The USDA Barley Core Collection: Genetic Diversity,Population Structure,and Potential for Genome-Wide Association Studies

New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define ‘mini-core’ sets of accessions capturing the majority of the allelic diversity present in the core collection. These ‘mini-core’ sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of ‘hull cover’, ‘spike row number’, and ‘heading date’ demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections.     

Genetic variation and diversity among loquat accessions

Loquat (Eriobotrya japonica (Thunb.) Lindl., Maloideae, Rosaceae) is a subtropical evergreen fruit tree indigenous of China, where the center of origin of the species is located. Loquat is grown in all subtropical areas and was introduced in the Mediterranean basin in late eighteenth century. In Europe, the largest germplasm bank is located at Instituto Valenciano de Investigaciones Agrarias (IVIA; Valencia, Spain). Thirteen microsatellites and a conserved region of S-allele were used to assess the genetic diversity of 102 accessions of the IVIA collection. A total of 38 SSR alleles and 11 putative S-alleles were used to study the genetic structure of the loquat germplasm bank using the STRUCTURE software, Factorial Correspondence Analysis (FCA), and unweighted pair-group method (UPGMA) cluster analyses. The total diversity was H _T?=?0.5682, the genetic differentiation G _ST?=?0.1660, and the standardized G _ST reached a much higher value of G′_ST?=?0.4948. The Evanno’s test indicated that the most informative number of populations was five, with accessions distributed according to their geographic origin in two, one, and two groups of Spanish, Italo-Spanish, and non-European origin, respectively. Knowledge of the substructure and diversity of the IVIA loquat collection and the self-incompatibility genotype data will allow us to select and incorporate useful materials into the loquat breeding program.     

Genetic variation for root architecture, nutrient uptake and mycorrhizal colonisation in Medicago truncatula accessions

Sustainable agriculture strives for healthy, high yielding plants with minimal agronomic inputs. Genetic solutions to increase nutrient uptake are desirable because they provide ongoing improvements. To achieve this it is necessary to identify genes involved in uptake and translocation of nutrients. We selected Medicago truncatula L. as a model because of its: i) close genetic relationship to food legumes, ii) use as a pasture legume in southern Australia and iii) availability of mapping populations generated from genetically diverse accessions. We discovered statistically significant differences between eight accessions for: root architecture in growth pouches, % root colonisation with the arbuscular mycorrhizal (AM) fungus Glomus intraradices, and plant tissue concentration of most macro- and micronutrients. Mycorrhizal colonisation had a significant effect on P concentration in roots but not shoots, Mg concentration in both roots and shoots, and the concentration of various micronutrients in shoots including Fe, Ca, but not Zn. Comparison of micronutrient uptake between root and shoot tissues showed that some M. truncatula accessions were more efficient at mobilisation of nutrients from roots to shoots. We are now in a position to use existing mapping populations of M. truncatula to identify quantitative trait loci important for human health and sustainable agriculture.     

鹅观草属三个物种及其居群间的醇溶蛋白分析

利用酸性聚丙烯酰胺凝胶电泳技术(APAGE)对小麦族鹅观草属3个物种:毛叶鹅观草、纤毛鹅观草和竖立鹅观草进行了醇溶蛋白电泳分析,23份材料电泳分离出22条相对迁移率不同的谱带,其中3条(16.6%)共同带,19条(83.4%)具多态性,每个材料可分离出9～16条谱带。结果表明:(1)三个物种具有相似的醇溶蛋白带型,但存在明显的种间差异;(2)同种不同居群间也存在遗传差异;(3)种间差异大于种内差异。     

Distribution of allozymic alleles and genetic diversity in the American Barley Core Collection

A survey of allozymic alleles and genetic diversity was made for 151 accessions of the American Barley Core Collection. A total of 25 alleles at ten loci were observed. Two loci were monomorphic. The average diversity index for individual loci ranged between 0.026 and 0.649. Most significant differences in allelic frequency and genetic diversity value were found between spring and winter barley. Spring barley showed a greatly higher average diversity than winter barley (t=2.124, P=0.071). The smallest differences in allelic frequencies and diversity values were observed between the two geographical regions, North and South America. Rare alleles were detected only in a few accessions. Seven rare alleles were associated with spring barley. The genetic similarities among the 151 accessions ranged from 0.20 to 1.00, which showed that a high level of genetic variability exists in this set of core accessions. Cluster analysis and principal coordinate analysis did not give clear-cut separation of different types of barley, but most of the winter barley accessions were closely associated. Received: 7 April 2000 / Accepted: 13 June 2000     

Nucleolar number variation in Hordeum species,their haploids and interspecific hybrids

Nucleolar number variation has been investigated in root tip cells by cytologically determining the number of nucleoli per cell in autoploids and alloploids of Hordeum species, their haploids and interspecific hybrids. The nucleolus organisers in autoploid types of H. vulgare or H. bulbosum did not show any alterations irrespective of the ploidy level. The nucleolar number variation in these species results from a definite pattern of fusion and the maximum number of nucleoli per nucleus corresponds to the number of secondary constrictions. Nucleolus formation in alloploids and interspecific hybrids is impaired on some of the NORs, suggesting differential amphiplasty or nucleolar dominance. A comparison of nucleolar formation in the alloploid species (brachyantherum, arizonicum, procerum and parodii), their haploids, and the interspecific hybrids revealed different degrees of variation from the expected mean and maximum numbers of nucleoli. While the deviations in hybrids between alloploids (H. arizonicum and H. brachyantherum or H. procerum and H. brachyantherum) are marginal, nucleolar dominance is more pronounced in hybrids involving H. vulgare or H. bulbosum as one of the parents and is invariably associated with the disappearance of the secondary constriction(s) from the NOR(s) contributed by one of the parents, and the number of nucleoli is appropriately reduced.     

Crossability variation in four South American Hordeum species

Andersson, 2. 1995. Crossability variation in four South American Hordeum species— Nord. J. Bot. IS: 355–364. Copenhagen. ISSN 0107–055X.
Intra- and interpopulation crosses within the four South American Hordeum species, H. cordobense, H. chilense, H. muticum and H. stenostachys were performed. Seeds were obtained in all intrapopulation crosses within all four species. Hordeum cordobense showed little variation in crossability of interpopulation crosses and the F₁-families had rather high fertility. A wide range in crossability between populations was observed in the three species H. chilense, H. muticum and H. stenostachys . Some combinations failed to set seed while others had high seed set. The fertility of the F₁-_- families varied from almost sterile to fully fertile. All parental plants, intra and interpopulation hybrids in the four species had very high meiotic pairing frequency with 12–14 chiasmata per cell. Hordeum cordobense is a homogeneous species while the other three species are heterogeneous and genetically diverse.     

Development of a Core Collection of Six-Rowed Hulless Barley from the Qinghai-Tibetan Plateau

Plant Molecular Biology Reporter - A core collection reflects the diversity of the larger germplasm collection and makes the evaluation of genetic resources more effective. To improve barley...     

Genetic variation and covariation in a population of tetraploid Dactylis L. accessions

Summary Efficient utilization of divergent germ plasm sources in breeding cultivated Dactylis glomerata L. ssp. glomerata Domin depends on knowledge of quantitative variation within and among accessions. This study was undertaken to quantify variation and covariation for forage yield, maturity, disease reaction, and ground cover within a population of tetraploid Dactylis accessions. Variation was observed among families within the population for each variable. Most genetic variation (73%–93% of the family sums of squares) was within country sources or within accessions. Thus, country boundaries, which are traditionally important factors used in defining limits of plant exploration expeditions, have limited expected use in targeting future exploration for specific sources of high yield, disease resistance, or ground cover. Maturity was the exception to this; late-maturing accessions were identified as originating exclusively from the USSR. Some relationships among traits, such as that for yield and disease reaction, differed for accessions and cultivars. Several accessions and families within accessions were identified to have performance superior to most or all cultivars included in this study. Existing germ plasm from several countries was identified to have potential in breeding orchardgrass, while that from other countries appeared to have little or no potential in supplying germ plasm for hay production in humid-temperate environments.     

Genetic variation in three species in the Lampropholis delicata (Lacertilia: Scincidae) complex

The Lampropholis delicata complex consists of three closely related species, which have very different habitat requirements and geographic distributions. Percentage polymorphism and average heterozygosity per population are lowest in the species with the narrowest habitat requirements. Genetic differentiation between populations is also lowest in this species, which had a very limited and almost continuous distribution. For one species, which occurs in a very wide range of habitats, both natural and disturbed, genetic variability is compared between samples from disturbed and undisturbed habitats. Average heterozygosity is significantly lower in samples from disturbed than in those from undisturbed sites.     

芝麻核心收集品中育成品种（系）的遗传多样性分析

利用SRAP分子标记技术对中国芝麻核心收集品的育成品种(系)进行遗传多样性分析,结果表明,14对引物组合在18份芝麻育成品种(系)间共扩增出稳定清晰的条带193条,其中多态性带124条,占64.2%.通过聚类分析和主坐标分析,表明育成品种(系)的遗传基础存在一定的多样性,但遗传相似系数较大(0.5342～0.9688),遗传距离较近.该研究结果表明,在芝麻育种的亲本选配中应积极引入地方种质、国外种质等,以拓宽遗传基础.     

豌豆资源遗传多样性及核心种质研究进展

豌豆是世界第四大食用豆类作物,我国是世界第二大豌豆生产国.本文对豌豆的起源、分布、遗传多样性及核心种质等研究进展进行综述,旨在为我国豌豆种质资源收集、保存、研究和利用提供参考.     

葡萄种质资源初级核心群的构建

以国家果树种质郑州葡萄圃保存的867份栽培种质为材料,对47项表型性状进行了主成分分析。采用欧氏遗传距离、离差平方和法进行种质初选。采用分组和逐步聚类法,分别以15%、20%、25%和30%的比例抽样,依次获得124、170、205和252份种质。通过对初选种质的遗传多样性指数、表型保留比例的分析,检验初级核心群的构建效果。结果表明,按种质类型分组,组内采用平方根策略、15%抽样比例获得的124份初选种质的表型保留比例和遗传多样性代表性均达到96%,表明构建的初级核心群对原始种质具有很好的代表性。     

Genetic evidence for three species of rockhopper penguins, Eudyptes chrysocome

The taxonomy of rockhopper penguins, Eudyptes chrysocome (Forster 1781), is contentious. Some authorities recognise three subspecies based on morphological differences and geographical separation of breeding populations while others suggest that morphological differences support classifying rockhopper penguins as two distinct species. The taxonomy of rockhopper penguins is of more than academic interest as breeding colonies worldwide have declined markedly in size since the 1930s and rockhopper penguins are currently listed as vulnerable by the IUCN. We compared the genetic distances between three mitochondrial gene regions from the three putative rockhopper penguin subspecies with the distances between various penguin sister species to clarify the taxonomy and systematics of rockhopper penguins. Genetic distances between the rockhopper penguin taxa, relative to other closely related penguin species, support reclassifying the three rockhopper penguin subspecies as species. Reclassification of rockhopper penguins as three species could result in their conservation status being upgraded from vulnerable to endangered.     

Genetic variation in three species of Epipactis (Orchidaceae): geographic scale and evolutionary inferences

The breeding system is expected to strongly influence the genetic structure of plant populations. In the present study, isozyme variation is documented in Danish populations of three species of Epipactis , varying in breeding system from allogamy to obligate autogamy. The allogamous and widespread E. helkborine subsp. helkborine shows high levels of polymorphism. Most of the genetic variation is found within local populations. A hierarchical analysis indicates significant among-population differentiation, but no regional differentiation in E. helkborine is apparent. This may be due to higher levels of gene flow in the past, before forest was fragmented. The ecotype from coastal dunes, E. helleborine subsp. neerlandka , does not differ from E. helkborine subsp. helkborine in any of the examined loci, but it has a significant population inbreeding coefficient that can probably be explained by higher levels of geitonogamy and the possibility of spontaneous autogamy. The entomophilous E. purpurata and the obligately autogamous E. phylhmthes are monomorphic at all loci examined. Several factors, including a founder effect at the time of colonization, high levels of geitonogamy, as well as habitat specialization combined with erratic flowering may have contributed to the lack of variation in E. purpurata. The lack of variation in the autogamous E. phyllanthes is probably due to inbreeding. It is proposed diat autogamy in Epipactis may in some cases have evolved through paedomorphosis of allogamous flowers and that the occurrence of local breeding groups may have facilitated the speciation process.     

大麦黄花叶病严重度的遗传分析

本文就大麦黄花叶病(BYMV)的抗性进行了遗传分析。研究表明,在本研究中,大麦黄花叶病抗性表现为多基因控制的数量性状,符合“加性-显性”遗传模型,但主要受加性效应控制。回归分析与平均显性度((H_1/D)~(1/2))测定均表明为部分显性。且控制BYMV的严重度的显性基因数约为3—6组。遗传力估算较高。最后就实验结果对BYMV抗性育种进行了初步分析讨论。     

Worldwide patterns of genetic variation among four esterase loci in Barley (Hordeum vulgare L.)

Summary Electrophoretic assays of 1506 accessions of domestic (Hordeum vulgare L.) and wild (H. spontaneum Koch.) barley, maintained in the USDA World Barley Collection, led to the following conclusions: (1) worldwide the four esterase loci, Est 1, Est 2, Est 3, and Est 4, have a minimum of 7, 12, 6, and 7 alleles, respectively; (2) little or no genetic differentation has developed between H. vulgare and H. spontaneum at these four esterase loci; (3) substantial genetic polymorphism and heterozygosity occur within many of the accessions despite the heavy inbreeding which results from the mating system of predominant self fertilization and from genetic drift associated with maintenance in small populations; (4) patterns of geographical distribution of alleles at these four loci are not at random over both small and large geographical areas, including differences on a continental scale; (5) four among 16 four-locus combinations of alleles are found in excess and all other combinations occur in deficiency on a worldwide basis.This work was supported in part by National Science Foundation Grant DEB 78-02046