cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1363147.08fu
title: SH1363147.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2043411.08fu
title: SH2043411.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2043412.08fu
title: SH2043412.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.5281/zenodo.15209294
title: Climate and local habitat conditions shape temporal stability of seedling dynamics in a temperate forest
DOI: 10.5281/zenodo.15209295
title: Climate and local habitat conditions shape temporal stability of seedling dynamics in a temperate forest
DOI: 10.15468/dl.wpkuky
title: Occurrence Download

description: A dataset containing 20630 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.countrycode = 'BT'
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence."year" &gt;= 2000 AND occurrence."year" &lt;= 2024)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 20630 records were derived from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021418-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.20038557.v1
title: Technical nuances of machine learning: implementation and validation of supervised methods for genomic prediction in plant breeding

description: Abstract The decision-making process in plant breeding is driven by data. The machine learning framework has powerful tools that can extract useful information from data. However, there is still a lack of understanding about the underlying algorithms of these methods, their strengths, and pitfalls. Machine learning has two main branches: supervised and unsupervised learning. In plant breeding, supervised learning is used for genomic prediction, where phenotypic traits are modeled as a function of molecular markers. The key supervised learning algorithms for genomic prediction are linear methods, kernel methods, neural networks, and tree ensembles. This manuscript provides an insight into the implementation of these algorithms and how cross-validations can be used to compare methods. Examples for genomic prediction come from plant breeding.
DOI: 10.6084/m9.figshare.20038557
title: Technical nuances of machine learning: implementation and validation of supervised methods for genomic prediction in plant breeding

description: Abstract The decision-making process in plant breeding is driven by data. The machine learning framework has powerful tools that can extract useful information from data. However, there is still a lack of understanding about the underlying algorithms of these methods, their strengths, and pitfalls. Machine learning has two main branches: supervised and unsupervised learning. In plant breeding, supervised learning is used for genomic prediction, where phenotypic traits are modeled as a function of molecular markers. The key supervised learning algorithms for genomic prediction are linear methods, kernel methods, neural networks, and tree ensembles. This manuscript provides an insight into the implementation of these algorithms and how cross-validations can be used to compare methods. Examples for genomic prediction come from plant breeding.
DOI: 10.6084/m9.figshare.20038558
title: Plant breeding in Brazil: Retrospective of the past 50 years

description: Abstract: The importance of plant breeding in Brazilian agriculture has grown a lot in the last 50 years. This occurred mainly because of the: increase in graduate programs, which qualified hundreds of professionals; creation of EMBRAPA and other research institutes or state companies, with an emphasis on the production of new cultivars and; promulgation of the cultivar protection law, which stimulates investments in seed production. The retrospective of what happened, enabling the country to move from being an importer of grains, fruits, and fibers to one of the largest exporters of these products worldwide, was the focus of this work. Taking as reference some agricultural products, this article highlights the significant contribution of plant breeding in recent years. Also, some of the enormous challenges that still have to be overcome, in which the participation of Brazilian breeders will be fundamental to continue the progress of agriculture in the coming years.
DOI: 10.6084/m9.figshare.20038558.v1
title: Plant breeding in Brazil: Retrospective of the past 50 years

description: Abstract: The importance of plant breeding in Brazilian agriculture has grown a lot in the last 50 years. This occurred mainly because of the: increase in graduate programs, which qualified hundreds of professionals; creation of EMBRAPA and other research institutes or state companies, with an emphasis on the production of new cultivars and; promulgation of the cultivar protection law, which stimulates investments in seed production. The retrospective of what happened, enabling the country to move from being an importer of grains, fruits, and fibers to one of the largest exporters of these products worldwide, was the focus of this work. Taking as reference some agricultural products, this article highlights the significant contribution of plant breeding in recent years. Also, some of the enormous challenges that still have to be overcome, in which the participation of Brazilian breeders will be fundamental to continue the progress of agriculture in the coming years.
DOI: 10.6084/m9.figshare.20038561
title: Recurrent selection in papaya: An effective strategy for the continuous development of new cultivars

description: Abstract: Part of the success of a breeding program depends on the composition of the base population. Superior genotypes and unimproved dioecious varieties are sources of genes for traits of interest and excellent options for the formation of segregating populations. Here we describe the first cycle of recurrent selection (RS) in papaya and propose an effective strategy, unprecedented in the crop, to generate variability and new cultivars. Initially, the RS base population (UCP-C0) was developed with wide variability. Subsequently, 196 S1 progenies were obtained, evaluated in a trial, and the superior 40 S1 progenies were recombined. Among the traits of the selected progenies, high fruit yield (producing two to five fruits per axil) stands out. The S1 progenies were recombined and their seed bulk corresponds to the base population for the second cycle (UCP-C1). The results of the first cycle demonstrate the genetic potential of this population for the development of superior cultivars, and the breeding strategy applied is promising.
DOI: 10.6084/m9.figshare.20038561.v1
title: Recurrent selection in papaya: An effective strategy for the continuous development of new cultivars

description: Abstract: Part of the success of a breeding program depends on the composition of the base population. Superior genotypes and unimproved dioecious varieties are sources of genes for traits of interest and excellent options for the formation of segregating populations. Here we describe the first cycle of recurrent selection (RS) in papaya and propose an effective strategy, unprecedented in the crop, to generate variability and new cultivars. Initially, the RS base population (UCP-C0) was developed with wide variability. Subsequently, 196 S1 progenies were obtained, evaluated in a trial, and the superior 40 S1 progenies were recombined. Among the traits of the selected progenies, high fruit yield (producing two to five fruits per axil) stands out. The S1 progenies were recombined and their seed bulk corresponds to the base population for the second cycle (UCP-C1). The results of the first cycle demonstrate the genetic potential of this population for the development of superior cultivars, and the breeding strategy applied is promising.
DOI: 10.25773/d91p-t507
title:   Storm Surge Simulation from Hurricane Isabel (2003) on the Virginia Shoreline
DOI: 10.6084/m9.figshare.20038563.v1
title: Germplasm enhancement and cultivar development: The need for sustainable breeding

description: Abstract: Farmers need sustainable cultivars to increase food supply and value with less production land, animals, and inputs. Next generation plant and animal breeders face climate change adaptation and mitigation challenges. These challenges need to be addressed with opportunities for significant reduction of environmental impact developing cultivars less addicted to fertilizers and soil moisture needs. Sustainable breeding can help balance agriculture with the environment. Sustainable breeders need to integrate long-term pre-breeding activities with cultivar development efforts providing farmers options to comply with environmental regulations. Good choice of germplasm is still the most important decision. The most sophisticated tools will have limited success if poor choices of germplasm are made. Seed companies need capable breeders developing the next generation of sustainable cultivars while public institutions need to mentor sustainable breeders capable to not only broadening and improving unique germplasm but also developing new cultivars carrying desirable traits. Graduates mentored in breeding programs integrating these needs will be selected for industry jobs without need for re-training. Sustainable breeders will need to operate in new breeding centers located in strategic environments for faster genetic improvement ahead of climate changes. Key factors for developing useful and unique sustainable cultivars will be the adaptation of exotic germplasm and the maximization of its genetic improvement before cultivar development through public and private partnerships. Inbreeding, genetic divergence, and reciprocal recurrent selection programs will continue to be essential to purify cultivars and exploit heterosis in economically important species.
DOI: 10.6084/m9.figshare.20038563
title: Germplasm enhancement and cultivar development: The need for sustainable breeding

description: Abstract: Farmers need sustainable cultivars to increase food supply and value with less production land, animals, and inputs. Next generation plant and animal breeders face climate change adaptation and mitigation challenges. These challenges need to be addressed with opportunities for significant reduction of environmental impact developing cultivars less addicted to fertilizers and soil moisture needs. Sustainable breeding can help balance agriculture with the environment. Sustainable breeders need to integrate long-term pre-breeding activities with cultivar development efforts providing farmers options to comply with environmental regulations. Good choice of germplasm is still the most important decision. The most sophisticated tools will have limited success if poor choices of germplasm are made. Seed companies need capable breeders developing the next generation of sustainable cultivars while public institutions need to mentor sustainable breeders capable to not only broadening and improving unique germplasm but also developing new cultivars carrying desirable traits. Graduates mentored in breeding programs integrating these needs will be selected for industry jobs without need for re-training. Sustainable breeders will need to operate in new breeding centers located in strategic environments for faster genetic improvement ahead of climate changes. Key factors for developing useful and unique sustainable cultivars will be the adaptation of exotic germplasm and the maximization of its genetic improvement before cultivar development through public and private partnerships. Inbreeding, genetic divergence, and reciprocal recurrent selection programs will continue to be essential to purify cultivars and exploit heterosis in economically important species.
DOI: 10.6084/m9.figshare.20038564
title: Contribution of breeding to agriculture in the Brazilian Amazon. I. Açaí palm and oil palm

description: Abstract Sustainable development in the Amazon involves moderate actions that combine technology-based agriculture with forest conservation. One of these actions is the genetic breeding of native species, which promotes cultural appreciation of the local society, and enables the opening of new markets. As an example, two breeding programs with solid results will be mentioned in this review: açaí palm (Euterpe oleracea Mart.) and oil palm (Elaeis guineensis Jacq. and E. oleifera (Kunth.) Cortés). Despite its importance, the prospects for breeding programs on Amazon are not optimistic. Factors intrinsic to plants, such as their incipient domestication, as well as their perennial nature and the difficulty linked to the improvement of plants in this category; and extrinsic factors, such as the lack of resources and specialized labour, in addition to the deficiency in logistics, are growing challenges that make it difficult to implementation of new programs and expansion of existing ones.
DOI: 10.6084/m9.figshare.20038564.v1
title: Contribution of breeding to agriculture in the Brazilian Amazon. I. Açaí palm and oil palm

description: Abstract Sustainable development in the Amazon involves moderate actions that combine technology-based agriculture with forest conservation. One of these actions is the genetic breeding of native species, which promotes cultural appreciation of the local society, and enables the opening of new markets. As an example, two breeding programs with solid results will be mentioned in this review: açaí palm (Euterpe oleracea Mart.) and oil palm (Elaeis guineensis Jacq. and E. oleifera (Kunth.) Cortés). Despite its importance, the prospects for breeding programs on Amazon are not optimistic. Factors intrinsic to plants, such as their incipient domestication, as well as their perennial nature and the difficulty linked to the improvement of plants in this category; and extrinsic factors, such as the lack of resources and specialized labour, in addition to the deficiency in logistics, are growing challenges that make it difficult to implementation of new programs and expansion of existing ones.
DOI: 10.6084/m9.figshare.20038566
title: The numbers game of soybean breeding in the United States

description: Abstract: Soybean [Glycine max (L.) Merr.] represents one of the most essential crops to the world’s economy and food security due to its unique seed composition. Public soybean breeding programs in the United States played an important role in developing the genetic basis of American soybean and discovering many economically important traits. After the passage of the Plant Variety Protection Act (PVP) in 1970 and the authorization to patent living matter in 1980, private companies have dominated the market share of commercial soybean varieties and public breeding programs shifted the efforts towards basic and applied research and education of the next generation of plant breeders. The short history of soybean breeding combined with a very narrow genetic basis derived from few ancestors can only make us reflect on all the innovations yet to be unveiled and the multiple possibilities to explore the unique traits that the golden miracle bean offers.
DOI: 10.6084/m9.figshare.20038566.v1
title: The numbers game of soybean breeding in the United States

description: Abstract: Soybean [Glycine max (L.) Merr.] represents one of the most essential crops to the world’s economy and food security due to its unique seed composition. Public soybean breeding programs in the United States played an important role in developing the genetic basis of American soybean and discovering many economically important traits. After the passage of the Plant Variety Protection Act (PVP) in 1970 and the authorization to patent living matter in 1980, private companies have dominated the market share of commercial soybean varieties and public breeding programs shifted the efforts towards basic and applied research and education of the next generation of plant breeders. The short history of soybean breeding combined with a very narrow genetic basis derived from few ancestors can only make us reflect on all the innovations yet to be unveiled and the multiple possibilities to explore the unique traits that the golden miracle bean offers.
DOI: 10.6084/m9.figshare.20038567.v1
title: Rice blast: strategies and challenges for improving genetic resistance

description: Abstract: Rice blast, caused by the fungus Pyricularia oryzae L., is considered one of the main threats to world rice production. The development of resistant cultivars is one of the best and sustainable control alternatives. Plant breeding efforts have been accelerated by genetic mapping (linkage and associative) and marker assisted selection. On the other hand, genomic editing techniques, such as meganucleases (MNs), Zinc-finger nucleases (ZFNs), Transcription Activator-like Effector Nucleases (TALENs) and Clustered Regularly Interspaced Short Palindrome Repeats/CRISPR-associated protein 9 (CRISPR/Cas9), can be used to promote specific genetic modifications. Likewise, transgenics can also be used to manipulate specific genes. In this sense, this work aims to characterize rice blast and elucidate available biotechnological alternatives to accelerate the development of improved rice cultivars resistant to rice blast.
DOI: 10.6084/m9.figshare.20038567
title: Rice blast: strategies and challenges for improving genetic resistance

description: Abstract: Rice blast, caused by the fungus Pyricularia oryzae L., is considered one of the main threats to world rice production. The development of resistant cultivars is one of the best and sustainable control alternatives. Plant breeding efforts have been accelerated by genetic mapping (linkage and associative) and marker assisted selection. On the other hand, genomic editing techniques, such as meganucleases (MNs), Zinc-finger nucleases (ZFNs), Transcription Activator-like Effector Nucleases (TALENs) and Clustered Regularly Interspaced Short Palindrome Repeats/CRISPR-associated protein 9 (CRISPR/Cas9), can be used to promote specific genetic modifications. Likewise, transgenics can also be used to manipulate specific genes. In this sense, this work aims to characterize rice blast and elucidate available biotechnological alternatives to accelerate the development of improved rice cultivars resistant to rice blast.
DOI: 10.6084/m9.figshare.20038569
title: Spray-induced gene silencing: an innovative strategy for plant trait improvement and disease control

description: Abstract Modern plant breeding is still a time-consuming and costly process, even with the most advanced technologies such as gene editing. Hence, there is an urgent need to develop alternative means for plant trait manipulation and plant protection. RNA interference (RNAi) is a conserved cellular mechanism mediated by naturally occurring double-stranded RNA (dsRNA) and small RNAs (sRNAs) that can target mRNAs for destruction or transcript reduction. Here, we review the potential of technology based on RNAi, called spray-induced gene silencing (SIGS), as an alternative or adjunct to breeding for manipulation of endogenous gene expression in plants or pathogen control. SIGS based on exogenous application of RNA molecules in plants may be especially useful in reducing pest or pathogen impacts, thereby ameliorating biotic stresses and increasing the agronomic performance of crops.