Genetic diversity of wild and cultured swamp eel (Monopterus albus) populations from central China revealed by ISSR markers

Asian swamp eel is a highly commercial fish, primarily for China and other Asian countries. The aim of this paper is to evaluate the genetic diversity of wild and cultured samples of Asian swamp eel Monopterus albus using ISSR markers. A total of 129 individuals belonging to three wild samples, Xiantao (XT), Huanggang (HG), Xinyang (XY) and three cultured samples, Wuhan (WH), Jingzhou (JZ) and Nanjing (NJ) were randomly selected for genetic analysis. Twelve ISSR primers were used for screening the six populations and 110 loci were obtained. The polymorphic loci were estimated to be 54%, 56.3%, 58.2%, 60.6%, 69.5% and 71% in NJ,WH, JZ, XT, HG and XY samples, respectively. Average heterozygosity value varied from 0.1956 to 0.2449. The three wild samples showed higher genetic diversity than the cultured samples (P < 0.05), including polymorphic bands (PPB), observed number of alleles per locus (_to), effective number of alleles per locus (Ne), Nei’s gene diversity index (H) and Shannon’s information index (I).     

Analysis of genetic diversity on 9 wild stocks of taimen (Hucho taimen) by microsatellite markers

Taimen (Hucho taimen) is a native fish species in China and it is in the state of endangerment. To explain clearly the genetic diversity and genetic structure, 9 wild populations of taimen were investigated using 20 microsatellite markers. The results showed that their observed heterozygosity ranged from 0.0994 to 0.8882, the expected heterozygosity varied from 0.2005 to 0.8759, and the range of PIC index was from 0.3432 to 0.5261 while population from Huma River had low genetic diversity. Fst of matching group ranged from 0.0246 to 0.2333 (P <0.0001)and Nm varied among 0.8216 to 9.9292, which indicated that the genetic differentiation was remarkable among populations.The half/full-sib family tests detected a proportion of half/full-sib family groups varying among 27.78% to 90.91%, showing a high inbred pressure and a risk of bottlenecks experienced by most groups. The AMOVA results showed that the global Fst was 0.1081; the clustering result showed that individuals from Beiji tributary of Heilongjiang River clustered as one clade, all individuals from Huma River and Wusuli River clustered as one clade and all individuals from the upper reaches of the Heilongjiang River clustered as another clade. All these results indicated that the decrease of taimen resource has affected the gene exchange among their populations. In order to achieve full protection of taimen germplasm resources, we should put an end to the destructive fishing for taimen and promotegene exchange among their populations.     

Genetic variation in wild and cultivated populations of the haploid-diploid red alga Gracilaria chilensis: how farming practices favor asexual reproduction and heterozygosity.

The extent of changes in genetic diversity and life-history traits associated with farming was investigated in the haploid-diploid red alga, Gracilaria chilensis, cultivated in Chile. This alga belongs to one of the most frequently cultivated seaweed genera around the world. Fifteen farmed populations, 11 wild populations, and two subspontaneous populations were sampled along the Chilean coast. The frequency of reproductive versus vegetative individuals and of haploid versus diploid individuals was checked in each population. In addition, the distribution of genetic variation in wild and cultivated populations was analyzed using six microsatellite markers. Our results first demonstrated that farmed populations are maintained almost exclusively by vegetative propagation. Moreover, the predominance of diploid individuals in farms showed that farming practices had significantly modified life-history traits as compared to wild populations. Second, the expected reduction in genetic diversity due to a cultivation bottleneck and subsequent clonal propagation was detected in farms. Finally, our study suggested that cultural practices in the southern part of the country contributed to the spread of selected genotypes at a local scale. Altogether, these results document for the first time that involuntary selection could operate during the first step of domestication in a marine plant.     

GENETIC VARIATION IN WILD AND CULTIVATED POPULATIONS OF THE HAPLOID– DIPLOID RED ALGA GRACILARIA CHILENSIS: HOW FARMING PRACTICES FAVOR ASEXUAL REPRODUCTION AND HETEROZYGOSITY

The extent of changes in genetic diversity and life-history traits associated with farming was investigated in the haploid–diploid red alga, Gracilaria chilensis , cultivated in Chile. This alga belongs to one of the most frequently cultivated seaweed genera around the world. Fifteen farmed populations, 11 wild populations, and two subspontaneous populations were sampled along the Chilean coast. The frequency of reproductive versus vegetative individuals and of haploid versus diploid individuals was checked in each population. In addition, the distribution of genetic variation in wild and cultivated populations was analyzed using six microsatellite markers. Our results first demonstrated that farmed populations are maintained almost exclusively by vegetative propagation. Moreover, the predominance of diploid individuals in farms showed that farming practices had significantly modified life-history traits as compared to wild populations. Second, the expected reduction in genetic diversity due to a cultivation bottleneck and subsequent clonal propagation was detected in farms. Finally, our study suggested that cultural practices in the southern part of the country contributed to the spread of selected genotypes at a local scale. Altogether, these results document for the first time that involuntary selection could operate during the first step of domestication in a marine plant.     

基于线粒体DNA控制区的斑翅草螽不同地理种群遗传分化研究

采用PCR扩增结合DNA克隆测序技术,分析了斑翅草螽Conocephalus maculates 9个地理种群mtDNA控制区序列的变异及遗传多样性。切除侧翼RNA基因序列后,最终获得的斑翅草螽mtDNA控制区比对后全长为676 bp,平均碱基组成T(37.8%),C(11.7%),A(41.3%)和G(9.1%)。共检测到98个可变位点,占总位点数的14.5%,其中,9处碱基插入/缺失,74处转换(40个T/C,34个A/G),50处颠换(18个A/T,11个T/G,15个A/C,6个C/G)。共定义46个单倍型,其中,4个为种群间共享单倍型(H02、H05、H08和H10),其余42个为各种群独有单倍型,包括6个种群内共享单倍型(H09、H11、H15、H18、H26和H38)。单倍型总数占实验个体总数的69.7%,除四川峨眉山外,其余种群单倍型百分比均﹥50%。通过两两地理种群间的FST值差异显著性检验,将这些群体分为4组,分别为SC+CQ,GX+FLB+HN+YN,XZ和HB。以长瓣草螽C.gladiatus、峨眉草螽C.emeiensis、悦鸣草螽C.melaenus、竹草螽C.bambusanus为外群,构建的斑翅草螽mtDNA控制区单倍型NJ法系统树形成3个自举支持度较高的分支,其中,分支A由28种单倍体组成,包括本研究中除四川峨眉山(SC)和重庆万州(CQ)以外的7个种群;分支B由12种单倍体组成,包含除菲律宾拉乌尼翁(FLB)和江西南昌(JX)以外的7个种群;分支C由6种单倍型组成,全部来自西藏林芝(XZ)的单倍型。聚类结果表明,斑翅草螽不同地理种群间的遗传分化并不明显,即使是两两群体间FST值差异显著的群体,也未能形成完全独立的分支。     

Phylogeography and Domestication of Chinese Swamp Buffalo

To further probe into whether swamp buffaloes were domesticated once or multiple times in China, this survey examined the mitochondrial DNA (mtDNA) Control Region (D-loop) diversity of 471 individuals representing 22 populations of 455 Chinese swamp buffaloes and 16 river buffaloes. Phylogenetic analysis revealed that Chinese swamp buffaloes could be divided into two distinct lineages, A and B, which were defined previously. Of the two lineages, lineage A was predominant across all populations. For predominant lineage A, Southwestern buffalo populations possess the highest genetic diversity among the three hypothesized domestication centers (Southeastern, Central, and Southwestern China), suggesting Southwestern China as the most likely location for the domestication of lineage A. However, a complex pattern of diversity is detected for the lineage B, preventing the unambiguous pinpointing of the exact place of domestication center and suggesting the presence of a long-term, strong gene flow among swamp buffalo populations caused by extensive migrations of buffaloes and frequent human movements along the Yangtze River throughout history. Our current study suggests that Southwestern China is the most likely domestication center for lineage A, and may have been a primary center of swamp buffalo domestication. More archaeological and genetic evidence is needed to show the process of domestication.     

圈养小熊猫遗传多样性与种群遗传结构分析

小熊猫是亚洲特有的珍稀濒危动物,目前受到栖息地减少、片断化和人类活动干扰等威胁。中国圈养小熊猫已经有60 多年历史,约55 个机构曾经饲养过小熊猫,现今圈养数量有400 多只,评估小熊猫圈养种群的遗传多样性和遗传结构对科学维持圈养种群和保存遗传种质资源意义重大。本研究利用19 个微卫星座位,对中国境内11 个小熊猫圈养种群的116 只个体进行了遗传多样性评估及遗传结构分析。结果显示11 个种群都具有较高的遗传多样性,平均基因丰富度3.505 ± 1.033 (北京)至4.026 ± 1.219 (冕宁),期望杂合度0.631 ± 0.225(黄山)至0.782 ±0.171 (温岭)。其中福州和无锡种群极显著偏离Hardy-Weinberg 平衡。整个圈养群体内各个种群遗传分化系数为0.055,呈显著分化,表明11 个种群遗传分化水平较高。Bayesian 遗传聚类分析将11 个种群聚为三个遗传簇,与野生种群的遗传聚类结果一致。结论:小熊猫圈养种群与野生种群相比,同样具有较高的遗传多样性。因此,圈养小熊猫遗传管理的重点不再是引进野生个体充实圈养种群,应制订科学的繁殖计划,避免近交,从而维持圈养种群的遗传多样性。     

西南地区6种魔芋属植物基于cpDNA序列的遗传多样性研究

研究野生作物资源的遗传变异及分化机制对种质资源的收集与改良具有重要意义。魔芋是我国西南地区的特色经济作物,但由于受到人为活动干扰,野生种群不断衰退。为评估西南地区魔芋属(Amorphophallus)野生群体的遗传多样性,探究代表性物种的系统发育地位,该研究利用3个叶绿体DNA(cpDNA)片段,分析了魔芋6个物种的遗传多样性,重建了种间系统发育关系。结果表明:(1)西南地区野生魔芋群体的遗传多样性普遍较低,虽然单倍型多样性(H_d)均值为0.428,但近一半群体只有1个单倍型,6个物种整体水平上的单倍型多样性在0.704到0.983之间。(2)在6个物种间检测到高水平的遗传分化,遗传分化系数(F_ST)值在0.481到0.967之间。(3)系统发育分析表明,选取的27个魔芋种主要聚成3个分支:非洲分支、东南亚分支和东亚大陆分支。疣柄魔芋(A. paeoniifolius)隶属于东南亚分支,而东亚大陆分支A包含花魔芋(A. konjac)和西盟魔芋(A. krausei),东亚大陆分支B由东亚魔芋(A. kiusianus)、滇魔芋(A. yunnanensis)和东京魔芋(A. tonkinensis)构成。生境隔离与人为干扰造成了西南地区野生魔芋群体较低的遗传多样性,魔芋属东亚大陆分支的分化可能与早期的快速扩张和生态适应有关。该研究为西南地区魔芋资源的合理保护、可持续利用和杂交育种提供了参考资料。     

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。     

Genetic differentiation of water buffalo (Bubalus bubalis) populations in China, Nepal and south-east Asia: inferences on the region of domestication of the swamp buffalo

Data from three published studies of genetic variation at 18 microsatellite loci in water buffalo populations in China (18 swamp type, two river type), Nepal (one wild, one domestic river, one hybrid) and south-east Asia (eight swamp, three river) were combined so as to gain a broader understanding of genetic relationships among the populations and their demographic history. Mean numbers of alleles and expected heterozygosities were significantly different among populations. Estimates of θ (a measure of population differentiation) were significant among the swamp populations for all loci and among the river populations for most loci. Differentiation among the Chinese swamp populations (which was due primarily to just one population) was much less than among the south-east Asian. The Nepal wild animals, phenotypically swamp type but genetically like river type, are significantly different from all the domestic river populations and presumably represent the ancestral Bubalus arnee (possibly with some river-type introgression). Relationships among the swamp populations (D(A) genetic distances, principal component analysis and structure analyses) show the south-east Asian populations separated into two groups by the Chinese populations. Given these relationships and the patterns of genetic variability, we postulate that the swamp buffalo was domesticated in the region of the far south of China, northern Thailand and Indochina. Following domestication, it spread south through peninsular Malaysia to Sumatra, Java and Sulawesi, and north through China, and then to Taiwan, the Philippines and Borneo.     

金沙江中下游圆口铜鱼遗传多样性与种群历史动态分析

以线粒体Cytb和CoⅠ基因作为分子标记,对金沙江中下游江段的圆口铜鱼进行遗传多样性和种群历史动态分析.结果显示,393尾圆口铜鱼样本共检测出91个串联基因序列单倍型,呈现较高的单倍型多样性(0.936±0.006)和较低的核苷酸多样性(0.00489±0.00009);基于单倍型构建的分子系统发育树及Median-j...     

Determination of genetic diversity of wild and cultured topmouth culter (Culter alburnus) inhabiting China using mitochondrial DNA and microsatellites

The topmouth culter (Culter alburnus) is one of the most commercially important freshwater fish species inhabiting China. However, very limited information is available regarding its genetic diversity and population structure, thus hindering the effective management of this fish stock. Understanding the genetic diversity of wild and cultured topmouth culter populations is highly relevant for successful hatchery management. This study evaluated the genetic diversity and structure of five wild and two cultured populations of topmouth culter in China by using microsatellites and mitochondrial DNA. The genetic diversity of wild populations was found to be lower than that of cultured populations. This finding indicates that wild topmouth culter resources should be protected to prevent further degeneration and extinction. Moreover, it demonstrated that cultured populations have greater breeding potential than wild ones. Subdivisions among wild populations were observed, which should be considered as different units for conservation and hatchery management.     

基于cpDNA trnL-F序列的胡黄连保护遗传学研究

胡黄连为特产中国-喜马拉雅特有高山植物,作为常用中、藏药材,受到灭绝性采挖,作为濒危和二级保护植物亟待科学的保护。该研究以云南和西藏7个野生居群91个个体为材料,基于 cpDNA trnL-F 非编码序列测序分析胡黄连的遗传多样性和遗传结构,分析显著进化单元,确立优先保护居群并提出科学的保护策略。结果表明：胡黄连 trnL-F 序列长度为871~876 bp,根据序列的核苷酸变异共鉴定出5个单倍型,西藏占有2个单倍型,云南占有3个单倍型,西藏和云南2个地区的所有单倍型均不共享。胡黄连具有较低的单倍型多样性(Hd ＝0.43419)和核苷酸多样性(Dij ＝0.00466)。种群间分化度(Fst ＝0.864520)和基因流(Nm ＝0.04)、居群间的遗传分化水平(GST ＝0.916)、AMOVA 分析(0.78％的遗传变异发生在居群内,60.97％的遗传变异发生在地区内居群间,38.25％的遗传变异发生在地区间)均表明,胡黄连居群间存在明显遗传分化。多数一致性树将胡黄连划分为3个进化分支(Ⅰ、Ⅱ、Ⅲ),这3个分支均与地理相关,分支Ⅰ分布于横断山区的4个居群,分支Ⅱ是分布于东喜马拉雅的一个居群,分支Ⅲ是分布于喜马拉雅中段的2个居群。3个分支分属于3个“进化显著单元(ESU)”。这3个 ESU 中白马雪山、茨中、定日、波密、聂拉木五个居群都需要保护,建议现阶段应优先保护的居群是云南白马雪山和西藏波密居群,以就地保护为主。     

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 (/) 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.     

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 diversity and conservation evaluation of a critically endangered endemic maple,Acer yangbiense,analyzed using microsatellite markers

The newly discovered endemic maple Acer yangbiense of China has only five individuals left in the wild, and thus has been classified as a plant species with extremely small populations (PSESP). PSESP species call for emergency protection procedures, such as ex-situ conservation and reintroduction. Our objectives were to examine the genetic diversity of A. yangbiense and to evaluate former conservation strategies from a genetic point of view. Our results suggested that A. yangbiense was not genetically depauperate, but its genetic loss at a species level was obvious. A parentage analysis indicated a high selfing-rate in A. yangbiense and suggested the existence of a previously unknown wild individual. Former conservation strategies did not include all genetic variations of the wild population, and gene diversity of the ex-situ conserved seedlings is lower than that of the wild population. From our findings, we make suggestions to guide the subsequent protection of this species.     

Genetic diversity of captive forest musk deer (Moschus berezovskii) inferred from the mitochondrial DNA control region

Forest musk deer ( Moschus berezovskii ) were once distributed widely in China. However, wild populations have declined dramatically because of poaching and habitat loss. Captive breeding populations have been established for several decades, but the genetic backgrounds of most captive populations were unclear and the population sizes increased very slowly. To provide useful information for conservation and management of this species, we investigated the genetic diversity and population structure of forest musk deer by analysing a 582-bp fragment of the mitochondrial DNA (mtDNA) control region (CR) in three captive breeding populations in Sichuan Province, China. Ninety-four variable sites and 27 haplotypes were observed in 109 individuals, and the nucleotide and haplotype diversities were relatively high compared with those of other endangered mammals. Of the three investigated populations, the Maerkang population had the highest nucleotide diversity ( π  = 0.0568), haplotype diversity ( h  =   0.836) and average intra-population genetic distance (0.062). The analysis of molecular variance demonstrated that most variation occurred within samples and that there was significant differentiation of the three populations. Estimates of gene flow indicated that there were few genetic exchanges among the three populations. Building pedigree records and increasing gene flow between populations will be helpful for conserving these populations and this species.     

中国桔小实蝇种群的微卫星多态性分析

为了研究桔小实蝇种群的遗传结构,本文采用微卫星分子标记技术,对中国南方9省区、越南和泰国的11个桔小实蝇地理种群共224个个体的遗传多样性水平及种群遗传结构进行了研究。用9对微卫星引物共检测到48个等位基因, 平均每个微卫星位点的等位基因数为5.33个。GENEPOP分析结果表明：11个桔小实蝇种群在9个微卫星位点上的多态位点百分率平均为94.45%。种群的Nei's基因多样性指数平均为0.4371,Shannon信息指数平均为0.7870,表明桔小实蝇种群具有非常丰富的遗传多样性。Nei's遗传多样性分析发现,各地理种群间产生了一定程度的遗传分化,种群间平均遗传分化系数F_st=0.2370。种群间一定程度的遗传分化可能是由地理隔离和基因流障碍（N_em = 0.8049）所引起。UPGMA聚类分析可知, 中国的桔小实蝇地理种群可分为华南支和西南支两大分支,华南分支包括福建、台湾、广东和海南4个种群,西南分支包括四川、云南、广西、贵州和湖南5个种群。由此推测, 中国桔小实蝇种群结构的形成与演变是在地理演化与经贸交流加强这两种因素的影响下不断进行的动态过程。     

秦岭细鳞鲑人工繁育群体与野生群体遗传变异分析

研究利用线粒体DNA（细胞色素b基因序列和D-loop区序列）序列对秦岭细鳞鲑（Brachymystax lenok tsinlingensis）野生群体和人工繁育群体的种群遗传结构进行了分析。结果表明, 在86个个体扩增出的线粒体D-loop区730 bp片段中, A+T含量（63.5%）明显高于G+C含量（36.5%）。Cyt b基因序列扩增1141 bp, A+T含量（52.8%）明显高于G+C含量（47.2%）。野生群体43个个体共检测到18个单倍型, 繁育群体43个个体中共检测到24个单倍型, 两个群体共享8个单倍型; 秦岭细鳞鲑野生群体的单倍型多样性和核苷酸多样性（h=0.9070.026; =0.002870.00074）低于繁育群体（h=0.9170.035; =0.003490.00083）, AMOVA分析显示, 98.37%的分子差异位于群体内, 1.63%的分子差异位于群体间, 两群体之间的遗传分化水平较低（Fst=0.01631, P=0.1075; Nm=30.16）。采用邻接法构建的系统发育树和单倍型网络图分析表明, 各群体内的个体不形成单系群, 两者之间互有交叉。总之, 秦岭细鳞鲑野生群体与繁育群体之间基因交流充分, 未出现遗传分化。       

Genetic differences between wild and hatchery populations of red sea cucumber (Stichopus japonicus) inferred from microsatellite markers: implications for production and stocking programs design

Red sea cucumber Stichopus japonicus is the most important and valuable commercial sea cucumber species in Korea. Its farming and stock enhancement started in the early 2000s and is still rapid expansion in Korea. Therefore, the analyses of genetic status of wild and hatchery populations are necessary to maintain the genetic diversity of this valuable marine resource. In this study, possible genetic similarity and differences between the wild population and hatchery population in Jeju, Korea were accessed using multiplex assays with eight highly polymorphic microsatellite loci. High levels of polymorphism were observed between the two populations. A total of 93 different alleles were found. Although a considerable loss of unique alleles and relatively high inbreeding coefficient value were observed in the hatchery samples, no statistically significant reductions were found in heterozygosity or allelic diversity in the hatchery population, compared with the wild population. However, significant genetic heterogeneity was found between two populations. These results suggest that genetic drift has probably promoted differentiation between populations, and stocking intensity in wild populations may correlate with loss of genetic integrity. Therefore, the sustainable exploitation plans of the fishery resource should be developed by applying basic genetic principles combined with molecular monitoring. This genetic baseline information of Korean red sea cucumber has important implications for designing of genetically sustainable restocking programs and more efficient conservation management guidelines for these valuable genetic materials.