Population genetic structure of Japanese wild soybean (Glycine soja) based on microsatellite variation

The research objectives were to determine aspects of the population dynamics relevant to effective monitoring of gene flow in the soybean crop complex in Japan. Using 20 microsatellite primers, 616 individuals from 77 wild soybean (Glycine soja) populations were analysed. All samples were of small seed size (< 0.03 g), were directly collected in the field and came from all parts of Japan where wild soybeans grow, except Hokkaido. Japanese wild soybean showed significant reduction in observed heterozygosity, low outcrossing rate (mean 3.4%) and strong genetic differentiation among populations. However, the individual assignment test revealed evidence of rare long-distance seed dispersal (> 10 km) events among populations, and spatial autocorrelation analysis revealed that populations within a radius of 100 km showed a close genetic relationship to one another. When analysis of graphical ordination was applied to compare the microsatellite variation of wild soybean with that of 53 widely grown Japanese varieties of cultivated soybean (Glycine max), the primary factor of genetic differentiation was based on differences between wild and cultivated soybeans and the secondary factor was geographical differentiation of wild soybean populations. Admixture analysis revealed that 6.8% of individuals appear to show introgression from cultivated soybeans. These results indicated that population genetic structure of Japanese wild soybean is (i) strongly affected by the founder effect due to seed dispersal and inbreeding strategy, (ii) generally well differentiated from cultivated soybean, but (iii) introgression from cultivated soybean occurs. The implications of the results for the release of transgenic soybeans where wild soybeans grow are discussed.     

中国花生核心种质的建立

以中国花生种质资源数据库中记录的6390份花生资源为材料,以其基本数据、特征数据和评价数据为信息,采用分层、层内分组聚类以及随机取样与必选资源相结合的方法,构建了由576份资源组成的花生核心种质,占基础收集品的9.01%。对核心种质的植物学类型组成和遗传多样性指数的分析,以及对各性状特征值、符合率和包含的主要抗病资源抗性等级及重要农艺性状资源的检测结果表明,本研究建立的核心种质是有效的。基础收集品中各种性状的遗传变异在核心种质中均存在,所用15个性状的各种特征值符合率均在90%以上,其中绝大部分性状的符合率达96%以上。     

中国花生核心种质的建立

以中国花生种质资源数据库中记录的6390份花生资源为材料,以其基本数据、特征数据和评价数据为信息,采用分层、层内分组聚类以及随机取样与必选资源相结合的方法,构建了由576份资源组成的花生核心种质,占基础收集品的9.01%。对核心种质的植物学类型组成和遗传多样性指数的分析,以及对各性状特征值、符合率和包含的主要抗病资源抗性等级及重要农艺性状资源的检测结果表明,本研究建立的核心种质是有效的。基础收集品中各种性状的遗传变异在核心种质中均存在,所用15个性状的各种特征值符合率均在90%以上,其中绝大部分性状的符合率达96%以上。     

中国野生大豆遗传资源搜集基本策略与方法

遗传资源搜集原则是通过种子采集追求样本具有最高程度的遗传多样性。为了合理而有效地搜集野生大豆资源,近年来通过野生大豆居群考察和遗传多样性分析,初步明确了野生大豆资源居群的遗传多样性分布动态:遗传多样性地理的和生态的区域性、生态系统内居群的遗传相关性及各种生境下居群遗传多样性差异,从理论上奠定了野生大豆资源合理有效搜集的依据。根据居群遗传多样性的分布规律,初步建立了居群野生大豆资源的搜集策略和方法。     

北京地区野生大豆种群SSR标记的遗传多样性评价

 使用40对SSR引物分析了北京地区野生大豆(Glycine soja)天然种群的遗传结构与遗传多样性。10个种群共检测到526个等位变异, 平均每对引物等位基因数为13.15个, 种群平均Shannon指数(I)为0.658, 群体平均位点预期杂合度(H_e)为0.369, 群体平均位点杂合度(H_o)为1.29 %。平均种群内遗传多样度(H_s)为0.362, 平均种群间遗传多样度(D_ST)为0.446, 基因分化程度(G_ST)为0.544。该研究显示, 中-西部生态区种群比北部和东部山区种群有较高的遗传多样性。在地理上, 环绕北京地区的太行山和燕山两大余脉区域野生大豆种群遗传分化表现出地理差异。可能是经过干旱选择而形成的有抗旱潜力的种群在遗传上表现单一化。期待该种群提供耐旱基因。     

Preservation of plant genetic resources in the biotechnology era

Thousands of years ago humans began domesticating crops as a food source. Among the wild germplasm available, they selected those that were best adapted for cultivation and utilization. Although wild ancestors have continued to persist in regions where domestication took place, there is a permanent risk of loss of the genetic variability of cultivated plants and their wild relatives in response to changing environmental conditions and cultural practices. Recognizing this danger, plant ex situ genebank collections were created since the beginning of the last century. World-wide, more than 6 million accessions have been accumulated including the German ex situ genebank in Gatersleben, one of the four largest global collections, housing 150,000 accessions belonging to 890 genera and 3032 species. This review summarizes the ex situ plant genetic resources conservation behavior with a special emphasis on German activities. Strategies for maintenance and management of germplasm collections are reviewed, considering modern biotechnologies (in vitro and cryo preservation). General aspects on genetic diversity and integrity are discussed.     

The genetic diversity and population structure of wild soybean evaluated by chloroplast and nuclear gene sequences

Glycine soja, also called wild soybean, is the wild ancestor of domesticated soybean (Glycine max), and one of the world's major cultivated crops. Wild soybean is a valuable resource for the breeding of cultivated soybean and harbors useful genes or agronomic traits. To use and conserve this valuable resource, we conducted a study to evaluate the genetic diversity and population structure of wild soybean using the sequencing data of two nuclear loci (AF105221 and PhyB) and one chloroplast locus (trnQ-rps16) of more than 600 individuals representing 53 populations throughout the natural distribution range. The results showed that most of the variation was found within the populations and groups, but significant genetic differentiation was also detected among different eco-geographical groups. Correlations between genetic and geographical distance at all the loci were consistent with the isolation by distance gene flow model. G. soja exhibited the highest genetic diversity in middle and downstream of Yangzi River (MDYR) region, followed by North East China (NEC), and was the lowest in North West China (NWC). We concluded that both in situ and ex situ conservation strategies required for wild soybean populations, especially which are native to MDYR and NEC regions.     

Development,validation and genetic analysis of a large soybean SNP genotyping array

Cultivated soybean (Glycine max) suffers from a narrow germplasm relative to other crop species, probably because of under‐use of wild soybean (Glycine soja) as a breeding resource. Use of a single nucleotide polymorphism (SNP) genotyping array is a promising method for dissecting cultivated and wild germplasms to identify important adaptive genes through high‐density genetic mapping and genome‐wide association studies. Here we describe a large soybean SNP array for use in diversity analyses, linkage mapping and genome‐wide association analyses. More than four million high‐quality SNPs identified from high‐depth genome re‐sequencing of 16 soybean accessions and low‐depth genome re‐sequencing of 31 soybean accessions were used to select 180 961 SNPs for creation of the Axiom^® SoyaSNP array. Validation analysis for a set of 222 diverse soybean lines showed that 170 223 markers were of good quality for genotyping. Phylogenetic and allele frequency analyses of the validation set data indicated that accessions showing an intermediate morphology between cultivated and wild soybeans collected in Korea were natural hybrids. More than 90 unanchored scaffolds in the current soybean reference sequence were assigned to chromosomes using this array. Finally, dense average spacing and preferential distribution of the SNPs in gene‐rich chromosomal regions suggest that this array may be suitable for genome‐wide association studies of soybean germplasm. Taken together, these results suggest that use of this array may be a powerful method for soybean genetic analyses relating to many aspects of soybean breeding.     

小麦地方品种繁殖更新过程中的遗传多样性变化分析

采用分别保存于长期库及中期库的3个小麦地方品种的6份材料,进行了9项农艺性状及35个与农艺性状相关的微卫星标记检测,每份材料选取30个单株进行遗传多样性与遗传结构分析。结果表明:(1)更新前,3个小麦地方品种均为遗传异质性群体,在SSR位点上的异质度分别为57.14%、48.57%和5.71%。(2)在农艺性状表现上,只有温泉小麦3在株高和穗粒数上更新后比更新前显著增加,其他材料无显著差异。(3)在SSR位点多态性表现上,3个品种在更新后均发生了遗传多样性变化,8个与粒重、产量、生育期性状相关位点存在等位位点丢失现象,其中2个与粒重、生育期相关位点频率变化显著。(4)综合农艺性状调查与SSR分子标记检测结果发现,3个品种更新前后在多样性指数上无显著差异,遗传分化系数Gst分别为0.0269、0.0324和0.0380,即更新前后遗传差异分别为2.69%、3.24%和3.80%。上述结果建议,经繁殖更新的小麦种质资源能够比较完好地保持其遗传多样性和遗传结构。对于遗传异质性小麦地方品种在繁殖更新后存在遗传多样性丢失的危险,为了保证更新前后的遗传完整性,建议在繁殖更新过程中每个品种至少应保持300个单株的群体。     

The genetic diversity of annual wild soybeans grown in China

Annual wild soybeans (Glycine soja), the ancestors of cultivated soybeans (G. max), are important sources of major genes for resistance to pests, diseases and environmental stresses. The study of their genetic diversity is invaluable for efficient utilization, conservation and management of germplasm collections. In this paper, the number of accessions, the variation of traits, the genetic diversity indexes (Shannon index) and the coefficient of variation were employed to study the geographical distribution of accessions, genetic diversity of characters and genetic diversity centers of annual wild soybean by statistical analysis of the database from the National Germplasm Evaluation Program of China. Most annual wild soybeans are distributed in Northeast China, and the number of accessions decreases from the Northeast to other directions in China. The genetic diversity indexes (Shannon index) were 0.49, 0.74, 0.02, 0.55, 1.45, 2.41, 1.27 and 1.89 for flower color, sootiness of seed coat, cotyledon color, pubescence color, hilum color, leaf shape, stem type and seed color, respectively. Coefficients of variation were 7.1%, 28.7%, 76.43% and 18.2% for protein content, oil content, 100-seed weight and days to maturity, respectively. Three genetic diversity centers, the Northeast, the Yellow River Valley and the Southeast Coasts of China, are proposed based on the geographical distribution of the number of accessions, genetic diversity and the multivariate variation coefficient. Based on these results and Vavilov’s theory of crop origination, two opposing possible models for the formation of the three centers are proposed, either these centers are independent of each other and the annual wild soybeans in these centers originated separately, or the Northeast center was the primary center for annual wild soybeans in China, while the Yellow River Valley center was derived from this primary center and served as the origin for the Southeast Coast center. Received: 25 June 2000 / Accepted: 18 October 2000     

Genetic divergence between North American ancestral soybean lines and introductions with resistance to soybean cyst nematode revealed by chloroplast haplotype

Domesticated soybean [Glycine max (L.) Merr.] is a major crop with an established ancestral relationship to wild soybean (Glycine soja Sieb. & Zucc.) native to Asia. Soybean genetic diversity can be assessed at different levels by identification of polymorphic alleles at genetic loci, in either the plastid or nuclear genomes. The objective of this study was to evaluate genetic diversity based on chloroplast haplotypes for soybean genotypes present in the USDA germplasm resource collection. Shared chloroplast haplotypes represent broad groups of genetic relatedness. Previous work categorized three-quarters of the cultivated soybeans from Asia into a single haplotype group. Our results confirmed the close relationship of North American soybean ancestors and G. max plant introductions previously identified as representing potential sources of soybean genetic variation with the finding that these genotypes belonged to a single chloroplast haplotype group. Genetic diversity was identified in soybean genotypes determined to have a high density of single nucleotide polymorphisms and in a screen of accessions with resistance to soybean cyst nematode. Characterization of soybean plant introduction lines into chloroplast haplotype group may be an important initial step in evaluating the appropriate use of particular soybean genotypes.     

Population structure of the wild soybean (Glycine soja) in China: implications from microsatellite analyses

Background and Aims Wild soybean (Glycine soja), a native species of East Asia, is the closest wild relative of the cultivated soybean (G. max) and supplies valuable genetic resources for cultivar breeding. Analyses of the genetic variation and population structure of wild soybean are fundamental for effective conservation studies and utilization of this valuable genetic resource. Methods In this study, 40 wild soybean populations from China were genotyped with 20 microsatellites to investigate the natural population structure and genetic diversity. These results were integrated with previous microsatellite analyses for 231 representative individuals from East Asia to investigate the genetic relationships of wild soybeans from China. Key Results Analysis of molecular variance (AMOVA) revealed that 43·92 % of the molecular variance occurred within populations, although relatively low genetic diversity was detected for natural wild soybean populations. Most of the populations exhibited significant effects of a genetic bottleneck. Principal co-ordinate analysis, construction of a Neighbor-Joining tree and Bayesian clustering indicated two main genotypic clusters of wild soybean from China. The wild soybean populations, which are distributed in north-east and south China, separated by the Huang-Huai Valley, displayed similar genotypes, whereas those populations from the Huang-Huai Valley were different. Conclusions The previously unknown population structure of the natural populations of wild soybean distributed throughout China was determined. Two evolutionarily significant units were defined and further analysed by combining genetic diversity and structure analyses from Chinese populations with representative samples from Eastern Asia. The study suggests that during the glacial period there may have been an expansion route between south-east and north-east China, via the temperate forests in the East China Sea Land Bridge, which resulted in similar genotypes of wild soybean populations from these regions. Genetic diversity and bottleneck analysis supports that both extensive collection of germplasm resources and habitat management strategies should be undertaken for effective conservation studies of these important wild soybean resources.     

An assessment of spatio-temporal genetic variation in the South African abalone (<Emphasis Type="Italic">Haliotis midae</Emphasis>), using SNPs: implications for conservation management

The South African abalone (Haliotis midae) is a gastropod mollusc of economic importance. In recent years natural populations have come under considerable pressure due to overharvesting and ecological shifts. The spatial genetic structure of H. midae has been determined; however there has not been a temporal assessment of abalone population dynamics around the South African coast. Using a population genomics approach this study aimed to assess fluctuations in genetic diversity among wild and cultured South African abalone populations through time and space. Various estimates of genetic diversity and population differentiation were calculated using EST-derived SNP markers. All populations had comparable levels of genetic diversity and the long-term effective population size appears to be sufficiently large for the wild populations, despite evidence of recent bottlenecks. Population differentiation was for the most part geographically correlated, with spatial genetic structure maintained across temporal samples. Significant genetic differentiation was, however, detected among temporal samples taken from the same locality. There was evidence for comparatively small short-term effective population sizes that could explain large changes in allele frequencies due to stochastic effects. Temporal heterogeneity could also be explained by changes in selection pressures over time. H. midae populations could, therefore, be more dynamic than previously estimated and this could have implications for effective conservation and fisheries management.     

野生小豆种质资源植株形态性状多样性分析

对来自中国、日本、韩国、缅甸4国的55份野生型、40份半野生型小豆种质资源植株形态性状的多样性进行分析,结果表明,野生型小豆与半野生型小豆在株高、平均成熟期、子粒颜色、百粒重等性状方面有明显的差别。95份小豆种质资源通过聚类分析,截值为1.488时可划分为5大类群。来源于缅甸和中国的野生型小豆种质各聚为1个类群,韩国和日本的种质混聚为3个类群。缅甸种质具平均成熟期长、茎秆粗、主茎分枝数多、百粒重轻等特点。中国贵州野生型种质植株较高、茎秆较细、单荚粒数较多、平均成熟期较长。日本野生型种质具有丰产特征。日本和韩国的半野生型小豆,平均成熟期较其他类群早、百粒重高、明度指数高。     

Nucleotide diversity of the upstream region of the putative MADS-box gene controlling soybean maturity

MADS-box genes are involved in plant reproductive development. However, the role of gene nucleotide diversity in soybean flowering and maturity remains unknown. Therefore, in this study, the distribution of DNA polymorphisms in the putative MADS-box gene located near the quantitative trait loci (QTL) for flowering time and maturity was targeted for association analysis using Glycine max (cultivated soybean) and Glycine soja (wild soybean). Sixteen single nucleotide polymorphisms identified in the upstream region of the putative MADS-box gene around QTL Pod mat 13-7 and Fflr 4-2 on chromosome 7 were found to be highly associated with maturity in soybean. The genetic diversity between cultivated soybeans and the wild relative was comparable, although the early maturity group (EMG) was less diverse than the late maturity group (LMG) of the cultivated soybean. Population size changes of the MADS-box gene in this soybean germplasm appeared to result from non-random selection. A selective pressure seemed to act on this gene in the EMG, while the LMG and G. soja were in genetic equilibrium. Neutrality tests and the constructed neighbor-joining tree indicate that the EMG of G. max has experienced strong artificial selection for its domestication and genetic improvement.     

No loss of genetic diversity in small and isolated populations of Medicago sativa subsp. falcata

Molecular allozyme markers of three polymorphic isozymes were used to estimate the genetic diversity among the seed progeny in fragmented Estonian populations of sickle medic Medicago sativa ssp. falcata L. depending on the population size and the isolation degree. Genetic diversity H_e was high in all populations, ranging between 0.795 and 0.893. No correlation between the genetic diversity measures and population size or isolation distance was found. Even the smallest population had equally high genetic diversity as about a hundred times larger population. Genetic differentiation of populations into two major groups was associated with the geographic position of populations, except one remote population. Elimination of seed progeny of reduced fitness by embryo abortion and continuous yearlong contribution of the highly heterozygous progeny through the soil seed bank are considered as important supplementary factors that have contributed to maintaining high levels of genetic diversity in populations of sickle medic in addition to its autotetraploid nature and perennial life form.     

High Genetic Diversity and Differentiation in Relict Lowland Populations of Gentianella austriaca (A. and J. Kern.) Holub (Gentianaceae)

Abstract: The biennial Gentianella austriaca (A. & J. Kern.) Holub, representing a nutrient-poor grassland taxon of low competition power, is becoming rare in the lowlands of eastern Austria due to changes in land use. To estimate effects of isolation and decreasing population sizes, as well as evolutionary relationships, we investigated variation in isozymes and morphological characters within and between seven populations from the mountains, foothills, and lowlands. Additionally, data on reproduction, habitat, germination and population sizes were collected to examine possible causes of variation and differentiation. We found highest genetic diversity (v_a, v_go) in the lowland and foothill populations, and highest genetic differentiation (D_ja, D_jgo) (i.e., lowest genetic identity: Nei's I) in the lowland populations. The low diversity of the mountain populations might indicate that they are derived from lowland populations. Surprisingly, highest genetic diversity was found in the smallest population. This indicates that in small remnant populations of taxa with a mixed mating system, genetic diversity might be maintained even after many generations after reducing population size dramatically. We found some relationship between genetic diversity and high fitness (germination success) and (inversely) with seed size. Plant size and reproductive success are negatively correlated with altitude, whereas flower size and seed size seem to be subject to other forces of selection. Combining all morphometric, reproductive and genetic traits, the lowland populations are most strongly differentiated and therefore of highest conservation priority.     

Evaluation of the geographical pattern of genetic diversity of Glycine soja and Glycine max based on four single copy nuclear gene loci: For conservation of soybean germplasm

Genetic diversity and its geographical patterns play a very important role in species conservation and exploitation. Here, nucleotide polymorphism patterns of four single copy nuclear gene loci in wild (Glycine soja) and cultivated soybean (Glycine max) populations from different geographical regions as well as their demographic history were analyzed. The results showed that: (1) Southern subpopulation has the highest, while central subpopulation revealed the lowest genetic diversity among three Chinese G. soja subpopulations. (2) Northern Chinese G. max subpopulation depicted higher genetic diversity than other two Chinese, Korean, Japanese and American G. max subpopulations. (3) Significant genetic differentiation (P < 0.001) was observed among Chinese G. soja subpopulations from three ecological zones. There was also a significant genetic differentiation（P < 0.01）between three Chinese and Japanese subpopulations of G. max. (4) The demographic dynamics revealed that effective population size of G. soja is expanding, while it was constant in G. max. G. soja is a useful germplasm resource to widen the genetic diversity of G. max. This study suggests that native populations of G. soja from different geo-ecological regions should be protected to conserve the genetic diversity.