years ago, it was widely assumed that traditional varieties would be
rapidly and completely replaced by modern varieties [130]; this did not happen in several
agricultural regions around the world [131]. For example, maize landraces in the U.S.
corn belt were completely replaced between 1925 and 1950, whereas those in Mesoamerica
continue to be cultivated [132]. A substantial amount of information has been documented
in the last few years on the continuing maintenance and use of traditional varieties bysmall-scale farmers around the world [131–133]. Farmers seem to find that diversity, inthe form of traditional varieties, remains important for their production systems. In fact,
traditional varieties seem to adapt better than modern varieties to climate change andrequire lower chemical inputs. There are different ways of supporting farmers and farming
communities in the maintenance of traditional varieties and crop genetic diversity within
their production systems: (i) on-farm diversity assessment; (ii) access to diversity andinformation; (iii) the extent of use of available materials and information; and (iv) benefits
derived by the farmer or farming community from their use of local crop diversity [131,133].
Different studies carried out around the world have demonstrated the value of the useof traditional varieties by small-scale farmers for conservation [131,134,135]. However, moststudies on this topic suggest that there is insufficient knowledge about the social, cultural,and methodological dimensions on the topic, particularly how seed exchange networks cope
under climate change, and under changes in socioeconomic factors, and family structuresthat have supported seed exchange systems to date [136,137]. Four core criteria have recently
been proposed that characterize diverse Seed Commons arrangements at local and regional
scales: (1) collective responsibility; (2) protection from private enclosure; (3) collective,
polycentric management; and (4) the sharing of formal and practical knowledge [138].
A successful in situ on-farm conservation programme would usually have awarenessraising as its first step. This will encourage not only the growing of local crops, but also
their use by consumers. Local policy makers, journalists, and rural leaders, including
farmers themselves, need to be educated through different activities, such as school programmes, poetry, essay and drama, village fairs, news, social media, etc. Through their
daily interactions with the on-farm crop diversity and with neighbouring farmers, a local
farming community is likely to know more about the local crop genetic resources than

Plants 2022, 11, 2038

18 of 36

anyone else. This is a good reason for the incorporation of farmers into the national plant
genetic resources (PGRs) system, making them partners. The interaction of genebank
operators with the local community helps make farmers aware of their activities. This
interaction will benefit both parties because it facilitates farmer access to genebank material,
and the genebank will receive farmer cooperation to maintain crop genetic diversity insitu. Genebanks can also facilitate the communication between farmer groups scatteredthroughout a country, sharing resources and learning from one another. In this model,
on-farm conservation recognises local farmers as the curators of the crop genetic diversity
and links it with indigenous knowledge.
On-farm conservation should be targeted at uplifting the livelihoods of resource-poor
farmers. This can be achieved if development efforts are targeted at local resources toempower farmers, leading to the sustainable development of their livelihoods. This canbe approached through infrastructure development, securing new marketing opportunities for underutilised crops and varieties with identified nutritional value or other traits
with consumer preference. With demand growing for organic foods, organic certification
programmes can be introduced at village level. In many developing countries, whereindustrialisation/mechanisation has yet to occur in some areas and farming traditions goback many centuries, farmers have developed a sense of community and collaborative
relationships where they exchange seeds, planting material, and labour. In contrast tothis, in industrialised countries, farmers compete with each other and decisions are madebased on economic reasons, with tradition having much less influence on how farming ispracticed—this makes it more difficult to introduce on-farm conservation. Increased mechanisation has also seen farm sizes increase and mono-cropping replacing traditional farming
systems. As a result of the introduction of modern agricultural practices in Germany, forexample, 90% of the original diversity of landraces has been lost [139]. Nevertheless, witha strong genebanking tradition, Germany has managed to introduce on-farm conservation
practices better than many other industrialised countries, with about 50 initiatives launched
for in situ conservation [139].
Some wild species are threatened by overexploitation by communities living in the
periphery of conservation areas. The domestication of such species and propagation
through seed gardens with the participation of users has been proposed as an approachfor the conservation of genetic diversity of such species [140]. Studies on the changes inthe diversity of landraces on farms have been critically analysed and recommendations forfurther studies and conservation measures needed have been proposed in a recent review
by Khoury et al. [132].
6.2. Ex Situ Conservation
6.2.1. Origin of Genebanks and Their Spread
Nicolai Vavilov was one of the first to realise that the traditional crop varieties andland races were being lost from farmers’ fields where they originated. This led him toestablish the genebank in Petrograd in the 1920s, with 50,000 seed samples collected from
more than 50 countries as a result of his expeditions. Since then, several genebanks havebeen established, and seed exchanges with Western Europe, the USA, Australia, and New
Zealand have commenced. Those that are large or with a particularly wide scope include
the All Union Institute for Plant Industry (VIR), Leningrad (Saint Petersburg), establishedin 1920; the Empire Potato Collection, Cambridge, UK (1938), now operating from James
Hutton Institute, Invergowrie, Scotland; the Rockefeller Foundation Collections of maize
under the Mexican Agricultural Programme (1943) [141]; and the National Seed Storage
Laboratory, Fort Collins, CO, USA (1958). Similar collection efforts were commenced
in many other South American countries in collaboration with American Land Grant
Universities. By 1952, the USA had established four plant introduction stations in Ames
(Iowa), Pullman (Washington), Geneva (New York), and Griffin (Georgia). In Europe,
other than the VIR in the Soviet Union, significant work was conducted at the Institut für
Kulturpflanzenforschung in Vienna, where Hans Stubbe carried out collection missions:Plants 2022, 11, 2038

19 of 36

this institute was moved to Gatersleben in 1946 and now operates as the Leibniz-Institut
fur Pflanzengenetik und Kulturpflanzenforschung (IPK).
6.2.2. International and National Genebanks
The FAO, despite commencing the Plant Introduction Newsletter as far back as 1957,
did not have any on-ground programmes for collection and conservation until 1964. This
started to be addressed following an FAO Technical Meeting on Plant Exploration andIntroduction, where the recommendation for setting up national and regional plant introduction centres was proposed and adopted. The FAO Expert Panel on Plant Exploration
and Introduction was established in 1965 and held six meetings up to 1974, when the International Board for Plant Genetic Resources (IBPGR) was established. By the 1970s, many
initiatives on international collaboration were in place, which gained further momentum
with the establishment of the IBPGR [142] which, in 1991, became the International Plant
Genetic Resources Institute—IPGRI. Within two decades, its network supported collectionsof over 200,000 accessions in 136 countries and coordinated the creation of an internationallylinked system of genebanks called the Registry of Base Collections (Figure 7). Its aim is
to conserve and make a subset of those materials available for national programmes [143].
The international genebanks were established in the centres of diversity of particular crops,
but circumstances required moving some. For example, the war in Syria resulted in therelocation of the International Centre for Agricultural Research in the Dry Areas (ICARDA)
from Aleppo, Syria, to Beirut, Lebanon, with most of the research activities moved to Morocco [144]. In addition to the traditional eight centres (Figure 7), Bioversity International
holds a banana collection and supports aroid and yam genebanks in the Pacific. The Centre
for International Forestry Research (CIFOR) and the World Agroforestry Institute have tree
Plants 2022, 11, x FOR PEER REVIEW
20 of 38
and fruit crop collections, and the International Livestock Research Institute (ILRI) has afodder crops collection.

Figure 7.
7. TheThe location
location ofof thethe major
major international
international cropFigurecrop genebanks
genebanks under
under thethe Consortium
Consortium ofof InternaInternational Agricultural Research Centres (CGIAR) network. CIMMYT—International Wheat and Maize
tional Agricultural Research Centres (CGIAR) network. CIMMYT—International Wheat and Maize
Improvement Centre, CIAT—International Centre for Tropical Agriculture, ICARDA—InternaImprovement Centre, CIAT—International Centre for Tropical Agriculture, ICARDA—Internationaltional Centre for Agricultural Research, IRRI—International Rice Research Institute, ICRISAT—InCentre
for Agricultural
Research,
IRRI—International
RiceTropics,
ResearchILRI—International
Institute, ICRISAT—International
ternational
Crops ResearchInstitutefor the Semi-Arid
Livestock ReCrops
Research
InstitutefortheSemi-Arid
Tropics,
ILRI—International
Livestock Research
Insearch Institute, IITA—International Institute for Tropical Agriculture, CIP—International
Potatostitute,Tropical
CIP—International
Potato Centre.
Centre. IITA—International
Inset—location of theInstitute
Svalbardfor
GlobalSeedAgriculture,
Vault in the Arctic
Circle.
Inset—location of the Svalbard Global Seed Vault in the Arctic Circle.

In 2006, IPGRI centres signed an agreement with the Governing Body of the ITPGRFA, as a result of which the work of the centres is now influenced by Plant-Treatyrelated activities. In the 1970s and 1980s, many national genebanks were set up both inindustrialised and developing countries. Generally poorer in crop genetic diversity, industrialised countries gave technical support for setting up national genebanks in devel-

Plants 2022, 11, 2038

20 of 36

In 2006, IPGRI centres signed an agreement with the Governing Body of the ITPGRFA,
as a result of which the work of the centres is now influenced by Plant-Treaty-related
activities. In the 1970s and 1980s, many national genebanks were set up both in industrialised and developing countries. Generally poorer in crop genetic diversity, industrialised
countries gave technical support for setting up national genebanks in developing tropicalcountries with a rich diversity of plant genetic resources. For example, Sri Lanka’s Plant
Genetic Resources Centre was set up with the Japanese Technical Cooperation in 1988.
The FAO estimates that 1750 genebanks exist worldwide with a total holding of about
7.4 million accessions. Of these, about 6.6 million are held in the national genebanks of individual countries [145]. For example, India’s National Genebank holds around 0.39 million
accessions, with similar numbers spread across 41 National Active Germplasm Sites [146].
To further safeguard the collections, the Svalbard Global Seed Vault (SGSV) was
opened in 2008 under a partnership between the Ministry of Agriculture and Food of theGovernment of Norway, the Nordic Genetic Resource Centre (NordGen), and the Crop
Trust. It is a backup facility for all the genebanks around the world and holds 1.15 million
accessions in some 5000 species. It has a capacity for 4.5 million accessions and seeds
are held under black box conditions, i.e., the seed boxes and containers stored in SGSV
will not be opened. The seeds are indisputably owned by the depositing genebank, andonly that genebank can request the return of seeds stored in SGSV [147]. For example,
when the access to ICARDA genebank in Syria was finally closed in September 2015 due towar, seed boxes safely deposited in SGSV were systematically retrieved, regenerated, andmultiplied in Lebanon and Morocco for the continuation of ICARDA operations [144]. Thus,
located halfway between Norway and the North Pole, carved into ice in the permafrost
110 m above sea level, SGSV provides back-up for individual collections in the event thatthe original samples in conventional genebanks are lost due to natural disasters, humanconflict, changing policies, mismanagement, or any other circumstances [147]. Engels andEbert [148] recently critically reviewed the current global system of ex situ collections in
the context of political and legal frameworks.
6.3. Management of Ex Situ Collections
6.3.1. Management in Time
Under ex situ conservation, once the plant or seed samples are removed from the centre
where they have evolved, natural processes of selection and adaptation to the environment
cease. Thus, the collected sample is a “frozen snapshot” of the genetic structure at thetime of collection [149]. In the case of seeds, particularly in cross-pollinated species, therepresentativeness of the sample is further reduced every time it is regenerated, because ofgenetic drift and natural selective pressures under different environmental conditions.
In the centres of diversity, on the other hand, crop evolution is an ongoing phenomenon: the “loss” and origin of “new” alleles frequently occur; indeed, land race cultivar
dynamics are quite high [149,150]. Even in extensive collections from the Mediterranean region, researchers have found low geographic coverage and poor representation of on-farmgenetic diversity in ex situ collections established in Europe [151]. This is perhaps because
as for wild species diversity, a stratified sampling strategy is required for full coverage [152].
Notwithstanding, no matter how well sampled, ex situ collections do not represent thenatural population in the diversity hotspot, after a few decades. Therefore, a regularand systematic monitoring programme of the landrace cultivar population dynamics inwell-defined in situ hotspots is needed to better understand the drivers of change [150]and to supplement existing collections. Systematic monitoring programmes would enableproper sampling at regular intervals to capture the changing allelic frequencies, which isparticularly important for meeting breeding challenges in a changing climate.
6.3.2. Identification of Duplicates
With large numbers of accessions in genebanks, another issue confronted by curators
is the duplication of samples resulting from poor passport data and collection strategies,

Plants 2022, 11, 2038

21 of 36

inconsistent documentation, and a lack of characterisation, amongst other factors. Labelling
errors, hybridisation between stocks, and confusion about origins have also been identified
as problems in ex situ collections. With over 7 million existing accessions in genebanks
around the world [145] and increasing storage demands and costs, methods for efficientcharacterization and curation are required to avoid duplication. Genebanks have usedmolecular markers, such as simple sequence repeat (SSR), single-nucleotide polymorphism(SNP), amplified fragment length polymorphic (AFLP), and chloroplast DNA markers
to characterise collections for their diversity and to identify duplicates with the aim ofrationalising future collection and conservation efforts.
Lately, genome sequencing is being used to identify new patterns of variation [153,154],
alleles of interest for breeding programmes [155], as well as duplicates [156] in collections.
Methods are being developed to sequence large populations at low cost, including complex
polyploid genomes [157–159]. Additionally, genome sequencing enables the unravellingof patterns of evolution of ancient crops, such as apple [160], grape [161], rice [114], andwheat [162], giving insights to their progenitors and conservation needs. Furthermore,they enable quantitative trait mapping and novel allele mining from large genetic collections [163]. When applied across different genebanks, these methods will enable thecost-effective and efficient management of germplasm and better stewardship of valuablegenetic resources.
6.3.3. What to Conserve and Use—The Concept of Core Collections
It is practically impossible to cover the entire range of landraces or the diversity within
CWR in a genebank. To manage the increasing number of accessions in collections andthe resultant difficulties in monitoring, regeneration, evaluation, etc., the concept of corecollections arose [164]. Identifying ‘representative’ samples within large collections helps
to better utilise genetic resources when there are tens of thousands of accessions to choose
from with just basic passport data. Such subsets in a collection represent the maximum
diversity without redundancy. This allows the supply of a set of accessions for evaluationor breeding purposes without compromising the diversity within the collection.
With the introduction of the core set concept, genebanks now has a tool to manage
their collections more efficiently. Core collections have since become focal points forconservation prioritisation, phenotypic evaluation, genotyping, and exchange. In the earlyyears, the objective was to develop a single entry point for users, providing them withthe widest diversity within a manageable number of accessions. Collections were defined
hierarchically using taxonomic characterisation, genomic distance, and geographic data,
dividing the collection into clusters and selecting ‘core’ genotypes within those clusters
using methods such as proportional allocation, log frequency allocation, and constantallocation groups. Once a core collection is developed, it can be validated using several
methods, such as mean comparisons with the entire collection, the homogeneity of variancesand frequency distributions among traits between the entire collection and the core, andoptimising correlations [165].
Alternatively, diversity can be assessed using molecular markers, and core sets developed using a maximization of the number of alleles observed in each marker locus
without relying on a stratification strategy. This M (maximization) strategy examines all theaccessions for the alleles in the collection and identifies those that maximize the numberof observed alleles at the marker loci. These can then be chosen as final candidates forthe core. The superiority of this marker-based method is derived from the correlation
between observed allelic richness at the marker loci and allelic richness at other loci. The
software uses iterative procedures to select samples with the highest diversity as measured
by the number of alleles and the trait classes that account for the greatest proportion of thecollection variability based on the M strategy. The method can also be applied for bothquantitative and qualitative data [166]. For example, this method enabled the production ofa mini core subset of 217 accessions representing a core of 1794 accessions from the UnitedStates Department of Agriculture Agricultural Research Service (USDA-ARS) collection of

Plants 2022, 11, 2038

22 of 36

rice, comprising more than 18,000 accessions [167], and to produce a core of 20 accessions
within 450 apple accessions of the New Zealand apple germplasm repository, which wastargeted for the first round of cryopreservation using winter dormant buds [168,169].
Core collections can also be developed using a multivariate distance approach [170] todevelop the clusters followed by selection within those. Applying these methods, the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) has developed core
sets from global collections of eleven crop species in ICRISAT genebank accessions [171].
Subsequently, mini core collections have been developed within the core collection using
the same principles.
Core subsets for global collections, such as those maintained by the CGIAR, often serve
as reference panels so that researchers around the world can evaluate the same genetic
resources in different environments. Individuals in those reference sets may be selected
as “controls” for phenotyping efforts (particularly relevant for disease and pathogen resistance/susceptibility and adaptation to different agro-ecological zones) so that results can becompared among research and breeding programmes. Some plant collections, particularly
those that are clonally propagated, are difficult to distribute across international borders.
Hence, multinational plantings of international core subsets for clonally propagated collections would help ensure that international communities have access to the same plantmaterials for comparative research.
6.4. Types of Collections in Genebanks, Their Management and Utilization
Ex situ collections are conserved in different forms depending on the reproductive behaviour, genetic composition of the population, use of the crop (seed, fruit, fibre, vegetative
materials, etc.) and other considerations. These aspects are briefly discussed below, withreferences to recent studies for details.
6.4.1. DNA Banks
Plant DNA banks were initially developed to create genetic libraries for evolutionary
studies, to understand biological diversity, and to collect genomic information [172]. However, with habitat loss, species extinction is happening at a rapid rate, particularly in areas
with high genetic diversity. Therefore, DNA banks are increasingly used to store genomic
and diversity information of species in these vulnerable hot spots. Additionally, our ability
to extract DNA from fossilised plant remains is providing new research opportunities inpaleoecology, phylogeography, and evolution, including crop domestication. Therefore,
the number of DNA specimens from extinct species is increasing in DNA banks.
Genomic research has seen unprecedented advances in recent years. However, thephysical DNA from the published sequences is generally not accessible to researchers.
Access to the original samples is important for conducting new studies, to extend or complement existing results, and to support good scientific practice, enabling the verificationof published results. To address these needs, the Global Genome Biodiversity Network(GGBN) was formed in 2011, with the aim of developing high-quality, well-documented,
and vouchered collections that store DNA or tissue samples, as well as to encourage and enable scientists to complete documentation chains between vouchers, tissues, physical DNA,
sequences, and publications [173,174]. The GGBN currently has 99 member organisations
from 35 countries, with over 4.1 million samples from 5152 families, covering 38,074 generaand 140,182 species. Their updates can be viewed in annual newsletters [175] and the data
can be accessed through their data portal [176].
DNA banking is considered the most economical way of conserving genetic information of plant genetic resources, and is also the easiest way of exchanging genetic information
across borders because DNA samples occupy less space, are more stable, and phytosanitarycertification is not needed.

Plants 2022, 11, 2038

23 of 36

6.4.2. Orthodox Seeds
There are three types of seeds from a conservation perspective. Orthodox seeds can bedried to low moisture contents (about 3% for oily seeds and about 7% for starchy seeds)
without damage and be stored dry at low temperatures without losing their viability overlong periods. Recalcitrant seeds cannot withstand desiccation to moisture contents below
20%. Intermediate seeds can be dried to a moisture content of 10% to 12%, but further
desiccation reduces viability and/or dry seeds are injured by low temperatures. Seeds ofmost of the main crop species belong to the orthodox category, meaning that they can besafely cooled to standard long-term storage conditions of −18 ◦ C without losing viability
once dried to appropriate moisture contents. Seed storage is well researched and is the mostefficient and cost-effective method of the conservation of plant germplasm, with about 96%
of accessions held in genebanks worldwide as seeds [177]. In most of the genebanks, theseed vaults are maintained at −18 ◦ C for long-term storage, whereas active collections aremaintained at 5 ◦ C to 10 ◦ C. Seeds may be stored in dedicated cold rooms (Figure 8) or inchest freezers or refrigerators, for which genebank standards and technical
Plants 2022, 11,domestic
x FOR PEERdeep
REVIEW
guidelines have been published by the FAO [178].

24 of 3FigureSeed vaults
for long-term
storage Statesat the UnitedStates Departmentof Agriculture—Agr
Figure 8. Seed vaults
for8.long-term
storageat the United
Departmentof Agriculture—Agrcultural Research Service genebank in Fort Collins, Colorado.
icultural Research Service genebank in Fort Collins, Colorado.

There are many advantages of conserving germplasm as seeds, including better se

There are many advantages of conserving germplasm as seeds, including better security than in the natural environment, less space required, methods being simple, easil
curity than in the natural environment, less space required, methods being simple, easily
accessed and exchanged, and long storage periods. Additionally, seed collections captur
accessed and exchanged,
and long storage periods. Additionally, seed collections capture
more allelic diversity of the population than clonal collections. Therefore, in the case omore allelic diversityofthepopulation
thanconservation
clonal collections.
Therefore,
in thecase offruit crop wild
relatives, seedis an option.
However,
as mentioned
abovfruit crop wild relatives,
seed conservation
is anoption.
However,
as mentioned
above, themethod, rethe evolutionary
processes arefrozenin time:as in any
ex situ conservation
evolutionary processes
are frozen
in time:in anyex situconservation
method,regenera-and initia
generationis required
fromastime
to time.
There
can be gaps
in the collection
tion is required fromtime
time. Therecan be gaps
the collection
initial set-up,
set-up,andtoongoing
maintenancecan beincostly,
includingand
providinga constant poweand ongoing maintenancesupply. can be costly, including providing a constant power supply.
Under the ITPGRFA
multilateralsystem,there system,
are overthere
730,000
accessions
Under
the ITPGRFA
multilateralare over730,000 available
accessions availabl
fromofthecollections
the CGIAR
Theof these accessions
from the collections
the
CGIAR ofsystem.
The system.
majority
ofmajority
these accessions
are heldare
inheld in thofonlyseeds,23,862
with only
23,862 conservedin vitro
andin
29,122field collection
the form of seeds,form
withconserved
as clones as
in clones
vitro and
29,122fieldincollec[143]. Theofnumberof accessions
accordingto the species
and11 participating genetions [143]. The number
accessions
accordingto the species
and the11theparticipating
banks
are
listed[143].
Additionally,
the
IBPGR
has
also
coordinatedthe creationof agenebanks are listed [143]. Additionally, the IBPGR has also coordinated the creationofinternationallylinkedsystemofgenebanks
known
as
the
RegistryofBaseCollection
an internationally linked system of genebanks known as the Registry of Base Collections(RBC)
conserve
and makea subsetof thosematerialsUnder
available.
this system(RBC) to conserve
andtomakea subsetof thosematerials
available.
thisUnder
system,144,000 accessions are available in 52 selected genebanks spread across all continents, cov
144,000 accessions are available in 52 selected genebanks spread across all continents, covering 80 genera and 250 species [179]. Engels and Ebert [177] recently critically reviewe
ering 80 genera and 250 species [179]. Engels and Ebert [177] recently critically reviewed
the current status of global seed banking with recommendations for improvement, em
the current status of global seed banking with recommendations for improvement, emphaphasising the role of functional genomics and phenomics as well as strengths and weaksising the role of nesses
functional
genomics
andphenomicsandas thewellstrategies
as strengths
and weaknesses
withinregulatory
frameworks
for linking
national programmewithin regulatorywith
frameworks
andthestrategies
forlinking
national
programmeswith thethe global network.
global network.
6.4.3. Genebanking of Clonal Crops and Recalcitrant Species
Field Collections

The traditional approach for maintaining germplasm of clonal species, species tha
are sterile or semi-sterile, and those producing recalcitrant seeds, is in field genebank
They provide an excellent opportunity for curators to assess the diversity by phenotypin

Plants 2022, 11, 2038

24 of 36

6.4.3. Genebanking of Clonal Crops and Recalcitrant Species
Field Collections
The traditional approach for maintaining germplasm of clonal species, species thatare sterile or semi-sterile, and those producing recalcitrant seeds, is in field genebanks.
They provide an excellent opportunity for curators to assess the diversity by phenotyping
and for plant breeders to directly use accessions in their breeding programmes. Woody
perennial crops (WPCs) represent about one-half of crop plant diversity and one-third of
the 167 major crops. WPCs are usually clonally propagated because they are obligately
outcrossing. Therefore, the conservation of germplasm through seed banks is not applicableto maintain the genetic characteristics of different heterozygous individuals. Moreover, theseeds of many species are recalcitrant, and therefore cannot be stored in traditional seedbanks. Additionally, WPC species have a juvenile stage that can last for several years. In
fact, plants generated from seeds usually exhibit strong, undesirable juvenile characters,such as a thorny habit and delayed flowering and fruit production [180]. In order to avoid
these problems, the long-term conservation of WPC germplasm can be effectuated as fieldcollections with clonal material in order to maintain the elite genotypes that form thefoundation of woody perennial agriculture. However, WPCs represents only 5.8% of ex
situ germplasm collections. Despite their importance, field collections are expensive toestablish, and maintenance requires high costs for specialized technical personnel andland. Usually, woody perennials have a large plant size and therefore need large areas formaintenance in the field. Moreover, field collections have high risks of loss because they
are exposed to natural disasters and are subject to biotic and abiotic stresses. In particular,
the risk of pathogen infections transmitted through vegetative propagation is high anddifficult to avoid. There are many examples of such cases, e.g., the loss of accessions in theapple germplasm collection in USDA due to fireblight (Erwinia amylovora) [181] and theloss of kiwifruit germplasm in New Zealand due to the incursion of Psuedomonas syringae
pv. actinidiae [182]. Therefore, many genebanks back up their field collections in separate
locations and also, more reliably, using lab-based conservation methodologies such as
in vitro storage or cryostorage.
Establishing field genebanks may seem straightforward, but there are established bestpractices for sampling, the duplication of collections, and cataloguing the accessions. Thesecan be found, for example, in the IPGRI training manual on “Establishment and management of field genebanks” [183], which has separate chapters on principles, legal issues,
plant health, choice of materials, genetic considerations, planting layout, management
characterisation and evaluation, utilisation, and economics. Another useful document is
the IPGRI handbook No 7 on “Technical guidelines for the management of field and in vitro
genebanks” [184]. Field genebanks of horticultural crops are a long-term commitment.
Therefore, in many countries, field collections and genebank operations are undertaken by
government departments.
In Vitro Collections
In general, lab-based germplasm conservation strategies fall under two major categories: slow growth procedures and cryopreservation. Both strategies require efficient
regeneration system with high regeneration efficiency via organogenesis and/or somatic
embryogenesis. In vitro storage has the advantage of maintaining collections under diseasefree conditions and the cultures have fewer biosecurity requirements when material isexchanged across borders. On the other hand, because collections have high genetic diversity, the response to tissue culture media will be variable, which therefore requires priorresearch to optimise media for different species and even genotypes within species. There
have been many studies on the tissue culture of cultivated species; therefore, this is not as
daunting as it used to be a few decades ago. In vitro genebanks enable the rapid multiplication of material when required and provide a safe environment for managing germplasm
collections in a confined space away from the field. To avoid somaclonal variation (genetic
variation induced under tissue culture conditions), pathways using dedifferentiation andPlants 2022, 11, 2038

25 of 36adventitious regeneration should be avoided. Therefore, intact shoot tips and axillary buds
are typically used with minimal use of plant growth regulators.
After initiation and the multiplication of accessions in tissue culture, they are stored
under slow-growth conditions to increase the period between subcultures, thus significantly
reducing the cost of labour and materials. Generally, this is achieved by a combinationof several factors: (a) decreased light (generally about 5–10% of the standard culture
conditions); (b) low temperature between 4 and 21 ◦ C with tropical species requiring higher
temperatures; (c) lower concentration of mineral nutrients and sucrose in media, often
without growth regulators; (d) smaller size of culture vessel/vial; (e) inclusion of growth
retardants in media; and (f) osmotic stress using chemicals [62,185,186]. Unless available in
the literature, these conditions need to be determined for each species by experimentation.
Many genebanks around the world have in vitro storage for some species. Genebanks
holding large numbers of accessions in vitro are given in Table 4.
Synthetic seed technology (SST) is an innovative and sustainable approach to preserve
the biodiversity of clonally propagated woody perennials. A synthetic seed is defined as
an artificially encapsulated somatic embryo, vegetative bud, or any other micropropagulethat plays the role of a seed and has the ability to give rise to a complete true-to-type plant.
SST offers opportunities to conserve clonal genetic resources safely at low cost.
General guidelines for the storage [187] and status of in vitro storage under the CGIAR
network, particularly CIP, IITA, CIAT, and Bioversity International [188], have been published. Additionally, in vitro techniques have proven useful in collecting germplasm whenseeds are not available (off-season), or in situations where seeds are not likely to remain
viable because of their recalcitrant nature. Pence et al. [189] recently reviewed basic approaches and principles of in vitro collection, and one of the crop species for which in vitro
collection is routinely used is coconut.
Table 4. Genebanks with large in vitro collections.
Genebank

Country

Crop

Number ofAccessions

Reference

International Potato Centre

Peru

Potato, Andean Rootand Tubers>11,000

CIP-Genebank [190]Cassava>2500

International Institute for Tropical Agriculture

Nigeria

Yam

>2500

Banana>500

EMBRAPA Genebank

Brazil24 genera, 63 species

1250

Cunha Alves, et al. [192]Agricultural Research Council

South Africa

Potato1100

Myeza and Visser [193]Fruit crops

743

Tuber crops

611

Spices380

Bulbous crops

171

National Bureau of Plant Genetic Resources

India

Medicinal and Aromatic

170

Total 24 Genera, 63 spp.

1250

IITA-GRC [191]Tyagi and Agrawal [194]Bioversity International Transit Centre

Belgium

Musa spp.

>1500

ITC [195]

International Centre for Tropical Agriculture (CIAT)

Columbia

Cassava

6632

Rondon [186]

The New Zealand Institute for Plant and Food
Research Limited

New ZealandKiwifruit (Actinidia spp.)

1012

Debenham andPathirana [62]United States Department of Agriculture
Agricultural Research Service

USA

Potato~1000

Bamberg et al. [196]Cryopreserved Collections—Stopping the Biological Clock
Cryopreservation is the storage of biological samples in liquid nitrogen (LN) at−196 ◦ C or in its vapour phase (LNV) at −165 ◦ C to −196 ◦ C. The demonstration that win-

Plants 2022, 11, 2038

26 of 36

ter shoots of woody species can be conserved in liquid nitrogen in 1960 by Sakai [197] gave
the impetus to undertake research on cryopreservation of fruit tree germplasm [198]. In themeantime, Latta [199] demonstrated the survival of carrot and sweet potato cell cultures in
LN when pre-treated with high concentrations of sucrose followed by freezing to −40 ◦ C
and subsequent transfer to LN. This method came to be called classical two-step freezing or
slow freezing. However, it was the advent of vitrification methods in the 1990s that allowed
genebanks to take up cryopreservation on a mass scale as it became applicable across different families and genera. The method relies on the dehydration of cellular content to theextent that sudden freezing does not allow water molecules to form lethal ice crystals, but
enters a state of metastable glass—hence the term vitrification. Vitrification can be applied
to naked meristematic explants, such as shoot tips and embryogenic cells, or to propagules
protected by encapsulation in alginate beads [200,201]. The most widely used vitrification
solution is Plant Vitrification Solution 2 [202] and the method is droplet vitrification, where
propagules are held on an aluminium strip covered in a droplet of vitrification solution
and directly immersed in LN. However, the recently developed V cryo-plate technique,where droplet vitrification and encapsulation techniques are combined, has shown an improvement in recovery over droplet vitrification in some crops [203–205]. The two methods
as applied to grapevine have been described by Bettoni et al. [206]. Another advantage ofcryopreservation using vitrification is its ability to eliminate viruses, phytoplasma, andbacteria [169,207–213] for the delivery of high-health propagation material.
Through cryopreservation, viable explants can be brought to a state where cellulardivision and metabolic processes are minimized to the extent that they cease, preserving
the structure and function of the biological system—virtually stopping the biological clock.
There are no biochemical processes or gene expression; therefore, the genetic material
is safe from any changes, and is hence ideal for conservation. Most of the protocols
depend on a tissue culture phase (except the dormant bud technique used mainly forapple cryopreservation); thus, it is important to ensure the precautions mentioned in
the previous section are taken to avoid somaclonal variation. It is also cost-effective tomaintain collections for extended periods of time in LN compared with field or in vitro
collections [214], and the cost effectiveness increases as more accessions are added to thecollection [215]. LN is used to freeze material, so the method is not dependent on an electric
power supply; hence, it is an attractive method for countries with an insecure power supply,
although it is dependent on a reliable LN supply.
The use of cryobanking in genebanks using vitrification methods has recently beensummarised by Wang et al. [200], and for the USDA, currently the world’s largest cryocollection, by Jenderek and Reed [216]. Panis [217] recently summarised the major cryopreserved collections worldwide. It is estimated that about 10,000 accessions are in long-term
cryostorage using explants from in vitro culture material (mainly vitrification methods). Of
these, over 80% belong to five species: potato (38%), cassava (22%), bananas and plantains(11%), mulberry (12%,) and garlic (5%). Other large collections are in apple, using winterdormant buds. Cryopreservation is also used for intermediate and recalcitrant seed cropconservation, such as coconut [218] and coffee [215], as well as for pollen. Pollen is naturally
dehydration-tolerant and can be used to conserve the nuclear genetic diversity of CWR,
recalcitrant species, endangered and rare species, and fruit and ornamental crops. The
cryopreservation of pollen allows access to pollen when needed by breeders, particularly
useful when breeding lines have differing flowering times, the use of CWR in breeding
programmes, and for hybrid seed production programmes. Cryopreserving the pollen of
male sterile lines for use on female lines can save large amounts of land in hybrid seedproduction fields and labour to collect pollen during busy periods of hybridisation. Pollenof many tropical plant species has successfully been cryopreserved: for example, the Indian
Institute of Horticultural Research in Bangalore holds 650 samples of pollen from 45 species
belonging to 15 plant families [219].
Synthetic seeds can be stored for long periods using vitrification-based cryopreservation [220,221]; both somatic embryos and other somatic tissues with meristematic regions

Plants 2022, 11, 2038

27 of 36

have been used in cryopreservation and methods have been optimized to achieve post-thaw
regeneration rates that meet genebank standards for the implementation of cryopreservation [201,206,222,223]. However, high genetic variability in the somatic embryogenesis
response [224,225] is a barrier to use this propagule in cryopreservation.
Cryopreservation is only applied to a limited number of crops in some tropicalgenebanks outside the CGIAR system. Interestingly, the banana genebank, including
the cryo-collection, is in Europe [226]. Since the introduction of vitrification methods, cryopreservation has become operationally simple and easily adaptable to any laboratory withtissue culture facilities. Collections of many tropical species, such as cassava, banana, sweet
potato, and taro, are already being cryopreserved for their long-term security. The challenge
is with CWR plus rare and endangered species of the tropics because their seeds are often
recalcitrant and therefore cannot be preserved in traditional seed banks. Botanic gardens
may only have one or a few specimens of each species in their field genebanks; however,the cryopreservation of seeds/embryonic axes and pollen enables the conservation of amuch broader genetic diversity of CWRs or endangered species. Genebanks therefore
need to invest in infrastructure and human resources for cryo-conservation. The integrated
conservation strategies described above were recently used to save iconic New Zealand
Myrtaceae species after the incursion of myrtle rust (Austropuccinia psidii) into New Zealandin 2017 [227]. The techniques used included the cryopreservation of pollen of Metrosideros
excelsa and zygotic embryos of recalcitrant Syzygium maire, along with the successful handpollination of flowers of Metrosideros bartlettii, a critically endangered species with only
a few plants in the wild. Ex situ conservation strategies in field genebanks, in vitro slow
growth, and the advantages and disadvantages of cryopreservation have recently beenreviewed by Panis et al. [226].
7. Challenges to Plant Breeding in Search of Right Germplasm
Germplasm resources including CWRs carry alleles that are integral to creating newcrop cultivars that can meet increasing consumer and environment demands. As changes
in environmental conditions accelerate, so does the need for germplasm resources to breed
more environmentally resilient crops. Properly characterised germplasm with information
available to the plant breeding community will enable the deployment of improved cultivars on an ongoing basis. New cultivars with better water use efficiency, tolerance to soil
toxicities, fertiliser response, and pest and disease tolerance will enable the replacementof at least some part of the costs for fertiliser, irrigation, and pesticides. Selection of theright genotype is the most effective means to achieve yield and quality improvements incrops, keeping other inputs to a minimum. Although plant breeders are often well awareof the necessity of maintaining genetic diversity in their breeding populations, they maylack the information to determine which of the thousands of accessions of a given cropwould prove most beneficial for their breeding objectives. They may also be reluctant tointroduce unadapted germplasm, with potentially negative impacts on quality, into theirelite breeding materials. In some cases, they may lack the technical expertise or facilities
to make interspecific crosses, for example, between CWR and cultivars of different ploidy
levels that often require embryo rescue, in vitro pollination, and other interventions. Therefore, plant breeders should have access to facilities and expertise in plant biotechnology forthe better utilisation of PGR.
Many international genebanks have a mandate to supply germplasm if the requests
are justified. With more and more accessions being characterised and accessible databases
made available, plant breeders should be trained in accessing the germplasm that matches
their needs. The USDA-ARS holds over 576,000 accessions from 15,116 species and in2015 alone, distributed over 239,000 accessions on request to national and international
researchers [228]. The accessions available for supply can be searched in the Germplasm
Resources Information Network-Global (GRIN-Global) database and ordered [229]. The
CGIAR system of 11 genebanks holds over 736,000 accessions, with wheat and rice accounting for >196,000 and >144,000, respectively. Other major collections are in sorghum

Plants 2022, 11, 2038

28 of 36(>39,200), beans (~38,000), barley (>31,500), maize (>29,700), pearl millet (>23,000), andforages and fodder (>44,000). The CGIAR system distributed over 3.9 million samples overa 10-year period from 2007 to 2016 [143]. The CGIAR system of networks has developed aGlobal Information System (GLIS), with an emphasis of assigning a unique digital object
identifier (DOI) to each accession; these are linked to the GRIN-Global searchable database
and to Genesys—an online database for global plant collections managed by the Crop
Trust [230]. The VIR collection holds 346,666 accessions of PGR and CWRs, representing
64 botanical families, 376 genera, and 2169 species. Annually, 12,000–14,000 accessions
are distributed by the genebank, of which 2000–3000 accessions are supplied outside
Russia [25].
8. Conclusions
Significant improvements have been made for the better management of PGRs withininternational and national genebanks in the last few decades. More attention is being
paid to managing ‘difficult’ species with recalcitrant seeds, clonal crops, and CWRs. Effective research and development mechanisms and policies have been established for theprotection and conservation of biodiversity worldwide. Many countries have signed international treaties on biodiversity, as well as PGR conservation and exchange. Coordination
among genebank curators, breeders, farming communities, government organisations, anddifferent stakeholders should be strengthened to meet global obligations for sustainable
management and the use of PGR for food and nutritional security. Genebank accessions
are of no use unless they are accessible online or can be observed in the field. Therefore,
conserved PGRs need to be characterised using advanced technologies and results withpassport data made available for online access by users. The emphasis should be on duplicating collections for better security, creating and securing core collections, identifying
gaps in collections and remediating them, and using advanced and integrated strategies
for the conservation and dissemination of information. CWR and landrace varieties need
to be secured for the future, using multiple strategies including in situ, on-farm, and ex situ
conservation. Further exploration and collection of PGR from diversity-rich centres should
also assume priority, recognising the high rate of loss of genetic diversity.
Author Contributions: Conceptualization, R.P. and F.C.; writing-original draft preparation, R.P. andF.C.; Writing-review and editing, R.P. and F.C. All authors have read and agreed to the publishedversion of the manuscript.
Funding: This research received no external funding.
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not applicable.
Data Availability Statement: Not applicable.
Conflicts of Interest: The authors declare no conflict of interest.

References
1.
2.
3.

4.

5.

FAO. The Food and Agriculture Organisation. The State of Food Security and Nutrition in the World 2019. Safeguarding against Economic
Slowdowns and Downturns. Available online: http://www.fao.org/3/ca5162en/ca5162en.pdf (accessed on 2 February 2022).
UN. United Nations 2030 Agenda for Sustainable Development—Sustainable Development Goals. Goal 2: Zero Hunger. Available
online: https://www.un.org/sustainabledevelopment/hunger/ (accessed on 7 June 2022).
FAO. The State of Food Security and Nutrition in the World 2021: Transforming Food Systems for Food Security, Improved
Nutrition and Affordable Healthy Diets for All. Available online: https://www.fao.org/3/cb4474en/online/cb4474en.html(accessed on 25 May 2022).
IPBES. Global Assessment Report of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services; The Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES)—IPBES Secretariat: Bonn, Germany, 2019;p. 1144.
IPCC. An IPCC Special Report on Climate Change, Desertification, Land Degradation, Sustainable Land Management, Food
Security, and Greenhouse Gas Fluxes in Terrestrial Ecosystems. Available online: https://www.ipcc.ch/site/assets/uploads/20
19/11/Headline-statements_Final.pdf (accessed on 5 May 2022).

Plants 2022, 11, 2038

6.
7.
8.
9.
10.
11.
12.

13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.

29.
30.
31.
32.

33.
34.
35.
36.
37.

29 of 36

Song, X.-P. Global estimates of ecosystem service value and change: Taking into account uncertainties in satellite-based land
cover data. Ecol. Econ. 2018, 143, 227–235. [CrossRef]
Xu, H.; Cao, Y.; Yu, D.; Cao, M.; He, Y.; Gill, M.; Pereira, H.M. Ensuring effective implementation of the post-2020 global
biodiversity targets. Nat. Ecol. Evol. 2021, 5, 411–418. [CrossRef] [PubMed]
CBD. A New Global Framework for Managing Nature Through 2030: First Detailed Draft Agreement Debuts. Available online:
https://www.cbd.int/article/draft-1-global-biodiversity-framework (accessed on 7 June 2022).
Stevenson, J.R.; Villoria, N.; Byerlee, D.; Kelley, T.; Maredia, M. Green Revolution research saved an estimated 18 to 27 million
hectares from being brought into agricultural production. Proc. Natl. Acad. Sci. USA 2013, 110, 8363–8368. [CrossRef] [PubMed]
Pingali, P.L. Green Revolution: Impacts, limits, and the path ahead. Proc. Natl. Acad. Sci. USA 2012, 109, 12302–12308. [CrossRef]
Karesh, W.B.; Dobson, A.; Lloyd-Smith, J.O.; Lubroth, J.; Dixon, M.A.; Bennett, M.; Aldrich, S.; Harrington, T.; Formenty, P.; Loh,
E.H.; et al. Ecology of zoonoses: Natural and unnatural histories. Lancet 2012, 380, 1936–1945. [CrossRef]
Jones, B.A.; Grace, D.; Kock, R.; Alonso, S.; Rushton, J.; Said, M.Y.; McKeever, D.; Mutua, F.; Young, J.; McDermott, J.; et al.
Zoonosis emergence linked to agricultural intensification and environmental change. Proc. Natl. Acad. Sci. USA 2013, 110,
8399–8404. [CrossRef]
Olivero, J.; Fa, J.E.; Real, R.; Márquez, A.L.; Farfán, M.A.; Vargas, J.M.; Gaveau, D.; Salim, M.A.; Park, D.; Suter, J.; et al. Recent
loss of closed forests is associated with Ebola virus disease outbreaks. Sci. Rep. 2017, 7, 14291. [CrossRef]
Rulli, M.C.; Santini, M.; Hayman, D.T.S.; D’Odorico, P. The nexus between forest fragmentation in Africa and Ebola virus disease
outbreaks. Sci. Rep. 2017, 7, 41613. [CrossRef]
Everard, M.; Johnston, P.; Santillo, D.; Staddon, C. The role of ecosystems in mitigation and management of COVID-19 and otherzoonoses. Environ. Sci. Policy 2020, 111, 7–17. [CrossRef]
Zhao, C.; Liu, B.; Piao, S.; Wang, X.; Lobell, D.B.; Huang, Y.; Huang, M.; Yao, Y.; Bassu, S.; Ciais, P.; et al. Temperature increase
reduces global yields of major crops in four independent estimates. Proc. Natl. Acad. Sci. USA 2017, 114, 9326–9331. [CrossRef]
Muehe, E.M.; Wang, T.; Kerl, C.F.; Planer-Friedrich, B.; Fendorf, S. Rice production threatened by coupled stresses of climate andsoil arsenic. Nat. Commun. 2019, 10, 4985. [CrossRef] [PubMed]
Meharg, A.A. Arsenic in rice—understanding a new disaster for South-East Asia. Trends Plant Sci. 2004, 9, 415–417. [CrossRef][PubMed]Hassan, F.I.; Niaz, K.; Khan, F.; Maqbool, F.; Abdollahi, M. The relation between rice consumption, arsenic contamination, andprevalence of diabetes in South Asia. EXCLI J. 2017, 16, 1132–1143. [CrossRef] [PubMed]
Morris, J.L.; Puttick, M.N.; Clark, J.W.; Edwards, D.; Kenrick, P.; Pressel, S.; Wellman, C.H.; Yang, Z.; Schneider, H.; Donoghue,
P.C.J. The timescale of early land plant evolution. Proc. Natl. Acad. Sci. USA 2018, 115, E2274–E2283. [CrossRef]
Petraglia, M.D.; Haslam, M.; Fuller, D.Q.; Boivin, N.; Clarkson, C. Out of Africa: New hypotheses and evidence for the dispersalof Homo sapiens along the Indian Ocean rim. Ann. Hum. Biol. 2010, 37, 288–311. [CrossRef]
Vavilov, N.I. Origin and Geography of Cultivated Plants; Nauka: Leningrad, Russia, 1987. (In Russian)
Cohen, B.M. Nikolai Ivanovich Vavilov: The explorer and plant collector. Econ. Bot. 1991, 45, 38–46. [CrossRef]
Zakharov, I.A. Nikolai I Vavilov (1887–1943). J. Biosci. 2005, 30, 299–301. [CrossRef]
Dzyubenko, N.I. Vavilov’s collection of worldwide crop genetic resources in the 21st Century. Biopreservation Biobanking 2018, 16,
377–383. [CrossRef]
Vavilov, N.I. The law of homologous series in variation. J. Genet. 1922, 12, 47–89. [CrossRef]
Voigt, W. Einige Gedanken zuVavilovs Gesetz der homologen Reihen und zu den Ursachen homologer genetischer Variationen
aus wissenschaftstheoretischer Sicht. Die Kulturpflanze 1988, 36, 163–168. [CrossRef]
Cheng, F.; Sun, R.; Hou, X.; Zheng, H.; Zhang, F.; Zhang, Y.; Liu, B.; Liang, J.; Zhuang, M.; Liu, Y.; et al. Subgenome parallel
selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea.
Nat. Genet. 2016, 48, 1218–1224. [CrossRef]
Maluszynski, M.; Ahloowalia, B.S.; Sigurbjörnsson, B. Application of in vivo and in vitro mutation techniques for crop improvement. Euphytica 1995, 81, 303–315. [CrossRef]
Pathirana, R. Plant mutation breeding in agriculture. CAB Rev. Perspect. Agric. Vet. Sci. Nutr. Nat. Resour. 2011, 6, 1–20. [CrossRef]
Foster, K.W.; Rutger, J.N. Inheritance of semidwarfism in rice Oryza sativa L. Genetics 1978, 88, 559–574. [CrossRef] [PubMed]
Rutger, J.N. Plant Mutation Breeding for Crop Improvement, Volume 1, Proceedings of the FAO/IAEA Symposium on Plant Mutation
Breeding for Crop Improvement, Vienna, Austria, 18–22 June 1990; International Atomic Energy Agency: Vienna, Austria, 1991;
pp. 155–165.
Pathirana, R. Gamma-ray-induced field tolerance to Phytophthora blight in Sesame. Plant Breed. 1992, 108, 314–319. [CrossRef]
Pathirana, R.; Weerasena, L.A.; Priyanthi, B. Development and release of gamma ray induced sesame mutant ANK-S2 in Sri
Lanka. Trop. Agric. Res. Ext. 2000, 3, 19–24.
Zhukovsky, P.M. Cultivated Plants and Their Progenitors; Kolos: Leningrad, Russia, 1971; p. 750. (In Russian)Harlan, J.R. Crops and Man; Crop Science Society of America: Madison, WI, USA, 1992.
Meyer, R.S.; DuVal, A.E.; Jensen, H.R. Patterns and processes in crop domestication: An historical review and quantitative
analysis of 203 global food crops. New Phytol. 2012, 196, 29–48. [CrossRef]

Plants 2022, 11, 2038

38.

39.
40.
41.
42.
43.
44.
45.
46.

47.
48.
49.
50.

51.
52.
53.
54.
55.
56.

57.
58.
59.
60.
61.
62.

63.
64.
65.
66.
67.

68.

30 of 36

Wang, M.; Yu, Y.; Haberer, G.; Marri, P.R.; Fan, C.; Goicoechea, J.L.; Zuccolo, A.; Song, X.; Kudrna, D.; Ammiraju, J.S.S.; et al. The
genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat. Genet. 2014, 46, 982–988.
[CrossRef]
Scarcelli, N.; Cubry, P.; Akakpo, R.; Thuillet, A.C.; Obidiegwu, J.; Baco, M.N.; Otoo, E.; Sonke, B.; Dansi, A.; Djedatin, G.; et al.
Yam genomics supports West Africa as a major cradle of crop domestication. Sci. Adv. 2019, 5, eaaw1947. [CrossRef]
Oumar, I.; Mariac, C.; Pham, J.-L.; Vigouroux, Y. Phylogeny and origin of pearl millet (Pennisetum glaucum [L.] R. Br) as revealedby microsatellite loci. Theor. Appl. Genet. 2008, 117, 489–497. [CrossRef]
Li, H.-L. The origin of cultivated plants in Southeast Asia. Econ. Bot. 1970, 24, 3–19.
Purugganan, M.D.; Fuller, D.Q. The nature of selection during plant domestication. Nature 2009, 457, 843–848. [CrossRef]
Hyten, D.L.; Song, Q.; Zhu, Y.; Choi, I.-Y.; Nelson, R.L.; Costa, J.M.; Specht, J.E.; Shoemaker, R.C.; Cregan, P.B. Impacts of genetic
bottlenecks on soybean genome diversity. Proc. Natl. Acad. Sci. USA 2006, 103, 16666–16671. [CrossRef] [PubMed]
Li, Y.-H.; Zhou, G.; Ma, J.; Jiang, W.; Jin, L.-G.; Zhang, Z.; Guo, Y.; Zhang, J.; Sui, Y.; Zheng, L.; et al. De novo assembly of soybean
wild relatives for pan-genome analysis of diversity and agronomic traits. Nat. Biotechnol. 2014, 32, 1045–1052. [CrossRef]
Khush, G.S. Green revolution: The way forward. Nat. Rev. Genet. 2001, 2, 815–822. [CrossRef]
Zakharova, E.S.; Epishin, S.M.; Vinetski, Y.P. An attempt to elucidate the origin of cultivated soybean via comparison of nucleotide
sequences encoding glycinin B4 polypeptide of cultivated soybean, Glycine max, and its presumed wild progenitor, Glycine soja.
Theor. Appl. Genet. 1989, 78, 852–856. [CrossRef] [PubMed]
Wang, K.-J.; Takahata, Y. A preliminary comparative evaluation of genetic diversity between Chinese and Japanese wild soybean(Glycine soja) germplasm pools using SSR markers. Genet. Resour. Crop Evol. 2007, 54, 157–165. [CrossRef]
Doyle, J.J. 5S ribosomal gene variation in the soybean and its progenitor. Theor. Appl. Genet. 1988, 75, 621–624. [CrossRef]
Mikel, M.A.; Diers, B.W.; Nelson, R.L.; Smith, H.H. Genetic diversity and agronomic improvement of North American soybean
germplasm. Crop Sci. 2010, 50, 1219–1229. [CrossRef]
Specht, J.E.; Williams, J.H. Contribution of Genetic Technology to Soybean Productivity—Retrospect and Prospect. In Genetic
Contributions to Yield Gains of Five Major Crop Plants; Fehr, W.R., Ed.; Crop Science Society of America: Madison, WI, USA, 1984;
pp. 49–74.
Bisaliah, S. Soybean Development in India; UN/ESCAP CGPRT Centre: Bogor, Indonesia, 1986; p. 111.
Agarwal, D.K.; Billore, S.D.; Sharma, A.N.; Dupare, B.U.; Srivastava, S.K. Soybean: Introduction, improvement, and utilization inIndia—Problems and prospects. Agric. Res. 2013, 2, 293–300. [CrossRef]
Herath, E. Cultivation and uses of soybeans in Sri Lanka. In INTSOY Series—International Soybean Program (USA); College ofAgricultural, University of Illinois at Urbana-Champaign: Champaign, IL, USA, 1976; Volume 10, pp. 250–252.
Chithrapala, N.H.M.S.; Aberathne, M.S.; Samarakoon Manike, S.M.; Pushpakumara, U. MISB 01—A new soybean [Glycine max(L.) Merill] variety for the dry and intermediate zones of Sri Lanka. Ann. Sri Lanka Dep. Agric. 2015, 17, 180–186.
Škorić, D. Achievements and future directions of sunflower breeding. Field Crops Res. 1992, 30, 231–270. [CrossRef]
Goryunova, S.V.; Goryunov, D.V.; Chernova, A.I.; Martynova, E.U.; Dmitriev, A.E.; Boldyrev, S.V.; Ayupova, A.F.; Mazin, P.V.;
Gurchenko, E.A.; Pavlova, A.S.; et al. Genetic and phenotypic diversity of the sunflower collection of the Pustovoit All-Russia
Research Institute of Oil Crops (VNIIMK). Helia 2019, 42, 45–60. [CrossRef]
Gavrilova, V.A.; Anisimova, I.N. Genealogy of the sunflower lines created on the basis of Russian varieties. Helia 2017, 40, 133–146.
[CrossRef]
Kumamoto, J.; Scora, R.W.; Lawton, H.W.; Clerx, W.A. Mystery of the forbidden fruit: Historical epilogue on the origin of thegrapefruit, Citrus paradisi (Rutaceae). Econ. Bot. 1987, 41, 97–107. [CrossRef]
Ferguson, A.R. Kiwifruit: The wild and the cultivated plants. Adv. Food Nutr. Res. 2013, 68, 15–32. [CrossRef]
Ferguson, A.R.; Huang, H. Genetic resources of kiwifruit: Domestication and breeding. Hortic. Rev. 2007, 33, 1–121.
Huang, H.; Wang, Y.; Zhang, Z.; Jiang, Z.; Wang, S. Actinidia germplasm resources and kiwifruit industry in China. Hortscience
2004, 39, 1165–1172. [CrossRef]
Debenham, M.; Pathirana, R. Establishment and management of an in vitro repository of kiwifruit (Actinidia spp.) germplasm. In
Meta-Topolin: A Growth Regulator for Plant Biotechnology and Agriculture; Ahmad, N., Strnad, M., Eds.; Springer Nature: Cham,
Switzerland, 2020; pp. 279–291.
Abraham, K.; Gopinathan Nair, P. Polyploidy and sterility in relation to sex in Dioscorea alata L. (Dioscoreaceae). Genetica 1991, 83,
93–97. [CrossRef]
Meyer, R.S.; Purugganan, M.D. Evolution of crop species: Genetics of domestication and diversification. Nat. Rev. Genet. 2013, 14,
840–852. [CrossRef]
Fuller, D.Q.; Harvey, E.L. The archaeobotany of Indian pulses: Identification, processing and evidence for cultivation. Environ.
Archaeol. 2006, 11, 219–246. [CrossRef]
Fuller, D.Q. Contrasting patterns in crop domestication and domestication rates: Recent archaeobotanical insights from the Old
World. Ann. Bot. 2007, 100, 903–924. [CrossRef] [PubMed]
Fuller, D.Q.; Denham, T.; Arroyo-Kalin, M.; Lucas, L.; Stevens, C.J.; Qin, L.; Allaby, R.G.; Purugganan, M.D. Convergent evolution
and parallelism in plant domestication revealed by an expanding archaeological record. Proc. Natl. Acad. Sci. USA 2014, 111,
6147–6152. [CrossRef] [PubMed]
Li, C.; Zhou, A.; Sang, T. Rice domestication by reducing shattering. Science 2006, 311, 1936–1939. [CrossRef]

Plants 2022, 11, 2038

31 of 36

Doebley, J.; Stec, A.; Hubbard, L. The evolution of apical dominance in maize. Nature 1997, 386, 485–488. [CrossRef]
Wang, H.; Nussbaum-Wagler, T.; Li, B.; Zhao, Q.; Vigouroux, Y.; Faller, M.; Bomblies, K.; Lukens, L.; Doebley, J.F. The origin of thenaked grains of maize. Nature 2005, 436, 714–719. [CrossRef]
71. Harlan, J.R. Lettuce and the Sycomore: Sex and romance in ancient Egypt. Econ. Bot. 1986, 40, 4–15. [CrossRef]
72. de Vries, I.M. Origin and domestication of Lactuca sativa L. Genet. Resour. Crop Evol. 1997, 44, 165–174. [CrossRef]
73. Vaughan, D.A.; Balázs, E.; Heslop-Harrison, J.S. From crop domestication to super-domestication. Ann. Bot. 2007, 100, 893–901.
[CrossRef] [PubMed]
74. Heslop-Harrison, J.S.; Schwarzacher, T. Domestication, genomics and the future for banana. Ann. Bot. 2007, 100, 1073–1084.
[CrossRef] [PubMed]
75. Trucchi, E.; Benazzo, A.; Lari, M.; Iob, A.; Vai, S.; Nanni, L.; Bellucci, E.; Bitocchi, E.; Raffini, F.; Xu, C.; et al. Ancient genomes
reveal early Andean farmers selected common beans while preserving diversity. Nat. Plants 2021, 7, 123–128. [CrossRef] [PubMed]
76. Hammer, K.; Laghetti, G. Genetic erosion—Examples from Italy. Genet. Resour. Crop Evol. 2005, 52, 629–634. [CrossRef]
77. Hammer, K.; Teklu, Y. Plant genetic resources: Selected issues from genetic erosion to genetic engineering. J. Agric. Rural. Dev.
Trop. Subtrop. (JARTS) 2008, 109, 15–50.
78. WCD. Dams and Development: A New Framework for Decision-Making. In The Report of the World Commission on Dams; Earthscan
Publications Ltd.: London, UK, 2000; p. 356.
79. Wu, J.; Huang, J.; Han, X.; Xie, Z.; Gao, X. Three-Gorges Dam–Experiment in Habitat Fragmentation? Science 2003, 300, 1239–1240.
[CrossRef] [PubMed]
80. Kleijn, D.; Bommarco, R.; Fijen, T.P.M.; Garibaldi, L.A.; Potts, S.G.; van der Putten, W.H. Ecological intensification: Bridging the
gap between science and practice. Trends Ecol. Evol. 2019, 34, 154–166. [CrossRef]
81. Ciotir, C.; Applequist, W.; Crews, T.E.; Cristea, N.; DeHaan, L.R.; Frawley, E.; Herron, S.; Magill, R.; Miller, J.; Roskov, Y.; et al.
Building a botanical foundation for perennial agriculture: Global inventory of wild, perennial herbaceous Fabaceae species.
Plants People Planet 2019, 1, 375–386. [CrossRef]
82. McClure, K.A.; Sawler, J.; Gardner, K.M.; Money, D.; Myles, S. Genomics: A potential panacea for the perennial problem. Am. J.
Bot. 2014, 101, 1780–1790. [CrossRef]
83. Audu, V.; Rasche, F.; Martensson, L.M.D.; Emmerling, C. Perennial cereal grain cultivation: Implication on soil organic matterand related soil microbial parameters. Appl. Soil Ecol. 2022, 174, 104414. [CrossRef]
84. Ledo, A.; Smith, P.; Zerihun, A.; Whitaker, J.; Vicente-Vicente, J.L.; Qin, Z.; McNamara, N.P.; Zinn, Y.L.; Llorente, M.; Liebig, M.;
et al. Changes in soil organic carbon under perennial crops. Glob. Chang. Biol. 2020, 26, 4158–4168. [CrossRef]
85. Means, M.; Crews, T.; Souza, L. Annual and perennial crop composition impacts on soil carbon and nitrogen dynamics at two
different depths. Renew. Agric. Food Syst. 2022, 1–8. [CrossRef]
86. Kreitzman, M.; Eyster, H.; Mitchell, M.; Czajewska, A.; Keeley, K.; Smukler, S.; Sullivan, N.; Verster, A.; Chan, K.M.A. Woody
perennial polycultures in the U.S. Midwest enhance biodiversity and ecosystem functions. Ecosphere 2022, 13, e03890. [CrossRef]
87. Félix, G.F.; Scholberg, J.M.S.; Clermont-Dauphin, C.; Cournac, L.; Tittonell, P. Enhancing agroecosystem productivity with woody
perennials in semi-arid West Africa. A meta-analysis. Agron. Sustain. Dev. 2018, 38, 57. [CrossRef] [PubMed]
88. DeHaan, L.; Larson, S.; López-Marqués, R.L.; Wenkel, S.; Gao, C.; Palmgren, M. Roadmap for accelerated domestication of an
emerging perennial grain crop. Trends Plant Sci. 2020, 25, 525–537. [CrossRef] [PubMed]
89. Van Tassel, D.L.; DeHaan, L.R.; Cox, T.S. Missing domesticated plant forms: Can artificial selection fill the gap? Evol. Appl. 2010,
3, 434–452. [CrossRef] [PubMed]
90. Lundgren, M.R.; Des Marais, D.L. Life history variation as a model for understanding trade-offs in plant–environment interactions.
Curr. Biol. 2020, 30, R180–R189. [CrossRef]
91. Friedman, J. The evolution of annual and perennial plant life histories: Ecological correlates and genetic mechanisms. Annu. Rev.
Ecol. Evol. Syst. 2020, 51, 461–481. [CrossRef]
92. DeHaan, L.R.; Van Tassel, D.L. Useful insights from evolutionary biology for developing perennial grain crops. Am. J. Bot. 2014,
101, 1801–1819. [CrossRef]
93. Vico, G.; Manzoni, S.; Nkurunziza, L.; Murphy, K.; Weih, M. Trade-offs between seed output and life span—A quantitative
comparison of traits between annual and perennial congeneric species. New Phytol. 2016, 209, 104–114. [CrossRef]
94. Smaje, C. The Strong perennial vision: A critical review. Agroecol. Sustain. Food Syst. 2015, 39, 471–499. [CrossRef]
95. Crews, T.E.; DeHaan, L.R. The strong perennial vision: A response. Agroecol. Sustain. Food Syst. 2015, 39, 500–515. [CrossRef]
96. Crews, T.E.; Carton, W.; Olsson, L. Is the future of agriculture perennial? Imperatives and opportunities to reinvent agriculture byshifting from annual monocultures to perennial polycultures. Glob. Sustain. 2018, 1, e11. [CrossRef]
97. Crews, T.E.; Blesh, J.; Culman, S.W.; Hayes, R.C.; Jensen, E.S.; Mack, M.C.; Peoples, M.B.; Schipanski, M.E. Going where no grains
have gone before: From early to mid-succession. Agric. Ecosyst. Environ. 2016, 223, 223–238. [CrossRef]
98. Jackson, W. New Roots for Agriculture; Friends of the Earth: San Francisco, CA, USA, 1980.
99. Yu, H.; Li, J. Breeding future crops to feed the world through de novo domestication. Nat. Commun. 2022, 13, 1171. [CrossRef]
100. Duhamel, M.; Vandenkoornhuyse, P. Sustainable agriculture: Possible trajectories from mutualistic symbiosis and plant neodomestication. Trends Plant Sci. 2013, 18, 597–600. [CrossRef] [PubMed]
101. Gaut, B.S.; Seymour, D.K.; Liu, Q.; Zhou, Y. Demography and its effects on genomic variation in crop domestication. Nat. Plants
2018, 4, 512–520. [CrossRef] [PubMed]
69.
70.

Plants 2022, 11, 2038

32 of 36102. Zhao, Y.; Zhong, L.; Zhou, K.; Song, Z.; Chen, J.; Rong, J. Seed characteristic variations and genetic structure of wild Zizania
latifolia along a latitudinal gradient in China: Implications for neo-domestication as a grain crop. AoB Plants 2018, 10, ply072.
[CrossRef]
103. Nooryazdan, H.; Serieys, H.; David, J.; Bacilieri, R.; Bervillé, A.J. Construction of a crop—Wild hybrid population for broadening
genetic diversity in cultivated sunflower and first evaluation of its combining ability: The concept of neodomestication. Euphytica
2010, 178, 159–175. [CrossRef]
104. Kantar, M.B.; Hüber, S.; Herman, A.; Bock, D.G.; Baute, G.; Betts, K.; Ott, M.; Brandvain, Y.; Wyse, D.; Stupar, R.M.; et al.
Neo-domestication of an interspecific tetraploid Helianthus annuus × Helianthus tuberosus population that segregates for perennial
habit. Genes 2018, 9, 422. [CrossRef]
105. Tomooka, N.; Naito, K.; Kaga, A.; Sakai, H.; Isemura, T.; Ogiso-Tanaka, E.; Iseki, K.; Takahashi, Y. Evolution, domestication andneo-domestication of the genus Vigna. Plant Genet. Resour. 2014, 12, S168–S171. [CrossRef]
106. Ciotir, C.; Townesmith, A.; Applequist, W.; Herron, S.; Van Tassel, D.; DeHaan, L.; Crews, T.; Schlautman, B.; Jackson, W.; Miller, A.
Global Inventory and Systematic Evaluation of Perennial Grain, Legume, and Oilseed Species for Pre-Breeding and Domestication; Missouri
Botanical Garden: St. Louis, MO, USA, 2016; Available online: http://www.tropicos.org/Project/PAPGI (accessed on 3 July2022).
107. Maxted, N.; Guarino, L.; Myer, L.; Chiwona, E.A. Towards a methodology for on-farm conservation of plant genetic resources.
Genet. Resour. Crop Evol. 2002, 49, 31–46. [CrossRef]
108. Kell, S.P.; Knüpffer, H.; Jury, S.L.; Ford-Lloyd, B.V.; Maxted, N. Crops and wild relatives of the EuroMediterranean region: Making
and using a conservation catalogue. In Crop Wild Relative Conservation and Use; Maxted, N., Ford-Lloyd, B.V., Kell, S.P., Iriondo, J.,
Dulloo, E., Turok, J., Eds.; CAB International: Wallingford, UK, 2008; pp. 69–109.
109. Harlan, J.R.; de Wet, J.M.J. Toward a rational classification of cultivated plants. Taxon 1971, 20, 509–517. [CrossRef]
110. Maxted, N.; Ford-Lloyd, B.V.; Jury, S.; Kell, S.; Scholten, M. Towards a definition of a crop wild relative. Biodivers. Conserv. 2006,
15, 2673–2685. [CrossRef]
111. Vaughan, D.A. A new rhizomatous Oryza species (Poaceae) from Sri Lanka. Bot. J. Linn. Soc. 1990, 103, 159–163. [CrossRef]
112. Phillips, J.; Yang, L. Oryza Rhizomatis. The IUCN Red List of Threatened Species. Available online: https://www.iucnredlist.org/
species/112680830/113899786 (accessed on 12 July 2020).
113. GBIF. Oryza Rhizomatis D.A.Vaughan. Available online: https://www.gbif.org/species/4135750 (accessed on 17 August 2020).
114. Huang, X.; Kurata, N.; Wei, X.; Wang, Z.-X.; Wang, A.; Zhao, Q.; Zhao, Y.; Liu, K.; Lu, H.; Li, W.; et al. A map of rice genome
variation reveals the origin of cultivated rice. Nature 2012, 490, 497–501. [CrossRef]
115. Nowicki, M.; Foolad, M.R.; Nowakowska, M.; Kozik, E.U. Potato and tomato late blight caused by Phytophthora infestans: An
overview of pathology and resistance breeding. Plant Dis. 2012, 96, 4–17. [CrossRef]
116. Brar, D.S.; Khush, G.S. Alien introgression in rice. In Oryza: From Molecule to Plant; Sasaki, T., Moore, G., Eds.; Springer: Dordrecht,
The Netherlands, 1997; pp. 35–47.
117. Ram, T.; Deen, R.; Gautam, S.K.; Ramesh, K.; Rao, Y.K.; Brar, D.S. Identification of new genes for Brown Planthopper resistance inrice introgressed from O. glaberrima and O. minuta. Rice Genet. Newsl. 2010, 25, 67–68.
118. Mondal, T.; Henry, R. The Wild Oryza Genomes; Springer: Cham, Switzerland, 2018.
119. Dey, S.; Badri, J.; Prakasam, V.; Bhadana, V.P.; Eswari, K.B.; Laha, G.S.; Priyanka, C.; Rajkumar, A.; Ram, T. Identification andagro-morphological characterization of rice genotypes resistant to sheath blight. Australas. Plant Pathol. 2016, 45, 145–153.
[CrossRef]
120. Ganeshan, P.; Jain, A.; Parmar, B.; Rao, A.R.; Sreenu, K.; Mishra, P.; Mesapogu, S.; Subrahmanyam, D.; Ram, T.; Sarla, N.; et al.
Identification of salt tolerant rice lines among interspecific BILs developed by crossing Oryza sativa × O. rufipogon and O. sativa x
O. nivara. Aust. J. Crop Sci. 2016, 10, 220–228.
121. Prasanth, V.V.; Chakravarthi, D.V.; Kiran, T.V.; Rao, Y.V.; Panigrahy, M.; Mangrauthia, S.K.; Viraktamath, B.C.; Subrahmanyam, D.;
Voleti, S.R.; Sarla, N. Evaluation of rice germplasm and introgression lines for heat tolerance. Ann. Biol. Res. 2012, 3, 5060–5068.
122. Prasanth, V.V.; Basava, K.R.; Babu, M.S.; V. G.N., V.T.; Devi, S.J.S.R.; Mangrauthia, S.K.; Voleti, S.R.; Sarla, N. Field level evaluationof rice introgression lines for heat tolerance and validation of markers linked to spikelet fertility. Physiol. Mol. Biol. Plants 2016, 22,
179–192. [CrossRef] [PubMed]
123. Surapaneni, M.; Balakrishnan, D.; Mesapogu, S.; Addanki, K.R.; Yadavalli, V.R.; Tripura Venkata, V.G.N.; Neelamraju, S.
Identification of major effect QTLs for agronomic traits and CSSLs in rice from Swarna/Oryza nivara derived backcross inbredlines. Front. Plant Sci. 2017, 8, 1027. [CrossRef] [PubMed]
124. Furuta, T.; Uehara, K.; Angeles-Shim, R.B.; Shim, J.; Nagai, K.; Ashikari, M.; Takashi, T. Development of chromosome segment
substitution lines harboring Oryza nivara genomic segments in Koshihikari and evaluation of yield-related traits. Breed. Sci. 2016,
66, 845–850. [CrossRef] [PubMed]
125. Zhai, W.; Wang, W.; Zhou, Y.; Li, X.; Zheng, X.; Zhang, Q.; Wang, G.; Zhu, L. Breeding bacterial blight-resistant hybrid rice withthe cloned bacterial blight resistance gene Xa21. Mol. Breed. 2002, 8, 285–293. [CrossRef]
126. Guo, S.-B.; Wei, Y.; Li, X.-Q.; Liu, K.-Q.; Huang, F.-K.; Chen, C.-H.; Gao, G.-Q. Development and identification of introgression
lines from cross of Oryza sativa and Oryza minuta. Rice Sci. 2013, 20, 95–102. [CrossRef]

Plants 2022, 11, 2038

33 of 36

127. Yoon, D.B.; Kang, K.H.; Kim, K.J.; Ju, H.G.; Kwon, S.J.; Suh, J.P. Mapping quantitative trait loci for yield components andmorphological traits in an advanced back cross population between Oryza grandiglumis and the O. sativa japonica cultivar
Hwaseongbyeo. Theor. Appl. Genet. 2006, 112, 1052–1062. [CrossRef]
128. Wairich, A.; de Oliveira, B.N.; Wu, L.B.; Murugaiyan, V.; Margis-Pinheiro, M.; Fett, J.P.; Ricachenevsky, F.K.; Frei, M. Chromosomal
introgressions from Oryza meridionalis into domesticated rice Oryza sativa result in iron tolerance. J. Exp. Bot. 2021, 72, 2242–2259.
[CrossRef]
129. Luo, Y.; Lao, L.Y.; Ai, B.; Zhang, M.; Xie, J.K.; Zhang, F.T. Development of a drought stress-resistant rice restorer line throughOryza sativa-rufipogon hybridization. J. Genet. 2019, 98, 55. [CrossRef]
130. Frankel, O.H.; Frankel, O.; Soulé, M.E. Conservation and Evolution; Cambridge University Press: Cambridge, UK, 1981.
131. Jarvis, D.I.; Hodgkin, T.; Sthapit, B.R.; Fadda, C.; Lopez-Noriega, I. An heuristic framework for identifying multiple ways of
supporting the conservation and use of traditional crop varieties within the agricultural production system. Crit. Rev. Plant Sci.
2011, 30, 125–176. [CrossRef]
132. Khoury, C.K.; Brush, S.; Costich, D.E.; Curry, H.A.; Haan, S.; Engels, J.M.M.; Guarino, L.; Hoban, S.; Mercer, K.L.; Miller, A.J.; et al.
Crop genetic erosion: Understanding and responding to loss of crop diversity. New Phytol. 2022, 233, 84–118. [CrossRef]
133. Jarvis, D.J.; Hodgkin, T.; Brown, A.H.D.; Tuxill, J.; Noriega, I.L.; Smale, M.; Sthapit, B. Crop Genetic Diversity in the Field and on the
Farm: Principles and Applications in Research Practices; Yale University Press: New Haven, CT, USA; London, UK, 2016.
134. Porcuna-Ferrer, A.; Fiala, V.; Freyer, B.; van Etten, J.; Vernooy, R.; Probst, L. Do community seed banks contribute to thesocial-ecological resilience of communities? A case-study from western Guatemala. Int. J. Agric. Sustain. 2020, 18, 232–249.
[CrossRef]
135. Diez, M.J.; De la Rosa, L.; Martin, I.; Guasch, L.; Cartea, M.E.; Mallor, C.; Casals, J.; Simo, J.; Rivera, A.; Anastasio, G.; et al. Plant
Genebanks: Present Situation and Proposals for Their Improvement. the Case of the Spanish Network. Front. Plant Sci. 2018, 9,
1794. [CrossRef] [PubMed]
136. Pautasso, M.; Aistara, G.; Barnaud, A.; Caillon, S.; Clouvel, P.; Coomes, O.T.; Delêtre, M.; Demeulenaere, E.; De Santis, P.; Döring,T.; et al. Seed exchange networks for agrobiodiversity conservation. A review. Agron. Sustain. Dev. 2012, 33, 151–175. [CrossRef]
137. Sievers-Glotzbach, S.; Euler, J.; Frison, C.; Gmeiner, N.; Kliem, L.; Mazé, A.; Tschersich, J. Beyond the material: Knowledge aspects
in seed commoning. Agric. Hum. Values 2021, 38, 509–524. [CrossRef]
138. Sievers-Glotzbach, S.; Tschersich, J.; Gmeiner, N.; Kliem, L.; Ficiciyan, A. Diverse seeds—Shared practices: Conceptualizing seedcommons. Int. J. Commons 2020, 14, 418–438. [CrossRef]
139. Hammer, K.; Gladis, T.; Diederichsen, A. In situ and on-farm management of plant genetic resources. Eur. J. Agron. 2003, 19,509–517. [CrossRef]
140. Bush, D.; Thomson, L.; Bolatolu, W.; Dutt, S.; Hamani, S.; Likiafu, H.; Mateboto, J.; Tauraga, J.; Young, E. Domestication provides
the key to conservation of Santalum yasi—A threatened Pacific sandalwood. Aust. For. 2020, 83, 186–194. [CrossRef]
141. Curry, H.A. From working collections to the World Germplasm Project: Agricultural modernization and genetic conservation at
the Rockefeller Foundation. Hist. Philos. Life Sci. 2017, 39, 5. [CrossRef]
142. FAO. Commission on Plant Genetic Resources: FAO Activities and Future Programme on Plant Genetic Resources. Available
online: http://www.fao.org/3/a-aj427e.pdf (accessed on 22 March 2022).
143. Noriega, I.L.; Halewood, M.; Abberton, M.; Amri, A.; Angarawai, I.I.; Anglin, N.; Blümmel, M.; Bouman, B.; Campos, H.; Costich,D.; et al. CGIAR Operations under the Plant Treaty Framework. Crop Sci. 2019, 59, 819–832. [CrossRef]
144. Westengen, O.T.; Lusty, C.; Yazbek, M.; Amri, A.; Asdal, Å. Safeguarding a global seed heritage from Syria to Svalbard. Nature
Plants 2020, 6, 1311–1317. [CrossRef]
145. FAO. The Second Report on the State of the World’s Plant Genetic Resources for Food and Agriculture. Available online:
http://www.fao.org/3/i1500e/i1500e.pdf (accessed on 22 March 2022).
146. Singh, A.K.; Varaprasad, K.S.; Venkateswaran, K. Conservation costs of plant genetic resources for food and agriculture: Seedgenebanks. Agric. Res. 2012, 1, 223–239. [CrossRef]
147. SGSV. Svalbard Global Seed Vault. Available online: https://www.croptrust.org/work/svalbard-global-seed-vault/ (accessedon 18 July 2022).
148. Engels, J.M.M.; Ebert, A.W. A critical review of the current global ex situ conservation system for plant agrobiodiversity. I. Historyof the development of the global system in the context of the political/legal framework and its major conservation components.
Plants 2021, 10, 1557. [CrossRef] [PubMed]
149. Bellon, M.R.; Dulloo, E.; Sardos, J.; Thormann, I.; Burdon, J.J. In situ conservation-harnessing natural and human-derived
evolutionary forces to ensure future crop adaptation. Evol. Appl. 2017, 10, 965–977. [CrossRef] [PubMed]
150. de Haan, S.; Núñez, J.; Bonierbale, M.; Ghislain, M.; van der Maesen, J. A Simple Sequence Repeat (SSR) marker comparison ofa large in- and ex-situ potato landrace cultivar collection from Peru reaffirms the complementary nature of both conservation
strategies. Diversity 2013, 5, 505–521. [CrossRef]
151. Casals, J.; Casanas, F.; Simo, J. Is it still necessary to continue to collect crop genetic resources in the Mediterranean Area? A casestudy in Catalonia. Econ. Bot. 2017, 71, 330–341. [CrossRef]
152. Smykal, P.; Hradilova, I.; Trneny, O.; Brus, J.; Rathore, A.; Bariotakis, M.; Das, R.R.; Bhattacharyya, D.; Richards, C.; Coyne, C.J.;
et al. Genomic diversity and macroecology of the crop wild relatives of domesticated pea. Sci. Rep. 2017, 7, 17384. [CrossRef]

Plants 2022, 11, 2038

34 of 36153. Abe, A.; Kosugi, S.; Yoshida, K.; Natsume, S.; Takagi, H.; Kanzaki, H. Genome sequencing reveals agronomically important loci inrice using MutMap. Nat. Biotechnol. 2012, 30, 174–178. [CrossRef]
154. Kumar, S.; Kirk, C.; Deng, C.; Wiedow, C.; Knaebel, M.; Brewer, L. Genotyping-by-sequencing of pear (Pyrus spp.) accessions
unravels novel patterns of genetic diversity and selection footprints. Hortic. Res. 2017, 4, 17015. [CrossRef]
155. Norelli, J.L.; Wisniewski, M.; Fazio, G.; Burchard, E.; Gutierrez, B.; Levin, E.; Droby, S. Genotyping-by-sequencing markers
facilitate the identification of quantitative trait loci controlling resistance to Penicillium expansum in Malus sieversii. PLoS ONE
2017, 12, e0172949. [CrossRef]
156. Singh, N.; Wu, S.Y.; Raupp, W.J.; Sehgal, S.; Arora, S.; Tiwari, V.; Vikram, P.; Singh, S.; Chhuneja, P.; Gill, B.S.; et al. Efficientcuration of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions. Sci. Rep. 2019,9, 650. [CrossRef]
157. Melo, A.T.O.; Bartaula, R.; Hale, I. GBS-SNP-CROP: A reference-optional pipeline for SNP discovery and plant germplasm
characterization using variable length, paired-end genotyping-by-sequencing data. BMC Bioinform. 2016, 17, 1–15. [CrossRef]
158. Schlotterer, C.; Tobler, R.; Kofler, R.; Nolte, V. Sequencing pools of individuals—mining genome-wide polymorphism data without
big funding. Nat. Rev. Genet. 2014, 15, 749–763. [CrossRef] [PubMed]
159. Wells, R.; Trick, M.; Fraser, F.; Soumpourou, E.; Clissold, L.; Morgan, C.; Pauquet, J.; Bancroft, I. Sequencing-based variant
detection in the polyploid crop oilseed rape. BMC Plant Biol. 2013, 13, 111. [CrossRef] [PubMed]
160. Duan, N.B.; Bai, Y.; Sun, H.H.; Wang, N.; Ma, Y.M.; Li, M.J.; Wang, X.; Jiao, C.; Legall, N.; Mao, L.Y.; et al. Genome re-sequencing
reveals the history of apple and supports a two-stage model for fruit enlargement. Nat. Commun. 2017, 8, 249. [CrossRef]
161. Bouquet, A. Sequencing of the grapevine genome: A brilliant demonstration of a 55-year-old hypothesis. Prog. Agric. Vitic. 2007,
124, 337–341.
162. Brenchley, R.; Spannagl, M.; Pfeifer, M.; Barker, G.L.A.; D’Amore, R.; Allen, A.M.; McKenzie, N.; Kramer, M.; Kerhornou, A.;
Bolser, D.; et al. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 2012, 491, 705. [CrossRef][PubMed]163. Graner, A.; Kilian, B. NGS technologies for analyzing germplasm diversity in genebanks. Brief. Funct. Genom. 2012, 11, 38–50.
[CrossRef]
164. Frankel, O.H.; Brown, A.H.D. Current plant genetic resources: A critical appraisal. In Genetics: New Frontiers; Oxford & IBH
Publishing Company: New Delhi, India, 1984; pp. 3–13.
165. Franco, J.; Crossa, J.; Díaz, J.; Taba, S.; Villaseñor, J.; Eberhart, S.A. A sequential clustering strategy for classifying gene bankaccessions. Crop Sci. 1997, 37, 1656–1662. [CrossRef]
166. Gouesnard, B.; Bataillon, T.M.; Decoux, G.; Rozale, C.; Schoen, D.J.; David, J.L. MSTRAT: An algorithm for building germplasm
core collections by maximizing allelic or phenotypic richness. J. Hered. 2001, 92, 93–94. [CrossRef]
167. Agrama, H.A.; Yan, W.; Lee, F.; Fjellstrom, R.; Chen, M.-H.; Jia, M.; McClung, A. Genetic assessment of a mini-core subset
developed from the USDA Rice Genebank. Crop Sci. 2009, 49, 1336–1346. [CrossRef]
168. Pathirana, R.; Molloy, C.; Erridge, Z.; McLachlan, A.; Seelye, J.; Kumar, S. Towards a cryopreserved germplasm collection ofapple—Results of dormant bud cryopreservation in the mild maritime winter climate of Hawkes Bay, New Zealand. Acta Hortic.
2018, 1205, 769–778. [CrossRef]
169. Pathirana, R.; Mathew, L.; Jibran, R.; Hunter, D.A.; Morgan, E.R. Cryopreservation and cryotherapy research on horticultural
crops in New Zealand. Acta Hortic. 2019, 1234, 29–36. [CrossRef]
170. Rana, J.C.; Sharma, T.R.; Tyagi, R.K.; Chahota, R.K.; Gautam, N.K.; Singh, M.; Sharma, P.N.; Ojha, S.N. Characterisation of 4274
accessions of common bean (Phaseolus vulgaris L.) germplasm conserved in the Indian gene bank for phenological, morphologicaland agricultural traits. Euphytica 2015, 205, 441–457. [CrossRef]
171. ICRISAT. ICRISAT Sorghum Core. Available online: http://genebank.icrisat.org/IND/Core?Crop=Sorghum (accessed on 20
May 2022).
172. Mattick, J.S.; Ablett, E.M.; Edmonson, D.L. The gene library-preservation and analysis of genetic diversity in Australasia. In
Conservation of Plant Genes; Academic Press: Cambridge, MA, USA, 1992; pp. 15–35.
173. Droege, G.; Barker, K.; Astrin, J.J.; Bartels, P.; Butler, C.; Cantrill, D.; Coddington, J.; Forest, F.; Gemeinholzer, B.; Hobern, D.; et al.
The Global Genome Biodiversity Network (GGBN) Data Portal. Nucleic Acids Res. 2014, 42, D607–D612. [CrossRef]
174. Gemeinholzer, B.; Dröge, G.; Zetzsche, H.; Haszprunar, G.; Klenk, H.; Güntsch, A.; Berendsohn, W.G.; Wägele, J. The DNA Bank
Network: The start from a German initiative. Biopreservation Biobanking 2011, 9, 51–55. [CrossRef]
175. GGBN. Newsletter. Available online: https://wiki.ggbn.org/ggbn/Newsletters (accessed on 20 June 2022).
176. GGBN. The GGBN Data Portal. Available online: http://www.ggbn.org/ggbn_portal/ (accessed on 27 June 2022).
177. Engels, J.M.M.; Ebert, A.W. A critical review of the current global ex situ conservation system for plant agrobiodiversity. II.
Strengths and weaknesses of the current system and recommendations for its improvement. Plants 2021, 10, 1904. [CrossRef][PubMed]178. FAO. Genebank Standards for Plant Genetic Resources for Food and Agriculture, Revised Edition. Available online: http://www.fao.org/3/a-i3704e.pdf (accessed on 20 May 2022).
179. Thormann, I.; Engels, J.M.M.; Halewood, M. Are the old International Board for Plant Genetic Resources (IBPGR) base collections
available through the Plant Treaty’s multilateral system of access and benefit sharing? A review. Genet. Resour. Crop Evol. 2019, 66,
291–310. [CrossRef]

Plants 2022, 11, 2038

35 of 36

180. Migicovsky, Z.; Warschefsky, E.; Klein, L.L.; Miller, A.J. Using living germplasm collections to characterize, improve, and conserve
woody perennials. Crop Sci. 2019, 59, 2365–2380. [CrossRef]
181. Forsline, P.L.; Aldwinckle, H.S. Natural occurrence of fire blight in USDA apple germplasm collection after 10 years of observation.
Acta Hortic. 2002, 590, 351–357. [CrossRef]
182. Datson, P.; Nardozza, S.; Manako, K.; Herrick, J.; Martinez-Sanchez, M.; Curtis, C.; Montefiori, M. Monitoring the Actinidia
germplasm for resistance to Pseudomonas syringae pv. actinidiae. Acta Hortic. 2015, 1095, 181–184. [CrossRef]
183. IPGRI-APO. Establishment and Management of Field Genebank, a Training Manual. Available online: https://www.
bioversityinternational.org/fileadmin/_migrated/uploads/tx_news/Establishment_and_management_of_field_genebank_78
6.pdf (accessed on 19 April 2022).
184. IPGRI. Technical Guidelines for the Management of Field and In Vitro Genebanks: IPGRI Handbooks for Genebanks No. 7.
Available online: https://cropgenebank.sgrp.cgiar.org/images/file/learning_space/genebankmanual7.pdf (accessed on 19
March 2022).
185. Carimi, F.; Pathirana, R.; Carra, A. Biotechnologies for germplasm management and improvement. In Grapevines—Varieties,
Cultivation and Management; Szabo, P.V., Shojania, J., Eds.; Nova Science Publishers: New York, NY, USA, 2012; pp. 199–249.
186. Aranzales, E.R. Use of Tissue Culture Techniques in the Conservation and Exchange of Cassava Germplasm Material: CIAT
Case. International Course on Modern Technologies for Production, Processing and Utilization of the Cassava Crop. “Support tosustainable development of the cassava sector in the Caribbean Region.” CIAT, Palmira, Colombia, 28 July 2014. Available online:
https://cgspace.cgiar.org/handle/10568/82943 (accessed on 15 February 2022).
187. CGIAR-SGRP. Refinement and Standardization of Storage Procedures for Clonal Crops—Global Public Goods Phase 2: Part III.
Multi-Crop Guidelines for Developing In Vitro Conservation Best Practices for Clonal Crops. Available online: https://cropgenebank.
sgrp.cgiar.org/images/file/learning_space/gpg2%20part%20iii_final%20for%20web.pdf (accessed on 5 April 2022).
188. CGIAR-SGRP. Refinement and Standardization of Storage Procedures for Clonal Crops—Global Public Goods Phase 2: Part II.
Status of In Vitro Conservation Technologies for: Andean Root and Tuber Crops, Cassava, Musa, Potato, Sweetpotato and Yam. Available
online: https://cropgenebank.sgrp.cgiar.org/images/file/learning_space/gpg2%20part%20ii%20_07022012.pdf (accessed on 5
April 2022).
189. Pence, V.C.; Engelmann, F.; Guarino, L.; RamanathaRao, V.; Goldberg, E. Collecting in vitro for genetic resources conservation. In
Collecting Plant Genetic Diversity: Technical Guidelines; Bioversity International: Rome, Italy, 2011; Volume 47, pp. 5–16.
190. CIP-Genebank. In Vitro Conservation. Available online: https://cipotato.org/genebankcip/process/in-vitro/ (accessed on 23
June 2022).
191. IITA-GRC. Genetic Resources Center. Available online: https://www.genebanks.org/genebanks/iita/; https://www.genebanks.
org/wp-content/uploads/2021/04/IITA-Closure-Report-IN-VITRO-CONS-2018-Round-2.xlsx (accessed on 22 May 2022).
192. Cunha Alves, C.; Azevedo, A.A.; Rennó, V.C. EMBRAPA Network for Brazilian Plant Genetic Resources Conservation. Biopreservation Biobanking 2018, 16, 350–360. [CrossRef]
193. Myeza, P.N.; Visser, A. Agricultural Research Council’s potato in vitro genebank. Acta Hortic. 2013, 1007, 727–731. [CrossRef]
194. Tyagi, R.K.; Agrawal, A. Genetic Resources Conservation: Ex Situ Conservation Strategies. Available online: http://www.nbpgr.
ernet.in/genomic_resources/03_rktyagi_ex-situ.pdf (accessed on 20 February 2022).
195. ITC. International Musa Germplasm Transit Center (ITC). Available online: https://www.bioversityinternational.org/bananagenebank/ (accessed on 22 August 2020).
196. Bamberg, J.B.; Martin, M.W.; Abad, J.; Jenderek, M.M.; Tanner, J.; Donnelly, D.J.; Nassar, A.M.K.; Veilleux, R.E.; Novy, R.G. In vitro
technology at the US Potato Genebank. Vitr. Cell. Dev. Biol.-Plant 2016, 52, 213–225. [CrossRef]
197. Sakai, A. Survival of the twig of woody plants at −196 ◦ C. Nature 1960, 185, 392–394. [CrossRef]
198. Sakai, A.; Nishiyama, Y. Cryopreservation of winter vegetative buds of hardy fruit-trees in liquid-nitrogen. Hortscience 1978, 13,
225–227.
199. Latta, R. Preservation of suspensions cultures of plant cells by freezing. Can. J. Bot. 1971, 49, 1253–1254. [CrossRef]
200. Wang, M.-R.; Lambardi, M.; Engelmann, F.; Pathirana, R.; Panis, B.; Volk, G.M.; Wang, Q.-C. Advances in cryopreservation ofin vitro-derived propagules: Technologies and explant sources. Plant Cell Tiss. Organ Cult. 2020, 144, 7–20. [CrossRef]
201. Carra, A.; Carimi, F.; Bettoni, J.C.; Pathirana, R. Progress and challenges in the application of synthetic seed technology for ex situ
germplasm conservation in grapevine (Vitis spp.). In Synthetic Seeds: Germplasm Regeneration, Preservation and Prospects; Faisal, M.,
Alatar, A.A., Eds.; Springer International Publishing: Cham, Switzerland, 2019; pp. 439–467.
202. Sakai, A.; Kobayashi, S.; Oiyama, I. Cryopreservation of nucellar cells of navel orange (Citrus sinensis Osb. var. brasiliensis Tanaka)
by vitrification. Plant Cell Rep. 1990, 9, 30–33. [CrossRef]
203. Niino, T.; Wunna; Watanabe, K.; Nohara, N.; Rafique, T.; Yamamoto, S.; Fukui, K.; Arizaga, M.V.; Martinez, C.R.C.; Matsumoto,T.; et al. Cryopreservation of mat rush lateral buds by air dehydration using aluminum cryo-plate. Plant Biotechnol. 2014, 31,
281–287. [CrossRef]
204. Yamamoto, S.; Rafique, T.; Fukui, K.; Sekizawa, K.; Niinois, T. V-cryo-plate procedure as an effective protocol for cryobanks: Casestudy of mint cryopreservation. Cryoletters 2012, 33, 12–23.
205. Yamamoto, S.; Rafique, T.; Priyantha, W.S.; Fukui, K.; Matsumoto, T.; Niino, T. Development of a cryopreservation procedureusing aluminium cryo-plates. Cryoletters 2011, 32, 256–265.

Plants 2022, 11, 2038

36 of 36206. Bettoni, J.C.; Pathirana, R.; Bonnart, R.; Shepherd, A.; Volk, G. Cryopreservation of grapevine shoot tips from in vitro plants using
droplet vitrification and V cryo-plate techniques. In Synthetic Seeds: Germplasm Regeneration, Preservation and Prospects; Faisal, M.,
Alatar, A.A., Eds.; Springer International Publishing: Cham, Switzerland, 2019; pp. 469–482.
207. Bettoni, J.C.; Mathew, L.; Pathirana, R.; Wiedow, C.; Hunter, D.A.; McLachlan, A.; Khan, S.; Tang, J.; Nadarajan, J. Eradication of
Potato Virus S, Potato Virus A, and Potato Virus M from infected in vitro-grown potato shoots using in vitro therapies. Front. Plant
Sci. 2022, 13, 878733. [CrossRef]
208. Bettoni, J.C.; Souza, J.A.; Volk, G.M.; Dalla Costa, M.; da Silva, F.N.; Kretzschmar, A.A. Eradication of latent viruses from apple
cultivar ‘Monalisa’ shoot tips using droplet-vitrification cryotherapy. Sci. Hortic. 2019, 250, 12–18. [CrossRef]
209. Farhadi-Tooli, S.; Ghanbari, A.; Kermani, M.J.; Zeinalabedini, M.; Bettoni, J.C.; Naji, A.M.; Kazemi, N. Droplet-vitrification
cryotherapy and thermotherapy as efficient tools for the eradication of apple chlorotic leaf spot virus and apple stem grooving
virus from virus-infected quince in vitro cultures. Eur. J. Plant Pathol. 2022, 162, 31–43. [CrossRef]
210. Mathew, L.; Tiffin, H.; Erridge, Z.; McLachlan, A.; Hunter, D.; Pathirana, R. Efficiency of eradication of Raspberry bushy dwarf
virus from infected raspberry (Rubus idaeus) by in vitro chemotherapy, thermotherapy and cryotherapy and their combinations.
Plant Cell Tiss. Organ Cult. 2021, 144, 133–141. [CrossRef]
211. Pathirana, R.; McLachlan, A.; Hedderley, D.; Carra, A.; Carimi, F.; Panis, B. Removal of leafroll viruses from infected grapevine
plants by droplet vitrification. Acta Hortic. 2015, 1083, 491–498. [CrossRef]
212. Wang, Q.; Valkonen, J.P.T. Elimination of viruses and phytoplasma by cryotherapy of in vitro-grown shoot tips: Analysis of allcases. Adv. Hortic. Sci. 2007, 21, 265–269.
213. Wang, Q.C.; Valkonen, J.P.T. Efficient elimination of sweetpotato little leaf phytoplasma from sweetpotato by cryotherapy ofshoot tips. Plant Pathol. 2008, 57, 338–347. [CrossRef]
214. Keller, E.R.J.; Zanke, C.D.; Senula, A.; Breuing, A.; Hardeweg, B.; Winkelmann, T. Comparing costs for different conservation
strategies of garlic (Allium sativum L.) germplasm in genebanks. Genet. Resour. Crop Evol. 2013, 60, 913–926. [CrossRef]
215. Dulloo, M.E.; Ebert, A.W.; Dussert, S.; Gotor, E.; Astorga, C.; Vasquez, N.; Rakotomalala, J.J.; Rabemiafara, A.; Eira, M.; Bellachew,
B.; et al. Cost efficiency of cryopreservation as a long-term conservation method for coffee genetic resources. Crop Sci. 2009, 49,
2123–2138. [CrossRef]
216. Jenderek, M.M.; Reed, B.M. Cryopreserved storage of clonal germplasm in the USDA National Plant Germplasm System. Vitr.
Cell. Dev. Biol.-Plant 2017, 53, 299–308. [CrossRef]
217. Panis, B. Sixty years of plant cryopreservation: From freezing hardy mulberry twigs to establishing reference crop collections for
future generations. Acta Hortic. 2019, 1234, 1–8. [CrossRef]
218. Wilms, H.; Rhee, J.H.; Rivera, R.L.; Longin, K.; Panis, B. Developing coconut cryopreservation protocols and establishingcryo-genebank at RDA; a collaborative project between RDA and Bioversity International. Acta Hortic. 2019, 1234, 343–348.
[CrossRef]
219. Rajasekharan, P.E.; Ravish, B.S.; Kumar, T.V.; Ganeshan, S. Pollen Cryobanking for Tropical Plant Species. In Conservation of
Tropical Plant Species; Normah, M.N., Chin, H.F., Reed, B.M., Eds.; Springer: New York, NY, USA, 2013; pp. 65–75.
220. Carimi, F.; Carra, A.; Panis, B.; Pathirana, R. Strategies for conservation of endangered wild grapevine (Vitis vinifera L. subsp.
sylvestris (C.C. Gmel.) Hegi). Acta Hortic. 2016, 1115, 81–86. [CrossRef]
221. O’Brien, C.; Hiti-Bandaralage, J.; Folgado, R.; Hayward, A.; Lahmeyer, S.; Folsom, J.; Mitter, N. Cryopreservation of woody crops:
The avocado case. Plants 2021, 10, 934. [CrossRef]
222. Pathirana, R.; Mathew, L.; McLachlan, A. A simplified method for high recovery of kiwifruit (Actinidia spp.) shoot tips after
droplet vitrification cryopreservation suitable for long-term conservation. Plant Cell Tiss. Organ Cult. 2021, 144, 97–102. [CrossRef]
223. Mathew, L.; Burritt, D.J.; McLachlan, A.; Pathirana, R. Combined pre-treatments enhance antioxidant metabolism and improvesurvival of cryopreserved kiwifruit shoot tips. Plant Cell Tiss. Organ Cult. 2019, 138, 193–205. [CrossRef]
224. Carra, A.; Sajeva, M.; Abbate, L.; Siragusa, M.; Pathirana, R.; Carimi, F. Factors affecting somatic embryogenesis in eight Italiangrapevine cultivars and the genetic stability of embryo-derived regenerants as assessed by molecular markers. Sci. Hortic. 2016,
204, 123–127. [CrossRef]
225. Niskanen, A.-M.; Lu, J.; Seitz, S.; Keinonen, K.; Von Weissenberg, K.; Pappinen, A. Effect of parent genotype on somatic
embryogenesis in Scots pine (Pinus sylvestris). Tree Physiol. 2004, 24, 1259–1265. [CrossRef]
226. Panis, B.; Nagel, M.; Van den houwe, I. Challenges and prospects for the conservation of crop genetic resources in field genebanks,
in in vitro collections and/or in liquid nitrogen. Plants 2020, 9, 1634. [CrossRef]
227. Nadarajan, J.; van der Walt, K.; Lehnebach, C.A.; Saeiahagh, H.; Pathirana, R. Integrated ex situ conservation strategies forendangered New Zealand Myrtaceae species. N. Z. J. Bot. 2020, 59, 72–89. [CrossRef]
228. Byrne, P.F.; Volk, G.M.; Gardner, C.; Gore, M.A.; Simon, P.W.; Smith, S. Sustaining the future of plant breeding: The critical role of
the USDA-ARS National Plant Germplasm System. Crop Sci. 2018, 58, 451–468. [CrossRef]
229. GRIN-Global. U.S. National Plant Germplasm System. Available online: https://npgsweb.ars-grin.gov/gringlobal/search.aspx(accessed on 25 March 2022).
230. CGIAR-Genebank-Platform. CGIAR Centers’ Use of Digital Object Identifiers (DOIs): A Submission to the Advisory Committee on
the Global Information System 10 p. Available online: https://cgspace.cgiar.org/handle/10568/102457 (accessed on 22 May 2022).