Sampling strategy for wild soybean ( Glycine soja ) populations based on their genetic diversity and fine-scale spatial genetic structure

A total of 892 individuals sampled from a wild soybean population in a natural reserve near the Yellow River estuary located in Kenli of Shandong Province (China) were investigated. Seventeen SSR (simple sequence repeat) primer pairs from cultivated soybeans were used to estimate the genetic diversity of the population and its variation pattern versus changes of the sample size (sub-samples), in addition to investigating the fine-scale spatial genetic structure within the population. The results showed relatively high genetic diversity of the population with the mean value of allele number (A) being 2.88, expected heterozygosity (He) 0.431, Shannon diversity index (I) 0.699, and percentage of polymorphic loci (P) 100%. Sub-samples of different sizes (ten groups) were randomly drawn from the population and their genetic diversity was calculated by computer simulation. The regression model of the four diversity indexes with the change of sample sizes was computed. As a result, 27–52 individuals can reach 95% of total genetic variability of the population. Spatial autocorrelation analysis revealed that the genetic patch size of this wild soybean population is about 18 m. The study provided a scientific basis for the sampling strategy of wild soybean populations. __________ Translated from Journal of Fudan University (Natural Science), 2006, 45(3): 322–327 [译自: 复旦学报 (自然科学版)]     

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人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0.171 4,香农指数(I)为0.271 4.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,而是呈从状分布.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.     

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。     

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.     

The effects of sample size on population genetic diversity estimates in song sparrows Melospiza melodia

To empirically determine the effects of sample size on commonly used measures of average genetic diversity, we genotyped 200 song sparrows Melospiza melodia from two populations, one genetically depauperate (n=100) and the other genetically diverse (n=100), using eight microsatellite loci. These genotypes were used to randomly create 10,000 datasets of differing sizes (5 to 50) for each population to determine what the effects of sample size might be on several estimates of genetic diversity (number of alleles per locus, average observed heterozygosity, and unbiased average expected heterozygosity) in natural populations of conservation concern. We found that at small sample sizes of 5 to 10 individuals, estimates of unbiased heterozygosity outperformed those based on observed heterozygosity or allelic diversity for both low- and high-diversity populations. We also found that when comparing across populations in which different numbers of individuals were sampled, rarefaction provided a useful way to compare estimates of allelic diversity. We recommend that standard errors should be reported for all diversity estimators, especially when sample sizes are small. We also recommend that at least 20 to 30 individuals be sampled in microsatellite studies that assess genetic diversity when working in a population that has an unknown level of diversity. However, research on critically endangered populations (where large sample sizes are impossible or extremely difficult to obtain) should include measures of genetic diversity even if sample sizes are less than ideal. These estimates can be useful in assessing the genetic diversity of the population.     

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.     

Mitochondrial DNA variation and population genetic structure in the small yellow croaker at the coast of Yellow Sea and East China Sea

Small yellow croaker is one of the most important fishery species in China. The mass–scale artificial propagation of this fish species was initially developed in 2015 with the aim of facilitating the fish production stock enhancement and aquaculture programs in the future. In the present study, the wild broodfish and its corresponding progeny along with three other wild populations were sampled and subjected to sequence analysis of the mitochondrial cytochrome c oxidase subunit I gene. The genetic diversity and population genetic structure were evaluated with a total sample size of 141 individuals representing the populations of the Yellow Sea (Qingdao and Lvsi populations) and the East China Sea (Xiangshan and Ningde populations). The wild populations were characterized by high haplotype diversity (0.925–0.976) and low nucleotide diversity (0.376%–0.560%). The hierarchical analysis of molecular variance (AMOVA) analysis and the values of pairwise Ф-statistics (Ф_ST) indicated non-significant genetic differentiation among the four wild populations. The hatchery stock XSH exhibited lower indices of genetic diversity compared with the wild populations that could be attributed to the small effective population size. The findings of the present study have valuable insight to the sustainable management and utilization of this resource.     

Fine-scale genetic structure enhances biparental inbreeding by promoting mating events between more related individuals in wild soybean (Glycine soja; Fabaceae) populations

Outcrossing between genetically distant individuals in a plant population enhances allelic heterozygosity-an important source for genetic diversity and adaptive evolution. Fine-scale spatial genetic structure (FSGS) can interfere with outcrossing by promoting mating between more related individuals. To test the influence of FSGS on outcrossing, FSGS and outcrossing rates were analyzed with four wild soybean (Glycine soja) populations from different habitats, using simple sequence repeat (SSR) fingerprints. Spatial autocorrelation analysis indicated variable FSGS (15.44-25.87 m) in all four populations. Multilocus mixed-mating analysis of 1605 progeny indicated substantial variation in single-locus outcrossing (T(s) = 6.3-12.6%) although the total outcrossing rates as estimated by multilocus outcrossing (T(m) = 12.8-17%) did not vary significantly among populations. The comparison between FSGS and outcrossing rates demonstrated that strong FSGS with large genetic patch size can enhance biparental inbreeding by promoting mating between more related individuals in a population. The results suggest that patch size management can aid in situ conservation by avoiding formation of strong FSGS and encouraging true outcrossing among individuals.     

Low genetic diversity in the bottlenecked population of endangered non-native banteng in northern Australia

Undomesticated (wild) banteng are endangered in their native habitats in Southeast Asia. A potential conservation resource for the species is a large, wild population in Garig Gunak Barlu National Park in northern Australia, descended from 20 individuals that were released from a failed British outpost in 1849. Because of the founding bottleneck, we determined the level of genetic diversity in four subpopulations in the national park using 12 microsatellite loci, and compared this to the genetic diversity of domesticated Asian Bali cattle, wild banteng and other cattle species. We also compared the loss of genetic diversity using plausible genetic data coupled to a stochastic Leslie matrix model constructed from existing demographic data. The 53 Australian banteng sampled had average microsatellite heterozygosity (HE) of 28% compared to 67% for outbred Bos taurus and domesticated Bos javanicus populations. The Australian banteng inbreeding coefficient (F) of 0.58 is high compared to other endangered artiodactyl populations. The 95% confidence bounds for measured heterozygosity overlapped with those predicted from our stochastic Leslie matrix population model. Collectively, these results show that Australian banteng have suffered a loss of genetic diversity and are highly inbred because of the initial population bottleneck and subsequent small population sizes. We conclude that the Australian population is an important hedge against the complete loss of wild banteng, and it can augment threatened populations of banteng in their native range. This study indicates the genetic value of small populations of endangered artiodactyls established ex situ.     

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.     

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.     

湖北星斗山台湾杉居群的遗传多样性研究

采用随机扩增多态性DNA(RAPD)方法对孑遗植物台湾杉分布于湖北星斗山的野生和栽培居群共42个个体进行了遗传多样性分析。从60个随机引物中筛选出13个引物,共扩增出155条清晰谱带,多态位点百分率为72.9%。野生居群和栽培居群的多态位点百分率分别为65.81%和59.35%;Nei’s基因多样性分别为0.2001和0.1911;Shannon’s信息指数分别为0.3120和0.2946。野生居群的遗传多样性高于栽培居群,表明这些原生古树的后代出现了一定程度的遗传衰退。用UPGMA方法对42个单株聚类可知,来自野生群体的个体和来自栽培群体的个体明显地各聚为一类。尽管孑遗物种台湾杉在湖北仅有一个野生群体,且为零星分布,总个体数40多株,但仍保持较高的遗传多样性水平,这说明遗传多样性不是导致其种群濒危的主要原因,导致台湾杉种群濒危的原因可能与台湾杉自然种群及群落所处生境的直接破坏及其本身生物学和生态学特性所导致的自然更新不良有着密切的联系。     

陕西省林麝mtDNA D-loop区序列结构和种群遗传多样性

林麝(Moschus berezovskii)曾广泛分布于中国,由于盗猎和栖息地缩小,秦岭地区野生种群数量迅速下降,圈养繁殖种群已成立了几十年,但大多数圈养种群的遗传背景不清,种群规模增长非常缓慢。为了给这一物种的保护和管理提供有用的信息,调查了陕西省林麝1个圈养种群3个野生种群线粒体DNA(mt DNA)D-Loop 632 bp片段的遗传多样性和种群结构。在69个个体中其碱基组成为A+T的平均含量63.2%高于G+C含量36.8%,共检测到变异位点171个(约占总位点数的27.05%)。核苷酸多样性(Pi)为0.04424,平均核苷酸差异数(K)为19.908。69个个体分属32个单倍型,单倍型间的平均遗传距离(P)为0.070。32个单倍型构建的NJ系统树聚为3个分支,4个林麝群体中的单倍型是随机分布的。4个群体的平均遗传距离为0.043(标准误SE为0.005),凤县养殖场群体与留坝和陇县群体的亲缘关系较远。单倍型间的平均遗传距离为0.043,可见其遗传分化尚未达到种群分化的水平。结果表明,陕西省林麝群体mt DNA D-loop区序列存在着较丰富的变异和遗传多样性,凤县野生群体和凤县养殖场群体的核苷酸多样性和单倍型多样较高,养殖场种群没有出现近亲繁殖及遗传多样性下降的情况。凤县野生群体和凤县养殖场群体两者遗传分化较小,存在着较高的基因流水平。     

Noninvasive genetic analyses for estimating population size and genetic diversity of the remaining Far Eastern leopard (Panthera pardus orientalis) population

Understanding and monitoring the population status of endangered species is vital for developing appropriate management interventions. We used noninvasive genetic analyses to obtain ecological and genetic data on the last remaining Far Eastern leopard population in the world. During seven winters from 2000–2001 to 2007–2008, we collected feces, hair, and saliva from most of the leopard habitat. Of the 239 leopard samples collected during the study period, 155 were successfully genotyped at 13 microsatellite loci and 37 individuals (18 males and 19 females) were identified. Population size estimates based on the Capwire model were 28 (95 % CI 19–38) in 2002–03 and 26 (95 % CI 13–33) in 2007–2008. The leopard population had a low level of genetic diversity (expected and observed heterozygosity = 0.43; average number of alleles per locus = 2.62), and effective population size was estimated to be low (N _e = 7–16) by two genetic-based methods. We observed little improvement in the genetic diversity during the study period and did find an indication of allele loss compared with individuals from the mid-1990s, suggesting that the remaining population will continue to suffer loss of genetic diversity. Given the small population size and the low genetic diversity, with little expectation of replenishment of the genetic variation by natural immigration, successful expansion of available habitat and development of a second population based on captive individuals may be crucial for persistence of this leopard subspecies in the wild.     

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。     

卧龙圈养大熊猫遗传多样性现状及预测,

以中国最大的大熊猫圈养种群—四川卧龙中国大熊猫保护中心的圈养种群为对象,以８个大熊猫微卫星位点为分子标记, 探讨了大熊猫圈养种群的遗传多样性, 并与邛崃野生种群及其他７个濒危物种进行比较。微卫星数据表明, 圈养种群的遗传多样性水平(A＝5.5, He ＝0.620, Ho＝0.574) 低于邛崃野生种群(A＝9.8,He＝0.779,Ho＝0.581),但高于其他7 个濒危物种的种群(He＝0.13~0.46)。在此数据的基础上对未来100个世代内圈养种群遗传多样性的变化情况做出了预测。结果表明假设种群数量比现在扩大一倍, 经历100个世代后也只会使平均等位基因数少减少0.4。因此继续增加野生个体对保持遗传多样性的意义已经不大, 建议该圈养种群的保护策略应将重点放到制定更有效的繁殖计划以避免近交上。     

Population and genetic status of a critically endangered species in Korea, Euchresta japonica (Leguminosae), and their implications for conservation

The conservation status of Euchresta japonica Hook. f. ex Regel in Korea was investigated, with an emphasis on its genetic diversity. From field surveys, we obtained the only locality record for a wild population in Korea, which contained eight individuals. Genotyping was performed using nine microsatellite markers for all 20 remaining individuals, including those in ex situ collections. Among nine microsatellite loci that amplified within this group, five showed polymorphism with low hererozygosities, and a total of 12 multilocus genotypes were detected. Wild-specific alleles were detected in two individuals, and ex situ-specific alleles were detected in six individuals. Five individuals proved to have individual-specific alleles. The Korean population was also distinguished from the previously reported Japanese population by different alleles and higher diversity. To conserve this species more effectively in Korea, we recommend the following: (1) fencing the remaining wild population; (2) no relocation of wild individuals, as nine ex situ plants are already available; (3) complete ex situ conservation of all genetic diversity via clonal propagation of wild individuals; and (4) continuous protection and monitoring of the wild population.     

Loss of genetic variation in hatchery-reared Indian major carp, Catla catla

The hypothesis that effective population sizes are low in hatchery-reared catla ( Catla catla ) from Bangladesh, possibly leading to inbreeding and loss of variation, was tested. The study was based on analysis of seven microsatellite loci in three samples of hatchery-reared catla and four samples representing wild populations. Pair-wise estimates of genetic differentiation between samples were low between wild samples (θ ranging from 0·012 to 0·034), but high between hatchery samples (θ ranging from 0·153 to 0·185), suggesting strong genetic drift in hatcheries. Genetic variation, both in terms of expected heterozygosity and allelic richness, was significantly lower in hatchery samples than in samples of wild catla. Application of a method for reconstructing families among offspring without parental genetic data showed that the hatchery samples consisted of very few half- and full-sib families, whereas the wild samples consisted of a high number of families, suggesting that most individuals were unrelated. Finally, estimation of the effective number of parents ( N _b) in the largest sample of hatchery fish confirmed that effective population size was low ( N _b= 14·9 for multiallelic loci and N _b= 10·6 if alleles were pooled into two composite alleles). The results show that low effective population sizes leading to loss of variation and possibly inbreeding depression should be a matter of serious concern in aquaculture production of catla.     

No relationship between individual genetic diversity and prevalence of avian malaria in a migratory kestrel

Insight into the genetic basis of malaria resistance is crucial for understanding the consequences of this parasite group on animal populations. Here, we analyse the relationship between genotypic variation at 11 highly variable microsatellite loci and prevalence of three different lineages of avian malaria, two Plasmodium (RTSR1, LK6) and one Haemoproteus (LK2), in a wild population of the endangered lesser kestrel (Falco naumanni). Although we used a large sample size (584 typed individuals), we did not find any significant association between the prevalence of the studied parasite lineages and individual genetic diversity. Although our data set is large, the 11 neutral markers typed may have had low power to detect such association, in part because of the low parasite prevalence observed (less than 5% of infected birds). However, the fact that we have detected previous correlations between genetic diversity and other traits (ectoparasitism risk, fecundity) in the study population using the same panel of neutral markers and lower sample sizes suggests that other factors could underlie the absence of such a similar correlation with avian malaria. Differences in the genetics of the studied traits and in their particular basis of inbreeding depression (dominance vs. overdominance) may have led to malaria prevalence, but not other traits, being uncoupled with individual genetic diversity. Also, we cannot discard the possibility that the absence of association was a consequence of a low pathogenic effect of these particular malaria lineages on our lesser kestrel population, and thus we should not expect the evolution of genetic resistance against these parasites.     

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.