Genetic Diversity and Population Structure Analysis in Indian Mustard Germplasm Using Phenotypic Traits and SSR Markers

Plant Molecular Biology Reporter - Indian mustard is an economically important oilseed crop in India; therefore, exploring the genetic diversity of various germplasm collections is quite relevant...     

Population Structure and Genetic Diversity in Popular Rice Varieties of India as Evidenced from SSR Analysis

We report here on the phylogenetic analysis, population substructure, and identification of molecular tags of 25 popular rice varieties and four landraces from different ecological belts of India employing a set of 52 simple sequence repeat (SSR) markers. Genetic analysis using the SSR markers categorized the genotypes into two major clusters, distributed according to their pedigree. Population structure analysis suggested that the optimum number of subpopulations was three (K?=?3) in the popular varieties and landraces. At K?=?5 the allelic distribution was much more similar to the phylogenetic dendrogram. The molecular diversity and population structure analysis indicated that there is not much variation among the popular rice cultivars of India. The study has identified SSR markers producing unique alleles, which should aid in the precise identification, maintenance, and genetic purity analysis of rice varieties.     

30个粳稻品种SSR标记遗传多样性分析

选用分布于水稻12条染色体上的64对SSR引物,对江苏省育成以及日本引进的粳稻品种共30份材料进行遗传多样性分析。结果表明,有50对SSR引物在30个品种间表现为多态性。共检测到140个等位基因,每对引物的等位基因数变幅为2～5个,平均为2．8个。有效等位基因为94．336个,平均为1．887。每个SSR位点的多态性信息量（PIC）变化范围为0．064～0．752,平均为0．410。30个品种间的遗传相似系数变幅为0．386～0．956之间,平均值为0．719,且81．4％的供试品种其遗传相似系数在0．600～0．800之间,亲缘关系较近;以遗传相似系数为原始数据,按UPGMA方法将30个品种划分为3大类群,结合系谱分析结果表明,江苏省育成的水稻品种遗传多样性不够丰富,多数品种间的亲缘关系较近,欲进一步提高江苏省水稻产量还需拓宽亲本选择范围,扩大遗传背景。     

黑龙江省近年审定水稻品种基于SSR标记的遗传多样性分析

为评估黑龙江省水稻品种的遗传基础,利用24个用于水稻DNA指纹图谱构建的SSR标记以及其他均匀分布于水稻12条染色体的38个SSR标记,对黑龙江省近年审定的73个水稻常规稻品种进行遗传多样性分析。结果表明,在62个SSR标记位点中,共检测到142个等位基因,平均每个标记2.3个,多态性比率平均为71.0%,多态性频率变幅为0~0.775,平均值为0.246。供试品种间两两遗传相似系数的平均值为0.759,变幅为0.622~0.966,且96.4%的品种间遗传相似系数在0.66~0.86之间,表明供试的73个品种亲缘关系较近。通过SSR标记基因型聚类分析将这些品种划分为6个类群,与系谱分析趋势一致,类群间的差异主要表现在生育期和米质方面。综上所述,黑龙江省近年审定的水稻品种遗传基础狭窄,在育种中需要导入新的种质资源,加强种质资源创新,以期丰富水稻品种的遗传多样性,进一步提高水稻产量和抗性。     

Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers

Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (F _st = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei’s genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These data provide comprehensive information for the development of conservation strategies of these valuable hazelnut resources.     

基于SSR标记的新疆野杏群体遗传多样性及遗传结构

利用27对SSR分子标记对新疆4个野杏群体遗传多样性和遗传结构进行分析,评价新疆野杏遗传多样性水平和分化程度,为新疆野杏合理保护与利用提供科学依据。结果显示：（1）27对SSR引物共检测到431个等位基因（N_a）,各位点平均等位基因数（N_a）和多态性信息含量（PIC）分别为15.96和0.84;物种水平上Shannons信息指数（I）和期望杂合度（H_e）分别为2.21和0.78。（2）群体水平上等位基因数（N_a）、有效等位基因（N_e）、Shannons信息指数（I）、期望杂合度（H_e）和观察杂合度（H_o）分别为10.98、5.85、1.92、0.79和0.55;其中新源县野杏群体遗传多样性最丰富,巩留县群体遗传多样性最低。（3）基于F统计量分析的遗传分化系数（F_st）为0.05,基因流（N_m）为5.26;分子方差分析显示新疆野杏群体大部分遗传变异来自群体内（95.4%）,群体间的遗传变异仅占4.6%。（4）新疆野杏群体遗传距离为0.06~0.49,平均为0.24;遗传相似度为0.61~0.94,平均为0.80;遗传相似度的聚类分析和遗传距离的主坐标分析结果一致,均将供试4个群体划分为两组;Mantel检测显示,新疆野杏群体遗传距离与地理距离无显著相关（r=0.332,P＝0.16）。研究表明,新疆野杏资源具有丰富的遗传多样性,群体遗传分化程度较低,群体间遗传距离较小,这与新疆野杏群体的大小和悠久的演化历史以及群体间频繁的基因交流相关。     

Genetic Diversity and Population Differentiation of Liaoning Weedy Rice Detected by RAPD and SSR Markers

Weedy rice refers to populations of usually annual Oryza species that diminish farmer income through reduction of grain yield and lowered commodity value at harvest. The genetic diversity and population genetic structure of weedy rice in Liaoning Province were studied by RAPD and SSR markers. The results indicate that the level of genetic diversity of Liaoning weedy rice is very low, with polymorphic loci being only 3.70% (RAPDs) and 47.62% (SSRs). On the other hand, high genetic differentiation was found among populations, in particular between two regions (Shenyang and Dandong), with Fst values of 0.746 (RAPDs) and 0.656 (SSRs), suggesting that more than two thirds of the genetic variation resides among regions. Combined with our investigations of cultural traditions, the low level of genetic diversity in Liaoning Province is attributed to its narrow genetic background enhanced by exchanges of cultivar seeds, whereas the high genetic differentiation between the two regions is most likely the result of different founding parents and gene flow from local rice varieties to weedy rice. The rice cultivars in the two regions are all local varieties and are different genetically. A comparison of the two marker systems demonstrates that SSR is more informative and powerful in terms of the assessment of genetic variability, although both RAPD and SSR provide useful genetic information on weedy rice.     

设施用厚皮甜瓜品种SSR标记遗传多样性分析

使用分布于甜瓜12条染色体上的72对SSR引物,对我国中东部设施内栽培的30个厚皮甜瓜品种进行分析;56对SSR引物在30个品种间表现为多态性。共检测到138个等位变异,每对引物的等位变异数变幅为2～6个,平均为2.6个。有效等位变异为86.16个,平均为2.25。每个SSR位点的多态性信息量(PIC)变化范围为0.045～0.725,平均为0.390。30个品种间遗传相似系数变幅为0.274～0.974之间,平均值为0.665,且90.4%的供试品种其遗传相似系数在0.474～0.824之间,亲缘关系较近;以遗传相似系数为原始数据,按UPGMA方法将30个品种划分为3大类群,结合系谱分析结果表明,我国中东部设施适宜种植的甜瓜品种遗传多样性不够丰富,多数品种间的亲缘关系较近,欲进一步提高中东部地区设施甜瓜产量和品质还需要拓宽亲本选择范围,扩大遗传背景。     

基于SSR标记的荔枝种质遗传多样性分析

从53对本课题组自主开发设计的SSR特异引物对中筛选出22对多态性引物,对46份荔枝材料的基因组DNA进行扩增,共得到54个等位基因,其中每对引物的平均等位基因数为2.4,共获得23个特异性标记,各标记的平均观察杂合度值、平均期望杂合度和PIC值分别为0.451、0.355和0.507。其中L it6位点各数值最高,是最理想的选择标记。利用22对多态性引物对46份荔枝种质进行聚类分析,构建树状图,结果表明:大多数种质相似系数在0.63～0.95之间,说明它们之间的亲缘关系较近,并发现淮枝(广东)与淮枝(海南)两者可能为同名异物品种。     

308个糯玉米审定品种SSR标记遗传多样性分析

随着中国糯玉米产业的蓬勃发展,每年通过审定的糯玉米品种逐渐增多,为了解其育成品种的遗传多样性和亲缘关系,本研究以308个糯玉米审定品种为材料,利用SSR标记从审定年份和适宜种植区2个角度分析近年来糯玉米审定品种遗传多样性特点和发展趋势.结果 表明,308份糯玉米审定品种在40个SSR标记上共检测出529个等位基因、14...     

中国甘薯登记品种SSR标记遗传多样性分析

该研究基于TP-M13-SSR分子标记荧光毛细管检测技术,以中国已入库登记的99份甘薯品种为材料,利用SSR标记建立登记品种的“01”数据库,导入DPS软件计算不同品种之间的遗传距离,采用MEGA的邻接法进行聚类分析,并利用Structure混合模型对材料进行遗传结构分析,以探讨各品种的遗传构成以及品种间的亲缘关系,揭示中国甘薯登记品种在DNA水平的相似度,为甘薯品种鉴定、亲本选配和品种改良等提供参考。结果显示:(1)28对引物共扩增出162条谱带,多态率为96.30%,每对引物平均获得5.57条多态性谱带。(2)构建了99份甘薯登记品种的遗传进化树,99份品种的遗传距离在0~0.4646之间,平均遗传距离为0.3077;在遗传距离为0.2670处将99份品种分为3个类群,且同一生态薯区的品种或具有同一亲本的品种首先被聚在一起,但不同生态薯区的品种在各类群中相对分散分布。(3)品种间的遗传基础较窄,部分生态薯区的品种相似性较高;群体结构分析将材料分为3个亚群,与聚类分析分群结果基本一致,其中31份材料拥有混合来源,遗传背景较为复杂。     

油菜品种及高油育种材料遗传多样性SSR分析

通过SSR标记分析91份油菜品种、骨干亲本和高油自交系,以及作为参考物种的芥菜型油菜、白菜型油菜、埃塞俄比亚芥等8份材料之间的亲缘关系及遗传多样性,为油菜杂种优势利用育种提供理论依据。筛选48对SSR引物对99份参试材料进行扩增,共检测到255个多态性条带。UPGMA聚类将99份材料聚为5组:第Ⅰ组包括89个材料,均为甘蓝型油菜;第Ⅱ组有埃塞俄比亚芥和‘G8白’2个白花材料;第Ⅲ组包括4个芥菜型材料;第Ⅳ组包括3个白菜型材料;第Ⅴ组仅有‘秦芥2008’。第Ⅰ组89个甘蓝型油菜又可分为5个亚组。第i亚组包括43个材料,主要为陕西的恢复系、华中农业大学和浙江材料;第ii亚组包括9个材料,以陕西材料为主;第iii亚组包括12个材料,以贵州和国外材料为主;第iv亚组包括19个材料,主要为中国农科院油料作物所、浙江农科院和安徽的材料;第v亚组包括‘浙油758’、‘147C’等6个材料。而且来自同一育种单位的大部分材料具有较高相似性,这可能是由于育种单位频繁使用少数核心骨干亲本所造成的。     

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.     

中国花生地方品种与育成品种的遗传多样性

以中国花生小核心种质中涉及来源于中国本土的145份地方品种和67份育成品种为材料,应用SSR技术从206对SSR引物中筛选出25对扩增效果好的多态性引物进行检测,并对其进行遗传多样性分析比较.结果表明:(1)地方品种与育成品种各具有特殊带型及各自独特的遗传特性.相似系数和多态性信息量均表明,地方品种的多样性比育成品种丰富,其中:地方品种之间的相似系数为0.57～0.99,平均0.795,多态性信息量0.530 0;育成品种之间的相似系数0.63～0.99,平均0.810,多态性信息量0.463 3.地方品种与育成品种之间的平均相似系数为0.794,变异范围0.56～0.99.(2)对不同生态区来源的分析表明,除黄河流域外其他各生态区地方品种的观测等位基因数和遗传多样性指数(分别为2.740 7～3.518 5和0.816 4～0.879 4)均比育成品种的对应值(分别为1.7012～2.145 6和0.4829～0.802 2)大,并以长江流域生态区地方品种的观测等位基因数和遗传多样性指数最大,分别为3.518 5和0.879 4.(3)聚类分析结果表明,花生核心种质中,中国本土资源分为3个品种群,即地方品种密枝亚种群、地方品种疏枝亚种群和育成品种群,与花生的亚种分类一致.(4)通过遗传多样性分析,鉴定出一批遗传差异较大的材料,其中zhh1398与zhh0041的遗传差异最大,相似系数为0.56,为花生品种的遗传改良及作图群体的构建奠定了基础.     

Genetic Diversity, Population Structure and Linkage Disequilibrium in Elite Chinese Winter Wheat Investigated with SSR Markers

To ascertain genetic diversity, population structure and linkage disequilibrium (LD) among a representative collection of Chinese winter wheat cultivars and lines, 90 winter wheat accessions were analyzed with 269 SSR markers distributed throughout the wheat genome. A total of 1,358 alleles were detected, with 2 to 10 alleles per locus and a mean genetic richness of 5.05. The average genetic diversity index was 0.60, with values ranging from 0.05 to 0.86. Of the three genomes of wheat, ANOVA revealed that the B genome had the highest genetic diversity (0.63) and the D genome the lowest (0.56); significant differences were observed between these two genomes (P<0.01). The 90 Chinese winter wheat accessions could be divided into three subgroups based on STRUCTURE, UPGMA cluster and principal coordinate analyses. The population structure derived from STRUCTURE clustering was positively correlated to some extent with geographic eco-type. LD analysis revealed that there was a shorter LD decay distance in Chinese winter wheat compared with other wheat germplasm collections. The maximum LD decay distance, estimated by curvilinear regression, was 17.4 cM (r(2)>0.1), with a whole genome LD decay distance of approximately 2.2 cM (r(2)>0.1, P<0.001). Evidence from genetic diversity analyses suggest that wheat germplasm from other countries should be introduced into Chinese winter wheat and distant hybridization should be adopted to create new wheat germplasm with increased genetic diversity. The results of this study should provide valuable information for future association mapping using this Chinese winter wheat collection.     

基于荧光SSR标记的玉米自交系遗传结构解析

利用多重SSR-PCR荧光标记检测技术,对本单位自育和引进的259份玉米自交系进行遗传多样性和亲缘关系分析,并以11个归属于不同杂种优势群的代表自交系为参照进行群体结构分析。结果显示,50对SSR引物共检测到214个等位基因变异,基因多态性指数的平均值为0.50,每个SSR标记的多态性信息量(PIC)平均值为0.44。用UPGMA方法将270份自交系划分成3大类群,进一步进行数值化杂种优势群分析,以明确所用种质资源的杂优类群利用方向,为玉米自交系的有效利用和品种的选育提供依据。     

303份甘薯地方种SSR遗传多样性与群体结构分析

利用SSR分子标记,对我国303份甘薯地方种进行了遗传多样性和群体结构分析。进一步明确了甘薯地方种间的遗传多样性和亲缘关系,为优异资源挖掘和品种改良提供了参考。利用SSR建立研究材料的0~1数据库,通过NTSYS-pc2.10软件计算Nei72遗传距离矩阵,将遗传距离矩阵导入MEGA 6.06,计算平均遗传距离和聚类分析;并利用STRUCTURE2.3.4对303份地方种进行群体结构分析。结果表明:30对SSR引物共检测出203条多态性位点,每对引物检测到1~14条多态性条带,平均每对引物获得6.77条。303份材料的平均遗传距离为0.564,聚类分析在遗传距离为0.477处可以把303份材料分成11个类群,其中第Ⅺ类群在遗传距离为0.452处可分为3个亚群。群体结构分析将303份材料划分成了5个稳定的群体,群体结构划分与聚类有相似的结果,其中70份材料Q值小于0.6,属于混合亚群。     

宁夏89份粳稻种质遗传多样性的SSR分析

选用分布于水稻12条染色体上的47对引物对宁夏89份粳稻种质材料进行SSR分析,以探讨宁夏粳稻品种的遗传多样性水平.结果表明,(1)47个位点上共检测到204个具有多态性的等位片段,每对引物检测出2～9个多态性片段,平均为4.16个;(2)聚类分析显示,89份材料的相似系数为0.63～0.91,平均为0.79.在相似系数0.718处聚为8个类群.研究表明,宁夏粳稻种质之间的相似性较高,遗传差异较小,遗传背景比较单一.     

Genetic Structure and Diversity of Glycyrrhiza Populations Based on Transcriptome SSR Markers

Plant Molecular Biology Reporter - Glycyrrhiza is a widely used traditional Chinese herb with medicinal value. Recently, however, Glycyrrhiza biodiversity has faced an unprecedented threat due to...     

编码区和非编码区SSR标记对水稻类群的比较研究

设计14对水稻编码区SSR引物和选取已公布的非编码区SSR引物12对、编码区SSR引物3对,采用SSR技术,对29个标记在60个水稻材料中的多态性进行分析。结果表明,编码区SSR标记平均检测到3.59个多态性位点,多态信息量PIC(polymorphism information conten)在0.032～P0.853之间,平均值为0.447;非编码区SSR标记平均检测到3.92个多态性位点,PIC在0.063～P0.795之间,平均值为0.521。聚类分析显示,非编码区SSR标记能更加精确地区分来自不同地区的水稻类群,编码区SSR标记也具有良好的多态性,同样可以用于分析水稻的亲缘关系。