湖栖鳍虾虎鱼微卫星DNA标记的开发与群体遗传多样性分析

为研究雷州半岛湖栖鳍虾虎鱼(Gobiopterus lacustris)遗传多样性,对湖栖鳍虾虎鱼雌雄性腺进行转录组测序,采用MISA软件进行微卫星分析,共获得25 452个微卫星标记,其中包含14 708个单碱基重复类型,6 175个2碱基重复类型,3、4、5和6碱基重复类型数目分别为4 223、327、15和4。随机选取50个微卫星位点设计引物,能够扩增出清晰稳定条带的有39对,其中,11个位点表现出不同程度的多态,28个位点呈现单态。利用11个具有多态性的微卫星位点分析湖栖鳍虾虎鱼在廉江市高桥镇红树林保护区、湛江东海岛、雷州市附城镇和雷州市九龙山红树林国家湿地公园4个野生群体中的遗传多样性及遗传结构,11个微卫星位点呈现出不同程度的多态性,等位基因数(Na)2～15,平均等位基因为(6?3.9)个,有效等位基因数(Ne)、平均观测杂合度(Ho)和期望杂合度(He)分别在1.919～2.485、0.343～0.465和0.381～0.483之间,平均多态信息含量(PIC)为0.348～0.465。Hardy-Weinber平衡分析显示,4个群体的大部分位点未偏离平衡。在每个群体中进...     

Analysis of Genetic Diversity and Structure of Guanzhong Horse Using Microsatellite Markers

To determine the genetic diversity and validate the pedigree record of Chinese Guanzhong horse, 67 individuals were genotyped with eight microsatellite markers. In our study, the mean observed and expected heterozygosities were 0.51 and 0.66, respectively. The mean observed number of alleles for the Guanzhong horse was 3.88. Nonetheless, the total value of F_ST multiloci clearly indicates that about 0.5% of overall genetic variation is due to line founder differences, while differences among individuals are responsible for the remaining 99.5%. In addition, the polymorphic information content (PIC) result showed that five loci (HTG7, HMS7, HMS2, AHT4, and HMS6) were highly polymorphic (PIC?>?0.5) and three loci (HMS3, HTG6, and COR071) were moderate polymorphic (PIC?>?0.25). Genetic distances and cluster analysis showed that the genetic relationship among 67 Guanzhong horse was generally consistent with pedigree recorded. Our results not only evaluated the genetic diversity of Chinese Guanzhong horse, but also suggested that the eight microsatellite markers might be used as subservient markers for parentage verification and individual identification in the Guanzhong horse.     

Genetic Diversity and Population Structure Analysis Between Indian Red Jungle Fowl and Domestic Chicken Using Microsatellite Markers

The present study was conducted to assess the genetic diversity, population structure, and relatedness in Indian red jungle fowl (RJF, Gallus gallus murgi) from northern India and three domestic chicken populations (gallus gallus domesticus), maintained at the institute farms, namely White Leghorn (WL), Aseel (AS) and Red Cornish (RC) using 25 microsatellite markers. All the markers were polymorphic, the number of alleles at each locus ranged from five (MCW0111) to forty-three (LEI0212) with an average number of 19 alleles per locus. Across all loci, the mean expected heterozygosity and polymorphic information content were 0.883 and 0.872, respectively. Population-specific alleles were found in each population. A UPGMA dendrogram based on shared allele distances clearly revealed two major clusters among the four populations; cluster I had genotypes from RJF and WL whereas cluster II had AS and RC genotypes. Furthermore, the estimation of population structure was performed to understand how genetic variation is partitioned within and among populations. The maximum ?K value was observed for K = 4 with four identified clusters. Furthermore, factorial analysis clearly showed four clustering; each cluster represented the four types of population used in the study. These results clearly, demonstrate the potential of microsatellite markers in elucidating the genetic diversity, relationships, and population structure analysis in RJF and domestic chicken populations.     

微卫星标记在玉米群体遗传多样性研究中的应用

简要综述了近几年利用微卫星(SSR)分子标记技术分析玉米群体遗传多样性过程中的研究进展对研究中混合取样,荧光标记技术,共享数据库等新方法的使用作了阐述.     

Genetic Diversity and Population Structure in Chinese Indigenous Poplar (Populus simonii) Populations Using Microsatellite Markers

Populus simonii Carr. is an important ecological and commercial breeding species in northern China; however, human interference during the last few centuries has led to the reduction and fragmentation of natural populations. To evaluate genetic diversity and differentiation within and among existing populations, we used 20 microsatellite markers to examine the genetic variation and structure of 16 natural populations. Our results indicated that the level of genetic diversity differed among populations, with average number of alleles per locus (AR) and expected heterozygosity (H _e) ranging from 3.7 to 6.11 and 0.589 to 0.731, respectively. A marginal population from Qilian in the Qinghai–Tibetan Plateau showed the highest values (AR?=?6.11, H _e?=?0.731), and the Zhangjiakou and Yishui populations showed the lowest values (AR?=?4.08, H _e?=?0.589 and AR?=?3.7, H _e?=?0.604). The inbreeding coefficient (F _IS) values for all populations were positive, which indicated an excess of homozygotes. The microsatellites allowed the identification of a significant subpopulation structure (K?=?3), consistent with an isolation by distance model for P. simonii populations. Additionally, molecular variance analysis revealed that 14.2 % of the variation resided among populations, and 85.8 % could be attributed to variation within populations. These data provide valuable information for natural resource conservation and for optimization of breeding programs in the immediate future.     

尼西鸡遗传多样性微卫星标记分析

尼西鸡抗病力强,产蛋性能高,适应高海拔及寒冷的气候条件,是具有独特群体遗传特性的高原地方鸡种。为了对其有效保护和合理利用提供遗传背景资料,筛选了家鸡基因组24条染色体上的33个微卫星标记,对随机选取的50个尼西鸡个体进行多态性检测,共检测到122个等位基因,每个座位平均等位基因数为3·7个。该群体平均多态信息含量和平均杂合度分别为0·5514和0·6350,大染色体较小染色体的微卫星多态性程度高。表明尼西鸡属多态性较丰富的群体。     

Characterization of the Genetic Diversity and Population Structure for the Yellow Cattle in Taiwan Based on Microsatellite Markers

In recent years, the population size of Taiwan yellow cattle has drastically declined, even become endangered. A preservation project, Taiwan Yellow Cattle Genetic Preservation Project (TYCGPP), was carried out at the Livestock Research Institute (LRI) Hengchun branch (1988–present). An analysis of intra- and inter- population variability was performed to be the first step to preserve this precious genetic resource. In this work, a total number of 140 individuals selected from the five Taiwan yellow cattle populations were analyzed using 12 microsatellite markers (loci). These markers determined the level of genetic variation within and among populations as well as the phylogenetic structure. The total number of alleles detected (122, 10.28 per locus) and the expected heterozygosity (0.712) indicated that these five populations had a high level of genetic variability. Bayesian cluster analysis showed that the most likely number of groups was 2 (K = 2). Genetic differentiation among clusters was moderate (F _ST = 0.095). The result of AMOVA showed that yellow cattle in Taiwan had maintained a high level of within-population genetic differentiation (91%), the remainder being accounted for by differentiation among subpopulations (4%), and by differentiation among regions (5%). The results of STRUCTURE and principal component analysis (PCA) revealed two divergent clusters. The individual unrooted phylogenetic tree showed that some Kinmen yellow cattle in the Hengchun facility (KMHC individuals) were overlapped with Taiwan yellow cattle (TW) and Taiwan yellow cattle Hengchun (HC) populations. Also, they were overlapped with Kinmen × Taiwan (KT) and Kinmen yellow cattle (KM) populations. It is possible that KMHC kept similar phenotypic characteristics and analogous genotypes between TW and KM. A significant inbreeding coefficient (F _IS = 0.185; P < 0.01) was detected, suggesting a medium level of inbreeding for yellow cattle in Taiwan. The hypothesis that yellow cattle in Taiwan were derived from two different clusters was also supported by the phylogenetic tree constructed by the UPGMA, indicating that the yellow cattle in Taiwan and in Kinmen should be treated as two different management units. This result will be applied to maintain a good level of genetic variability and rusticity (stress-resistance) and to avoid further inbreeding for yellow cattle population in Taiwan.     

First Records on Genetic Diversity and Population Structure of Algerian Peanut (Arachis hypogaea) Using Microsatellite Markers

Peanut (Arachis hypogaea L) is one of the wide cultivated plants with a narrow genetic base, hence the interest in prospecting, rescuing, and characterizing germplasm of this species is continuously carried out. In this work, eleven microsatellite markers were used to assess the genetic diversity and population structure of 68 Algerian peanut accessions originated from four geographic regions in the north and south of Algeria. A total of 83 alleles were amplified with a mean number of 7.545 alleles per locus and polymorphic information content (PIC) ranged from 0.625 to 0.874. The observed and expected heterozygosity varied from 0.31 to 1.00 and from 0.61 to 0.84 with a mean of 0.704 and 0.732, respectively. Genetic structure analysis showed a strong population at K?=?2, separating accessions according to their subspecies affiliation (hypogeae ssp. and fastigiata ssp.). It was also able to quantify the genetic correlations between genotypes using principal component analysis (PCA) and the method of groups of unweighted pairings with arithmetic means (UPGMA). Analysis of molecular variance (AMOVA) revealed high genetic variation within individuals (90.7%) and low genetic differentiation between subspecies (10.3%) and among populations (8.9%) from different geographical origin. Genetic diversity analysis in this study provides useful information for the exploration and utilization of these peanut cultivars.

     

用SSR研究栲树群体遗传结构

利用微卫星（SSR）分子标记对福建省内4个栲树（Castanopsis fargesii Franch.）群体遗传结构进行了研究。SSR标记揭示了栲树群体丰富的遗传变异：平均等位基因数A＝9.0,平均有效等位基因数Ne=4.8,平均期望杂合度He=0.65,而群 具有较低的Fst值（Fst=0.031）。SSR每个位点的等位基因频率分布在栲树群体间都存在显或极显差异,表明根据SSR等位基因频率分布亦能了解各体的分化。SSR标记使栲树群体中一些稀有等位基因得以表现,54个SSR等位基因中有15个等位基因仅出现在1个或2个群体中,且频率较低,在遗传多样性保护中更应注重保护这些稀有的等位变异。     

Study on Population Genetic Structure in Castanopsis fargesii with Microsatellite Markers

Genetic structure of four populations in Castanopsis fargesii Franch. in Fujian Province was studied with microsatellite (SSR) markers. A high level of genetic variation was detected in the populations of C. fargesii by using SSR with A=9.0, Ne=4.8, He=0.65 and the population differentiation coefficient ( Fst ) was only 0.031. The distributions of alleles of all loci were significantly different among the populations of C. fargesii , and the population differentiation could be found according to the distributions of SSR alleles. Some rare alleles in the populations of C. fargesii were revealed by SSR: Fifteen of 54 alleles appeared in one or two populations with lower frequencies; conservation of these rare alleles is of great importance.     

Genetic Diversity and Natural Population Structure of Cacao (Theobroma cacao L.) from the Brazilian Amazon Evaluated by Microsatellite Markers

A sample of 94 accessions of Theobroma cacao L. (cacao), representing four populations from the Brazilian Amazon (Acre, Rondônia, lower Amazon and upper Amazon) were analyzed using microsatellite markers to assess the genetic diversity and the natural population structure. From the 19 microsatellite loci tested, 11 amplified scorable products, revealing a total of 49 alleles, including two monomorphic loci. The Brazilian upper Amazon population contained the largest genetic diversity, with the most polymorphic loci, the highest observed heterozygosity; and the majority of rare alleles, thereby this region might be considered part of the center of diversity of the species. The observed heterozygosity for all the Brazilian populations (H _o = 0.347) was comparable with values reported for other similar upper Amazon Forastero cacao populations, with the Acre and Rondônia displaying the lowest values. The lower Amazon population, traditionally defined as highly homozygous, presented an unexpectedly high observed heterozygosity (H _o = 0.372), disclosing rare and distinct alleles, with large identity with the upper Amazon population. It was hypothesized that part of the lower Amazon population might derive from successive natural or intentional introduction of planting material from other provenances, mainly upper Amazon. Most of the loci exhibited a lower observed heterozygosity than expected, suggesting that self-pollination might be more common than usually assumed in cacao, but excess of homozygotes might also derive from sub-grouping (Wahlund effect) or from sampling related individuals. Most of the gene diversity was found to occur within groups, with small differentiation between the four Brazilian Amazon populations, typical of species with high gene flow.     

Microsatellite Markers and Genetic Diversity of Four Scleractinian Corals

Russian Journal of Marine Biology - Eighteen microsatellite sequences were isolated from Platygyra acuta through magnetic bead hybridization enrichment method, and the site primers were used to...     

基于SSR标记的宁夏水稻遗传多样性分析

选择自上世纪80年代以来的59份宁夏水稻种质,利用分布于12条染色体的82对SSR引物进行遗传多样性和遗传相似性分析。共检测到339个等位基因,品种间不同位点等位基因数目2~19个,平均4.13个。Nei基因多样性指数变幅为0.0333~0.9164,平均为0.4394。按种质释放或审定年代,55份水稻分为3组分析,随着年代的增加,等位基因数和遗传多样性指数均呈增大趋势,且3群体间等位基因数和多样性指数差异均达极显著水平（P<0.001）。UPGMA聚类分析表明,参试59份水稻种质在遗传相似系数0.78水平上聚为5大类,其中第Ⅰ类为1份香稻种质;第Ⅱ、Ⅳ类均为3份种质;第Ⅲ类有5份种质,与吉林水稻相似;绝大多数品种被聚为第Ⅴ类,占参试材料数的79.7％。对比宁夏水稻选育品种系谱,大多数种质具有宁夏骨干亲本红旗12、京引39、东方红2号、京引59等的血缘,种质间亲缘关系较近。虽然近年来宁夏水稻的遗传多样性有增加的趋势,但遗传基础狭窄,参试种质的相似系数在0.75以上,最高达0.97。应继续加大力度引进和创新亲本材料,拓宽宁夏水稻的遗传基础。     

利用微卫星标记分析四川8个地方鸡品种遗传多样性

通过选用30个多态性较好的微卫星标记,检测了四川省8个地方鸡品种：峨嵋黑鸡、泸宁鸡、旧院黑鸡、米易鸡、石棉草科鸡、凉山崖鹰鸡、兴文乌骨鸡、沐川乌骨鸡的遗传多样性。利用等位基因频率计算出各群体的平均遗传杂合度（H）、多态信息含量（PIC）和群体间的DA遗传距离。结果表明：30个微卫星位点中有24个微卫星位点在8个鸡群体中的多态信息含量均为高度多态,可作为有效的遗传标记用于各鸡品种的遗传多样性和系统发生关系的分析。各鸡种的杂合度都较高,平均杂合度范围是0.629~0.681,最高的是泸宁鸡（0.681）,最低的是旧院黑鸡（0.629）。据分析可能是由于交通闭塞,形成了家禽品种的多种多型,而且杂合度的高低与PIC值的大小体现了较高的一致性。对DA遗传距离的计算表明：用UPGMA法进行聚类分析,结果8个鸡品种被聚为3类：Ⅰ类：峨嵋黑鸡、米易鸡、泸宁鸡、旧院黑鸡聚为一类。米易鸡、泸宁鸡先聚在一起,然后又与峨嵋黑鸡在较近的距离聚在一起,然后再与旧院黑鸡聚在一起;Ⅱ类：石棉草科鸡、兴文乌骨鸡、沐川乌骨鸡聚为一类。兴文乌骨鸡、沐川乌骨鸡在较近的距离聚在一起,然后又与石棉草科鸡在较近的距离聚在一起;Ⅲ类：凉山崖鹰鸡独自聚为一类。这与几个鸡品种的来源、分化、选育历史及地理分布是一致的。     

茶花鸡群体遗传多样性

茶花鸡是我国具有独特遗传特性的地方家禽品种,为了进一步阐明其群体遗传变异和遗传结构状况,采用了33个家鸡特异性的微卫星标记对该鸡种自然群体中30个个体进行了多态性电泳检测。33个微卫星座位共检测到105个等位基因,所有座位都呈现出多态性,每个座位的等位基因数在2~5个之间,平均每个座位等位基因数3.20个。群体平均杂合度和平均多态信息含量分别为0.612 9和0.527 6。结果表明,茶花鸡自然群体遗传多样性较丰富。     

Genetic Diversity of Plasmodium falciparum in Haiti: Insights from Microsatellite Markers

Hispaniola, comprising Haiti and the Dominican Republic, has been identified as a candidate for malaria elimination. However, incomplete surveillance data in Haiti hamper efforts to assess the impact of ongoing malaria control interventions. Characteristics of the genetic diversity of Plasmodium falciparum populations can be used to assess parasite transmission, which is information vital to evaluating malaria elimination efforts. Here we characterize the genetic diversity of P. falciparum samples collected from patients at seven sites in Haiti using 12 microsatellite markers previously employed in population genetic analyses of global P. falciparum populations. We measured multiplicity of infections, level of genetic diversity, degree of population geographic substructure, and linkage disequilibrium (defined as non-random association of alleles from different loci). For low transmission populations like Haiti, we expect to see few multiple infections, low levels of genetic diversity, high degree of population structure, and high linkage disequilibrium. In Haiti, we found low levels of multiple infections (12.9%), moderate to high levels of genetic diversity (mean number of alleles per locus = 4.9, heterozygosity = 0.61), low levels of population structure (highest pairwise F_st = 0.09 and no clustering in principal components analysis), and moderate linkage disequilibrium (ISA = 0.05, P<0.0001). In addition, population bottleneck analysis revealed no evidence for a reduction in the P. falciparum population size in Haiti. We conclude that the high level of genetic diversity and lack of evidence for a population bottleneck may suggest that Haiti’s P. falciparum population has been stable and discuss the implications of our results for understanding the impact of malaria control interventions. We also discuss the relevance of parasite population history and other host and vector factors when assessing transmission intensity from genetic diversity data.     

Evaluation of Genetic Diversity and Population Structure Analysis among Germplasm of Agaricus bisporus by SSR Markers

Agaricus bisporus is a popular edible mushroom that is cultivated worldwide. Due to its secondary homothallic nature, cultivated A. bisporus strains have low genetic diversity, and breeding novel strains is challenging. The aim of this study was to investigate the genetic diversity and population structure of globally collected A. bisporus strains using simple sequence repeat (SSR) markers. Agaricus bisporus strains were divided based on genetic distance-based groups and model-based subpopulations. The major allele frequency (MAF), number of genotypes (NG), number of alleles (NA), observed heterozygosity (HO), expected heterozygosity (HE), and polymorphic information content (PIC) were calculated, and genetic distance, population structure, genetic differentiation, and Hardy–Weinberg equilibrium (HWE) were assessed. Strains were divided into two groups by distance-based analysis and into three subpopulations by model-based analysis. Strains in subpopulations POP A and POP B were included in Group I, and strains in subpopulation POP C were included in Group II. Genetic differentiation between strains was 99%. Marker AB-gSSR-1057 in Group II and subpopulation POP C was confirmed to be in HWE. These results will enhance A. bisporus breeding programs and support the protection of genetic resources.     

Genetic Diversity and Geographic Population Structure of Bovine Neospora caninum Determined by Microsatellite Genotyping Analysis

The cyst-forming protozoan parasite Neospora caninum is one of the main causes of bovine abortion worldwide and is of great economic importance in the cattle industry. Recent studies have revealed extensive genetic variation among N . caninum isolates based on microsatellite sequences (MSs). MSs may be suitable molecular markers for inferring the diversity of parasite populations, molecular epidemiology and the basis for phenotypic variations in N . caninum , which have been poorly defined. In this study, we evaluated nine MS markers using a panel of 11 N . caninum -derived reference isolates from around the world and 96 N . caninum bovine clinical samples and one ovine clinical sample collected from four countries on two continents, including Spain, Argentina, Germany and Scotland, over a 10-year period. These markers were used as molecular tools to investigate the genetic diversity, geographic distribution and population structure of N . caninum . Multilocus microsatellite genotyping based on 7 loci demonstrated high levels of genetic diversity in the samples from all of the different countries, with 96 microsatellite multilocus genotypes (MLGs) identified from 108 N . caninum samples. Geographic sub-structuring was present in the country populations according to pairwise F _ST. Principal component analysis (PCA) and Neighbor Joining tree topologies also suggested MLG segregation partially associated with geographical origin. An analysis of the MLG relationships, using eBURST, confirmed that the close genetic relationship observed between the Spanish and Argentinean populations may be the result of parasite migration (i.e., the introduction of novel MLGs from Spain to South America) due to cattle movement. The eBURST relationships also revealed genetically different clusters associated with the abortion. The presence of linkage disequilibrium, the co-existence of specific MLGs to individual farms and eBURST MLG relationships suggest a predominant clonal propagation for Spanish N . caninum MLGs in cattle.     

利用微卫星标记分析东平湖黄颡鱼的遗传多样性

采用27对鲤微卫星引物对山东东平湖黄颡鱼进行全基因组扫描,结果有19对引物能获得稳定的扩增条带,其中有6个微卫星位点具有多态性。对这6个位点的扩增产物进行分析,结果显示:6个位点共检测到22个等位基因,每个位点的等位基因数从2个到6个不等;平均基因纯合率为41.67%,平均多态信息含量(PIC)为0.488,平均杂合度为0.5833。这表明东平湖黄颡鱼种群结构合理,群体遗传多样性较丰富,种质资源处于安全状态。