bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inference of allelic dosages and inheritance modes in tetraploids: a case study in Betula apoiensis with a putative hybrid origin
Authors: Nagamitsu Teruyoshi , Kawahara Takayuki , Kanazashi Ayako 
Published: June 2017

AbstractIn tetraploids, inference of allelic dosages and inheritance modes is difficult due to the ambiguous number of allele copies and the variation between disomic and tetrasomic patterns. Considering the biases of amplification and the overlaps of stutter products in polymerase chain reactions, we inferred tetraploid genotypes at three nuclear microsatellite loci in progeny arrays from six reciprocal crosses among three parents of Betula apoiensis with a putative hybrid origin. In each cross, we assigned diploid genotypes to gametes on the basis of the tetraploid genotypes of the parents and their progeny and observed the frequencies of the gamete genotypes. Segregation patterns of the observed gamete genotypes indicated few null alleles in the progeny arrays and tetrasomic inheritance with rare double reduction. This mode of inheritance was consistent between genders and between mates in the crosses. This result suggests that our method to infer tetraploid genotypes in nuclear microsatellites is successful in family samples with few null alleles when the amplification biases and the stutter-product overlaps are accessed properly.
Novel nuclear microsatellites in the endangered neotropical timber tree Lecythis ampla (Lecythidaceae)
Authors: Hernández G. , Konrad H. , Krumböck S. , Geburek Thomas 
Published: June 2017

Abstract
For the first time, nuclear microsatellite (nSSRs) primers were developed in the endangered tree species Lecythis ampla (Lecythidaceae) as molecular tools. An enrichment protocol with genomic DNA libraries for nSSRs was used to identify candidate loci. A large number of candidate loci were identified. Consecutively population genetic parameters of these loci were tested in two available populations. Eventually 17 microsatellite loci have been identified that show no or only low evidence for linkage disequilibrium, deviations from Hardy-Weinberg expectations or high levels of null alleles. These markers are apt for future molecular population studies.
Genetic heterogeneity in age classes of naturally regenerated old growth forest of Picea abies (L.) Karst
Authors: Wojnicka-Półtorak A. , Wachowiak W. , Prus-Głowacki W. , Celiński K. , Korczyk A. 
Published: June 2017

AbstractThe Białowiez·a Primeval Forest is located northeastern Poland. It is one of Europe’s most precious old growth forests in terms of abundance and richness of vegetation, retaining features of a primeval lowland forest which cannot be found anywhere else on the European continent. The aim of the study was to assess the genetic heterogeneity of the naturally regenerated Picea abies population using five chloroplast microsatellite markers. In total, 290 trees representing five age classes were studied. Clear patterns of genetic differentiation in relation to demographic substructuring were found within the population. The class of embryos exhibited the greatest genetic richness as evident from the highest number of alleles and haplotypes, the highest mean number of private alleles and haplotypes and the highest haplotype diversity. In the subsequent age classes, a significant decrease in the level of genetic variation was observed. Our data demonstrate that long-lived, highly outcrossing tree species growing in continuous stands can be genetically heterogeneous on a small geographic scale. The heterogeneity is related to age structure and it is likely due to the underlying mating system and selection processes.
Comparison of allelic diversity between native gene resource plantings and selections in open-pollinated progeny test of Pinus radiata D. Don.
Authors: Zhang L. , Huanqiong N. , Gapare Washington J. , Dillon S. K. , Li X. , Wu H. X. 
Published: June 2017

AbstractGenetic diversity within radiata pine first generation of open-pollinated selections (OPS) from the native resource stands was compared with that observed in native populations to monitor potential changes in genetic diversity during domestication. Genetic diversity was estimated using 58 single nucleotide polymorphisms (SNPs) from 8 expressed genes. Nucleotide diversity maintained in first generation of selections (OPS) (mean π = 0.0036; mean θw= 0.0058) was similar to that found within the native population material (mean π = 0.0043; mean for θw= 0.0065). Likewise, mean values for expected heterozygosity (HE) within and between native population material and OPS were similar (mean = 0.27 ± 0.04) and not significantly different (P = 0.068). Also, the overall distribution of allele frequency classes was not significantly different between native population material and OPS. These results point to no evidence of loss of diversity in OPS due to artificial selection. One possible reason is that the domestication of the OPS is at a very early stage. Another may be that artificial selection in the OPS was based on tree growth and form, not wood properties. The genes selected in this study are mostly involved in cell wall formation, thus genetic diversity of these genes should remain stable between natural population and OPS, unless there was a significant sampling bias in the OPS. Although the SNP information suggests similarities among mainland populations, results from quantitative genetic studies found large provenance differences for growth-, morphological-, stem-form traits, and disease resistance. Determining the threshold at which genetic diversity levels will be significantly reduced during selection should help breeders to make informed decisions regarding the intensity of selection in managed breeding populations as well as gene resource populations.
Promotion of resistance of black alder clones (Alnus glutinosa (L.) Gaertn.) against Phytophthora alni ssp. alni by cyclolipopeptide producing bacteria
Authors: Zaspel I. , Naujoks G. , Krüger L. , Pham L. H. 
Published: June 2017

Summary
This study demonstrated the promotion of the ability of black alder clones to resist to Phytophthora alni ssp. alni with the cyclolipopeptide (CLP)-producing Pseudomonas veronii isolate PAZ1. The bacterial strain, isolated from an association with P. alni ssp. alni, and characterised by its production of the secondary metabolites viscosin and massetolides, possessed inhibitory ability against isolates of the oomycete tree pathogen in vitro. In plant experiments with alder clones in vitro, the treatment with living bacteria showed an earlier start of the rooting process and a promoted root and shoot growth. Compared to non-treated plants, the root system was improved by longer primary roots with abundant secondary roots. The treatment with a methanol extract prepared from strain PAZ1 had no comparable effect. After protective application of strain PAZ1 14 days before the pathogen, the disease incidence was lower and biomass production was higher than in the pathogen control. These results were completed by a greenhouse experiment for a period of 13 months. Bacteria application prior to the pathogen led to reduced Phytophthora incidence at two of five clones in the combined treatment.
Analysis of absolute nuclear DNA content reveals a small genome and intra-specific variation in Cashew (Anacardium occidentale L.), Anacardiaceae
Authors: Aliyu Olawe Mashood 
Published: June 2017

Abstract
There are scanty data on genome size of Anacardiaceae, and none has been reported for cashew, Anacardium occidentale till date. This study aimed at determining the absolute nuclear DNA content (genome size) that could facilitate research into bio-systematics, genomics and genetic improvement of this important tropical tree crop species. Here, isolated nuclei of preparations from 43 cashew accessions selected across five growing regions were flow cytometrically analyzed for genome size determination using Solanum lycopersicum var. Stupicke with a genome size of 1.96 pg/2C as an internal reference standard.
Mean genome size was significantly different (P<0.01) across the 43 cashew accessions suggesting intra-specific variation (about 3.6% coefficient of variation) for absolute nuclear DNA content in this species, but with no evidence of endopolyploidy or endoreduplication. Flow cytometric analysis data presented here showed that absolute genome size of cashew is about 0.857 pg/2C (419 Mb/1C). However, there was a slight gradual increment in genome size from south to north gradient across sampled populations. The data also showed significant correlation (r=0.368, P<0.01) between nuclear DNA content (genome size) and phenotypic trait, nut weight. The results obtained here confirmed relatively small genome size in this tree species, almost twice genome size of diploid Arabidopsis thaliana but slightly lower than mango, Mangifera indica, a close relative in Anacardiaceae. Similarity in genome size between Mangifera indica and Anacardium occidentale could be a further proof of genetic relatedness between these two important species of Anacardiaceae.
How small and constrained is the genome size of angiosperm woody species
Authors: Ohri Deepak 
Published: June 2017

AbstractAngiosperm hardwood species are generally considered to show an average smaller genome size with a narrow range of variation than their herbaceous counterparts. Various explanations pertaining to limitations of cell size exerted by wood fibers, the requirement of smaller stomata, longer generation time, large population size, etc., have been put forward to account for their small and constrained genome size. Yet studies done in the past several years show that genomically as well as evolutionarily, hardwoods are as diverse and active as their herbaceous counterparts. This is entirely supported by the presence of well developed inter and intraspecific polyploid series and natural triploidy in many genera. Polyploidy, in some instances has been shown to confer adaptability to arid and salt stress conditions and in colonization of new areas. Moreover, hardwoods also show reasonable amenability to the induced polyploidy which abruptly changes the balance between nuclear and cell size. Polyploidy has been induced in many hardwoods to restore fertility in interspecific hybrids and for the production of triploids.Furthermore, some cases studied show that genome size variation in hardwoods can be as variable as that of herbaceous species. Genome size has been shown to vary remarkably both at homoploid level as well as by polyploidy in certain genera. In the same way, the genome size is not correlated with the habit in certain groups having both herbaceous and woody taxa. This point is further proved by the presence of secondary and insular woody habit in certain cases where either the transition to woodiness is not followed by any diminution in the genome size, or the genome size of insular woody species may be even more than that of the congeneric herbaceous species. This shows that woody habit does not by itself put any constraints on the genome size either at homoploid or at polyploidy levels. The genome size in fact, not only varies significantly in many congeneric woody species but also may not show any correlation with the habit when woody and herbaceous species are compared in some narrow taxonomic groups studied.
Near rotation-length performance of selected hybrid larch in Central Maine, U.S.A
Authors: Greenwood M. S. , Roth Brian E. , Maass D. , Irland L. C. 
Published: June 2017

AbstractTwenty-two year measurements of a test of inter- and intraspecific larch hybrids among European (E), Japanese (J) and tamarack (T) parents growing in central Maine reveal significant hybrid vigor, especially among crosses involving J and E parents. The mean heights and diameters of all the interspecific crosses between J and E parents exceeded those of intraspecific crosses among either of the parents. The mean height after 22 years for all 17 JxE and ExJ crosses was 19.2 m (63 feet), which compares favorably with heights of loblolly pine plantations at age 25 growing in the southeastern USA, where site index ranged from 12.2 m to 24.4 m (40 and 80 feet respectively). In addition the mean height of these larch crosses was 30% greater than that of a control hybrid seed lot of German origin. Crosses between E and T parents also performed well, but exhibited relatively poor form, and seed set was very low. Seed set and viability for crosses between J and E were as good as intraspecific parental crosses. Therefore propagation of hybrid larch crosses via controlled pollination and rooted cuttings is feasible, and the potential benefits of larch plantations for Maine’s forest economy are briefly discussed.
Differentiation of six Eucalyptus trees grown in Mexico by ITS and six chloroplast barcoding markers
Authors: Fladung M. , Schroeder H. , Wehenkel C. , Kersten B. 
Published: June 2017

Abstract
Different species of the genus Eucalyptus, originally native to Australia, are being cultivated in different parts of the world due to their fast growth and beneficial wood properties. In Mexico, probably up to 25 different Eucalyptus species (many of them with unknown species declaration) were introduced early in the 20th century. Many Eucalyptus species are cross compatible and information about provenances of the single eucalypt species is rare. In this study, an experimental plantation established in 1984 and located in Northeast of Mexico was chosen as example to re-assign the species name of six randomly selected Eucalyptus trees growing in this plantation. First, a phylogenetic tree was constructed from complete chloroplast sequences of 31 Eucalyptus species available in the NCBI database. The phylogenetic tree includes three of the nine Eucalyptus species known to be introduced to Mexico, namely E. camaldulensis, E. saligna and E. grandis, which belong to a clade named “Symphyomyrts”. By employing combined BLASTN and UPGMA analyses of six chloroplast (cp) regions, three of the six unknown eucalypt samples (Euc4, 5, 6) cluster together with E. microtheca and E. cladocalyx, whereas the other three (Euc1, 2, 3) were more similar to a group containing E. camaldulensis, E. grandis and E. saligna. UPGMA analysis of the ITS region overall shows the same rough clustering, but provide more detailed information for two samples being most likely assigned to E. camaldulensis.
Expression of three phenylpropanoid pathway genes in Scots pine (Pinus sylvestris L.) in open-pollinated families with differing relative wood densities during early and late wood formation
Authors: Kanberga-Silina K. , Jansons A. , Rungis Dainis 
Published: June 2017

Abstract
Wood volume and quality are the most important aspects of commercial forestry production, and studies of wood formation are important in order to increase the value and efficiency of forestry production. The phenylpropanoid pathway produces various compounds with diverse functions both for plant defence against biotic and abiotic stress as well as structural development. One of the main roles is monolignol production for lignin biosynthesis, which is a crucial aspect of wood formation. For this study three candidate genes involved in lignin biosynthesis were selected: phenylalanine ammonialyase (PAL1), cinnamyl alcohol dehydrogenase (CAD) and cinnamoyl-CoA reductase (CCR). Candidate gene expression was analysed in selected individuals with high and low wood density from open-pollinated Scots pine families during early wood (EW) and late wood (LW) formation and correlation between expression of these genes, total lignin content, and wood density was determined. Wood density values for analysed trees were similar within tree families but differed significantly between families with high and low wood density (p=1,06E-20). Wood density was slightly negatively correlated with lignin content (r=-0.36, p=0.038), but only in individuals in the high density wood group. In trees with low wood density, expression of the CAD gene was significantly lower in late wood formation compared to early wood (p=0.00179). In trees with high wood density, expression of the PAL1 gene was five times higher during early wood formation compared to late wood formation. A positive correlation was detected between PAL1 and CCR gene expression during early wood formation (r=0.804) and late wood formation (r=0.466).
PCR-RFLP analysis of cpDNA in Gigantochloa scortechinii (Poaceae: Bambuseae) in Peninsular Malaysia and implications for the use of cpDNA markers in systematic studies
Authors: Dhanendiren N. , Ong H.Y. , Khoo G. , Wong K.M. , Goh W.L. 
Published: June 2017

Abstract
Gigantochloa is a paleotropical woody bamboo genus that has been widely cultivated in SE Asia because of its usefulness. Recent studies have shown that species of this genus enter into an introgression complex with other genera of the same subtribe Bambusinae. Within G. scortechinii, a common species indigenous to Malay Peninsula and common in Peninsular Malaysia, two distinct chloroplast DNA (cpDNA) lineages, the Gombak- and Langat-type, were recovered. We report the development of a PCR-based restriction fragment length polymorphism (RFLP) marker for depicting the genetic differentiation in G. scortechinii based on cpDNA. We determined a cpDNA region and its corresponding restriction enzyme which can produce different RFLP profiles for the two cpDNA lineages. Our design was verified with empirical studies. The Gombak-type was the dominant cpDNA genotype for G. scortechinii in Peninsular Malaysia. Implications for the continued use of cpDNA markers in systematic studies are discussed.
Genetic diversity and spatial genetic structure in populations of Orbignya phalerata Mart. under different exploitation intensities in the Brazilian savanna
Authors: Ibanes Bruna , Sebbenn A.M. , Azevedo V.C.R. , Moreno M.A. , Gandara F.B. , Tambarussi E.V. , Ferraz E.M. , Damasceno-Silva K.J. , Lima P. S.C. , Carvalhaes M.A. 
Published: June 2017

AbstractGenetic studies in tropical tree species have found signs of decreased genetic diversity and increased levels of inbreeding and spatial genetic structure (SGS) in fragmented and exploited populations. The aim of this paper was to investigate genetic diversity, structure, and intrapopulation SGS using eight microsatellite loci for three Orbignya phalerata populations that have undergone different intensities of seed harvesting. From each population, we georeferenced and sampled 30 seedlings, 30 juveniles, and 30 adult trees. The total number of alleles over all loci (k), and observed (Ho) and expected heterozygosity (He) presented lower values for the population experiencing more intense fruit harvesting than less heavily exploited populations, suggesting that fruit harvesting may decrease genetic diversity. Null alleles were detected in practically all loci among seedlings, juveniles, and adults in all populations, indicating that the estimates of Ho, He, and fixation index (F) are biased. When corrected for null alleles (FNull), the fixation index decreased for all samples, resulting in significantly higher than zero results for seedlings of all populations, but not for juveniles and adults of all populations. The comparison of FNullvalues between cohorts in the most heavily exploited population (ESP) suggests that inbred individuals are eliminated between seedling and adult stages. Significant SGS was detected up to 60 m in all populations, which indicates short distance seed dispersal. Genetic differentiation (G’ST) between pairwise populations was related to spatial distance between populations, with the greatest difference between more distant populations.
Mating system variation among populations, individuals and within and among fruits in Bertholletia excelsa
Authors: Wadt L.H.O. , Baldoni A. B. , Silva V. S. , Campos T. , Martins K. , Azevedo V.C.R. , Mata L.R. , Botin A.A. , Hoogerheide E.S. S. , Tonini H. , Sebbenn Alexandre M. 
Published: June 2017

Abstract
The aim of this study was to investigate variation in mating system among three Brazilian Amazon populations of the tree Bertholletia excelsa with different levels of anthropogenic interventions. We collected open-pollinated seeds from one natural population, remnant trees dispersed in a pasture, and trees from a plantation. Outcrossing rate not varied among the populations and indicates that all seeds were originated from outcrossing (tm=1.0). Mating among relatives was significant higher in the plantation than forest and pasture populations, probably due the fact that many trees are related in the plantation. Correlated mating was significantly higher in pasture (rp=0.47) and plantation (rp=0.51) than in the natural population (rp=0.22), suggesting that trees in natural population are pollinated by a higher number of pollen donors. The paternity correlation was significantly higher within (rp(w)=0.41) than among fruits (rp(a)=0.18), showing a higher probability to find full-sibs within than among fruits. The fixation index was generally lower in seed trees than in their seedlings, suggesting selection for heterozygous individuals from seedling to adult stages. Progeny arrays collected from the natural population had a lower proportion of pairwise full-sibs than in pasture and plantation and higher variance effective size (2.75) than trees in pasture (2.15) and plantations (2.22). Results highlight that seed collections for conservation, breeding and reforestation programs preferentially should be carried out in natural populations due low proportion highest variance effective size within progeny.
PCR-based detection of single sequence variants from a natural collection of the non-model tree species European Aspen Populus tremula (L.)
Authors: Winkler S. , Linke K. , Gscheidel N. , Meyer M. , Krabel Doris 
Published: June 2017

Abstract
In the present study we present and discuss the identification of species-specific SNPs to rule out any experimental influence of species-specific primer design (Populus tremula vs. the closely related model-species Populus trichocarpa) on the detectability of SNPs. Applying a species-optimized method, partial sequences of 14 genes involved in xylem cell development, xylogenesis, pectin formation, and drought stress reaction were analyzed at the genomic level. About 3 Mb of sequence information were generated by Sanger sequencing technology and 258 sequence variants were identified. 15 out of these represent insertions /deletions located exclusively in non-coding regions and the remaining 243 are SNPs found in coding and non-coding regions of candidate genes.
The introduction of a species-specific SNP detection pipeline will help to detect nucleotide variants in P. tremula and to conduct association mapping in natural P. tremula populations.