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。     

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.     

Importance of genetic characterization and conservation of plant genetic resources: The breeding system and genetic diversity of wild soybean (Glycine soja)

Abstract Plant genetic resources play an important role in the improvement of cultivated plants. To characterize and evaluate the ecological and reproductive features of wild soybean ( Glycine soja Sieb. et Zucc.), which is the most probable ancestor of cultivated soybean ( G. max (L) Merr.), the breeding system and genetic diversity of G. soja were investigated. The extent of natural cross-pollination of G. soja was estimated in four populations along the Omono River in Akita Prefecture, Japan by examining allozyme variation. Although it has been previously believed that G. soja is autogamous, as is cultivated soybean, the mean multilocus outcrossing rate ( t m) estimate was 13%. These values are much higher than the outcrossing rate previously reported for both G. soja and G. max . Frequent visits by honeybees and carpenter bees to flowers were also observed, which supported this conjecture. Furthermore, to evaluate the genetic variation of G. soja as a genetic resource, the genetic structure of 447 populations over Japan were analyzed. Wild soybean populations had a higher degree of variation of isozyme loci. The G ST coefficient of gene differentian values among the sites within the district were particularly high, revealing that the isozyme genotype was greatly different among site populations and homogeneous within the sites. The genetic differentiation among nine districts was observed in the allele frequencies of a few loci, indicating that geographic isolation in the wild soybean population was effectively created through the distance between the districts. The difference in the allele frequency among the districts may be produced under genetic drift. Finally, the importance of the preservation of natural plant populations and the habitats of wild progenitors (i.e. the in situ conservation of plant genetic resources) was emphasized.     

An Improved Method to Detect Allozymes of Spl and Ti Loci in Soybean Seed Proteins

In order to exploit and conserve the genic resources in soybean, it is necessary to analyse the genetic structure of soybean population. The modified procedures detecting the allozymes of Sp 1 (coding β-amylases) and Ti (coding soybean trypsin inhibitors) are summarized as follows: After proteins of soybean seed were separated by using 7% polyacrylamide slab gel electrophoresis (Davis system), gel was soaked in starch solution for half an hour. After that, gel was washed by distilled water twice. Finally, gel was stained by using I2-KI solution (in 0.05N HCl) for 2–3 h. The blank bands in blue back-ground are β-amylases. The products of Sp1a and Sp 1b located at Rf=0.38–0.40 and Rf=0A4–0.47 respectively. The dark blue bands are proteins. The altozymes of Ti can be identified by co-electrophoresis with standard soybean trypsin inhibitors.     

湖南新田野生大豆自然居群遗传多样性分析

利用SSR分子标记技术对8个来自湖南新田的野生大豆自然居群遗传多样性进行了分析.结果表明:(1)所分析的材料中73对SSR引物共检测到397个等位变异,等位变异数范围为2～10个,平均为5.4个;期望杂合度(He)的变化范围从0.16～0.82,平均为0.64.(2)分子方差分析发现,居群间存在着严重的遗传分化,群体69%的变异存在于居群间,31%的遗传变异存在于居群内.(3)新田的8个居群中桑梓路边(SZLB)和桑梓(SZ)两个居群的遗传多样性比其他群体的高,而新田1 km处(XT1)、新田2 km处(XT2)和新田6 km处(XT6)野生大豆居群的遗传多样性较低.(4)根据遗传距离可将8居群分为3类:新田1 km处和新田2 km处为一类;新田6 km处单独为一类;大冠岭上龙秀、龙秀后山、桑梓、桑梓路边和青龙等处为一类.(5)居群遗传距离和地理距离之间存在线性相关,相关系数为0.837(P<0.01);海拔与期望杂合度呈显著正相关,相关系数为0.92(P=0.001).研究结果表明,湖南新田野生大豆具有较高的遗传多样性,但不同居群的遗传多样性差异很大;位于该县高海拔山区大冠岭一带的野生大豆居群是湖南新田地区的一个多样性中心.     

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.     

Genetic spatial clustering: significant implications for conservation of wild soybean (Glycine soja: Fabaceae)

Knowledge of spatial patterns of genetic variation within populations of wild relative species has significant implications with respect to sampling strategies for ex situ and in situ conservation. To study spatial genetic structure of wild soybean (Glycine soja Sieb. et Zucc.) at the fine scale, three natural populations in northern China were analyzed using inter-simple sequence repeat (ISSR) fingerprints for estimating kinship coefficients. A regression analysis of kinship coefficients against spatial distances revealed that individuals occurring close together tended to be more genetically related. The Sp statistic further indicated a comparable spatial pattern among the three wild soybean populations with similar Sp values (mean = 0.0734, varied from 0.0645 to 0.0943) detected across the three populations. Genetic patches were on average ca. 20 m in size, and the effective neighborhood sizes varied between 10 and 15 m. The spatial genetic structure evident in the wild soybean populations may be attributed to the restricted seed dispersal and predominant inbreeding mating system of this species. The detection of family structure in the populations of wild soybean has a significant implication for the effective conservation of the important genetic resources.     

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。     

Population genetic structure of wild Phaseolus lunatus (Fabaceae), with special reference to population sizes

To set up an in situ conservation strategy for Phaseolus lunatus, we analyzed the genetic structure of 29 populations in the Central Valley of Costa Rica. Using 22 enzyme loci, we quantified the proportion of polymorphic loci (P(p)), the mean number of alleles per locus (A), and the mean effective number of alleles per locus (A(e)), which equaled to 10.32%, 1.10, and 1.05, respectively. The total heterozygosity (H(T)), the intrapopulation genetic diversity (H(S)), and the interpopulation genetic diversity (D(ST)) were 0.193, 0.082, and 0.111, respectively. The genotypic composition of the analyzed populations showed a deviation from the Hardy-Weinberg proportions (F(IT) = 0.932). This disequilibrium was due to either genetic differentiation between populations (F(ST) = 0.497) or nonrandom mating within populations (F(IS) = 0.866). From the level of genetic differentiation between populations and the private alleles frequencies estimates, gene flow was calculated: Nm(W) = 0.398 and Nm(S) = 0.023, respectively. The results suggested that wild Lima bean maintains most of its isozyme variation among populations. Significant positive correlation was observed between population size and P(p), A, and H(o) (observed heterozygosity), whereas no correlation was observed with the average fixation index of population (F). The loss of genetic variability in populations was attributed to inbreeding and the bottleneck effects that characterized the target populations. In situ conservation and management procedures for wild Lima bean 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.     

Genetic differentiation in relation to seed weights in wild soybean species (Glycine soja Sieb. & Zucc.)

Seed weight is one of the most important botanical and phylogenetic characteristics. The study objective was to understand whether there is genetic difference in different seed weights of wild soybean (Glycine soja Sieb. & Zucc.). A total of 563 wild soybean samples, which belonged separately to genebank germplasm accessions (220 samples), one regional population samples (293 plants) and one natural population (150 plants), were analyzed using microsatellite markers. Of four size classes, the smallest seed size type had the highest coefficient of variation in seed weight; small and large seed types had relatively great genetic differences. In the national genebank germplasm accessions, genetic diversity gradually decreased from quantitatively dominant small and middling seed types to less frequent large seed types. In the regional and natural populations, generally, small to middling seed sizes had higher genetic diversity than the smallest and larger seed sizes. Cluster analysis revealed genetic differences in seed size traits. The semi-wild type (Glycine gracilis Skvortzow) was the most genetically differentiated from other seed sizes. However, it was also clearly shown that the phylogenic genetic differentiation among seed sizes was less than the genetic differentiation among geographical habitat populations in the wild soybean species.     

Genetic diversity and peculiarity of annual wild soybean (<Emphasis Type="Italic">G. soja</Emphasis> Sieb. et Zucc.) from various eco-regions in China

Annual wild soybean (Glycine soja Sieb. et Zucc.) is believed to be a potential gene source for future soybean improvement in coping with the world climate change for food security. To evaluate the wild soybean genetic diversity and differentiation, we analyzed allelic profiles at 60 simple-sequence repeat (SSR) loci and variation of eight morph-biological traits of a representative sample with 196 accessions from the natural growing area in China. For comparison, a representative sample with 200 landraces of Chinese cultivated soybean was included in this study. The SSR loci produced 1,067 alleles (17.8 per locus) with a mean gene diversity of 0.857 in the wild sample, which indicated the genetic diversity of G. soja was much higher than that of its cultivated counterpart (total 826 alleles, 13.7 per locus, mean gene diversity 0.727). After domestication, the genetic diversity of the cultigens decreased, with its 65.5% alleles inherited from the wild soybean, while 34.5% alleles newly emerged. AMOVA analysis showed that significant variance did exist among Northeast China, Huang-Huai-Hai Valleys and Southern China subpopulations. UPGMA cluster analysis indicated very significant association between the geographic grouping and genetic clustering, which demonstrated the geographic differentiation of the wild population had its relevant genetic bases. In comparison with the other two subpopulations, the Southern China subpopulation showed the highest allelic richness, diversity index and largest number of specific-present alleles, which suggests Southern China should be the major center of diversity for annual wild soybean. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

广东省猴耳环遗传多样性研究

为了解猴耳环(Archidendron clypearia)种质资源的遗传多样性,以广东省12个野生猴耳环群体的146份种质资源为材料,采用SSR分子标记技术对其遗传多样性和亲缘关系进行分析.结果表明,21对SSR引物共检测到249个等位基因,平均每对SSR引物检测的等位基因数(Na)为11.857,有效等位基因数(N...     

利用ISSR标记研究野大豆居群内遗传变异及其取样策略

为了有效地保护野大豆(Glycine soja Sieb.et Zucc.)并制定合理的居群取样策略,对上海江湾机场的一个天然野大豆居群进行了100个单株(个体)的随机取样,并用ISSR分子标记对其进行了遗传多样性分析。利用筛选出的15条ISSR引物在这个居群中检测到较高的遗传变异,样本内个体间的相似系数变化在0．17～0．89之间。居群内平均每个位点的平均预期杂合度(He)为0．1714,香农指数(I)为0．2714。PCA分析显示,江湾野大豆居群内的遗传变异不是呈均匀分布,而是呈丛状分布。该野大豆居群遗传多样性和样本内个体数量间的相关性分析显示：在个体数少于40的情况下,遗传多样性随个体数的增加而迅速增加：当样本中的个体数大于40时,遗传多样性的增加减慢并很快趋于饱和。研究表明：对野大豆居群进行异地保护时,对各居群的采样植株数不应当低于35～45;在居群内采样时,所采集的个体之间最好相隔一定的空间距离。     

野生杏和栽培杏的遗传多样性和遗传结构分析

利用SSR分子标记结合荧光毛细管电泳检测技术,研究了野生杏和栽培杏的遗传多样性和遗传结构,结果显示:27个SSR位点,平均每个位点检测到17.82个等位基因(Na)和7.44个有效等位基因(Ne),平均Shannon's信息指数(I)为2.23,平均期望杂合度(He)和观察杂合度(Ho)分别为0.70和0.52。基于SSR位点,群体水平上平均等位基因数、有效等位基因数、期望杂合度、观察杂合度和Shannon's信息指数分别为6.59、4.15、0.70、0.53和1.50,说明我国杏种质资源遗传多样性丰富,其中野生杏资源遗传多样性明显高于栽培杏资源,野生杏中西伯利亚杏种质遗传多样性最高且具有较多的特异等位基因,而栽培杏中仁用杏遗传多样性最低,特有等位基因较少。聚类分析将供试159份种质分为4组。群体遗传结构分析将159份种质划分为5个类群,分类情况与传统形态指标划分基本一致。通过本研究可知,我国杏资源遗传多样性丰富,遗传结构较为复杂;西伯利亚杏与栽培杏亲缘关系较远;野生普通杏与栽培杏具有类似的遗传结构,推测野生普通杏为栽培杏原始种;仁用杏遗传多样性较低,遗传背景狭窄。本研究结果可为杏资源新品种选育及持续利用提供重要的理论依据。     

Genetic Variation and Differentiation of Larix decidua Populations in Swiss Alps (in English)

Genetic diversity within and among six subpopulations of Larix decidua Mill. from two altitudinal transects of Swiss Alps was investigated using 6 enzyme systems coding for 8 loci. Globally, the mean proportion of polymorphic loci was 22.9%, the average number of alleles per locus was 1.3, and the mean expected heterozygosity was 0.095. Only 5.8% of the genetic variation resided among populations. The mean genetic distance was 0.006. Several significant differences of gene frequencies were found between different age classes. Positive values of the species mean fixation index observed in this study suggested a considerable deficit of heterozygotes in the populations of L. decidua of Swiss Alps. At one of the sites (Arpette), the highest subpopulation in elevation gave the lowest level of genetic diversity (as evidenced by the lowest proportion of polymorphic loci and the lowest mean expected heterozygosity) and the largest value of genetic distance when compared to other subpopulations. The genetic differences between the highest subpopulation and the other ones suggest that the founder effect may be an important factor influencing genetic differentiation of L. decidua populations at Arpette transect.     

不同尺度下野大豆种群的遗传分化

为了阐明不同尺度范围内野大豆种群的遗传分化情况,应用随机扩增多态性DNA（RAPD）方法,分别对我国5个纬度8个不同地点的野大豆（Glycine soja)种群及浙江金华地区5个野大豆种群,进行了分子生态学研究。根据RAPD数据计算相似系数及遗传距离并进行聚类分析,发现无论是不同纬度野大豆种群还是金华地区野大豆小种群均存在较高的遗传变异,且不同纬度野大豆种群间的遗传变异与地理纬度有一定正相关。在对金华地区野大豆种群遗传多样怀的研究,利用Shannon指数估算了5个野大豆种群的遗传多样性,发现大部分的遗传变异存在于野大豆种群间（78．5％）,只有少部分的遗传变异存在于种群内。本就此探讨了不同尺度下野大豆种群的遗传多样性与环境因子的关系,并对其成因及维持机制进行了讨论。     

Microsatellite markers reveal genetic diversity of wild soybean in different habitats and implications for conservation strategies (Glycine soja) in China

Wild soybean individuals were sampled from ten habitat sites in Beijing region, China and were assessed using 36 SSR markers for the genetic variation among the habitat subpopulations. AMOVA analysis showed 57.46 % inter-population and 42.54 % intrapopulation genetic variation. The genetic variation had geographical regionality. The drought-stressed and founder subpopulations intensively reduced genetic diversity, and along-river system habitats appeared to have closer genetic similarity. The bottleneck impact of drought stress appeared to be inferior to the founding effect on subpopulation genetic diversity but superior on genetically geographical grouping. Here, all the subpopulations were found to contain unique alleles. The phenotypic and genetic diversities had similarly fluctuated patterns across the subpopulations. These results here suggest that a conservation strategy should be taken: theoretically as many as possible populations are sampled to maximize the genetic diversity in ex situ conservation of wild soybean within an area in China. Spatial distance should be considered for isolating wild soybean populations when genetically modified soybeans are cultivated in China.     

瑞士阿尔卑斯山欧洲落叶松居群的遗传变异和分化

应用等位酶分析技术,沿两个海拔梯度在瑞士阿尔卑斯山研究了欧洲落叶松（Larix decidua Mill.)居群内和居群间的遗传多态性,结果表明,多态性位点的比例为22.9%,平均每个位点的等位基因数为1.3,平均期望杂合度为0.095,遗传变异的5.8%存在于居群之间,平均遗传距离为0.006。几个有统计意义的基因频率差别在不同树龄类被发现,正在繁育系数值表明在瑞士阿尔卑斯山欧洲落叶松居群有相当的杂合体缺乏,在阿尔拜特（Ar-pette),海拔最高的亚居群与其他亚居群相比较显示最低的遗传多态性（如显示最低的我态性位点比例和最低的平均期望杂合度）和最大的遗传距离值,在最高亚居群和其他亚居群间的遗传差别暗示奠基效应可能是影响这个定样场所欧洲落叶松居群遗传分化的主要因素。