基于SSR标记构建葡萄种质资源分子身份证

以国家葡萄品种资源圃内保存的80份葡萄种质为试材,对构建葡萄种质分子身份证的方法进行探讨研究。利用筛选后的SSR标记对供试品种进行区分,然后根据引物对不同品种扩增条带分子量的大小进行编码。从62对引物中筛选出来自葡萄19条染色体上的28对SSR引物,在供试种质间共检测出等位基因169个,每对引物平均检测到等位基因数为6.0个。将等位基因赋值后仅用9对引物构建了供试种质的分子身份证编码,平均每对引物区分种质达8.9份,达到了区分品种更加简洁明了,用最少的引物区分不同品种的目的,表明SSR标记技术可有效用于建立葡萄种质资源分子身份证。     

河北省大豆推广品种遗传多样性分析

利用主要农艺性状以及SSR和AFLP2种分子标记,对河北省41个大豆推广品种进行遗传多样性分析,以便为种质资源利用和创新提供依据。农艺性状聚类结果将41个材料划分为3个类群和2个特殊品种,聚类结果与材料系谱来源相差悬殊,不能反映材料间亲缘关系。SSR和AFLP数据聚类结果将41个材料划分为4个SAG（SSR and AFLP—basedgroups）分子类群。30对SSR引物共检测出135个等位变异,平均每个位点上有4．47个等位变异,SSR的遗传多样性指数（Simpson）分布范围为0．0928～0．7800,平均值为0、6442。10对AFLP引物共扩增出93个多态性标记,平均每对引物9．3个多态性标记。品种间的遗传相似系数（GS）变化范围为0．5877～0．9868,平均值变化范围为0．6732～0．7653,总体平均值为0.7237,遗传相似系数较高,说明材料间遗传变异较小。     

糯玉米种质品质性状鉴定和SSR标记遗传多样性分析

对165份来源不同的糯玉米农家种和自交系的穗粒性状和淀粉品质性状进行了鉴定,并利用60对SSR标记进行了遗传多样性分析。结果表明,165份糯玉米种质穗长、秃顶长、行数、行粒数和穗粗变异较大,粗淀粉含量、支链淀粉含量和淀粉糊化特性RVA特征谱带值各指标变异丰富。60 对SSR引物在165份材料间共检测到281个等位基因变异,PCR扩增片段大小介于90～690bp,每对引物检测到2～9个等位基因,平均为4.68个;每对SSR 引物的多态信息量( PIC) 在0.332～0. 860之间,平均为0. 690。利用UPGMA 聚类分析方法将供试种质自交系分为3类,划分结果基本符合品系的来源情况,生产应用的多数糯玉米自交系材料与我国西南地区糯玉米地方品种材料具有较远的亲缘关系。显示出165份糯玉米种质具有丰富的遗传多样性,可为糯玉米杂优利用和遗传改良提供遗传基础。     

基于SSR标记的广东栽培益智群体遗传多样性分析

为了解广东栽培益智(Alpinia oxyphylla)群体的遗传多样性,采用SSR分子标记技术对166份种质的遗传差异进行研究。结果表明,14对SSR引物共检测到88个等位基因,每对引物检测的有效等位基因为1.198～3.279,平均2.599;Shannon多样性信息指数为0.736～1.890,平均1.107。方差分析表明20.87%的变异来自组间,79.13%的变异来自组内。基于主成分分析和遗传结构分析表明,供试166份益智样本可分为4大类群,但没有反映出形态特征的规律性。因此,益智种质资源具有较高遗传多样性,且遗传变异主要发生在群体内,群体间的遗传分化较低,且基于表型性状的类型划分和基于SSR分子标记的聚类未能实现一致性。     

基于SSR标记的132份甘薯种质指纹图谱的构建及遗传多样性分析

利用SSR分子标记技术,构建132份甘薯种质的DNA指纹图谱,并进行遗传多样性分析,旨在为甘薯种质资源亲缘关系鉴定、分类提供理论依据。利用筛选的核心引物进行PCR扩增,通过聚丙烯酰胺凝胶电泳检测显示,19对引物共扩增出232个条带,其中多态性条带165条,多态性比率为71.1%,平均每对引物扩增出8.68个条带,多态性信息含量变化范围在0.6706~0.9331之间,平均为0.8158;其中引物SSR9和引物C33可将132份种质完全区分开,并构建供试材料的DNA指纹图谱,供试材料遗传距离在0.0363~0.5939之间,平均为0.4087,表明种质资源间遗传多样性丰富。基于SSR标记对供试材料进行聚类分析,将供试材料分为2个类群,第Ⅰ类群分为两个亚类,第Ⅰ-1亚类包括济薯25和3份日本引进品种日本金千贯、安納芋、日本薯;第Ⅰ-2亚类包括济徐薯23、苏丹、济薯09281。第Ⅱ类群分为两个亚类,第Ⅱ-1亚类由S07甘薯品系和与其亲缘关系较近的20份甘薯种质组成;第Ⅱ-2亚类由剩余的70份甘薯种质组成,为甘薯分子辅助育种中亲本的选择提供理论依据。     

棉花SSR标记种质资源纯度鉴定及遗传多样性分析

采用前期筛选出的26对SSR核心引物,对收集保存的58份棉花种质资源进行纯度检测和遗传多样性分析。结果显示,供试材料的纯度概率介于20%-90%,分子标记检测结果与田间表型相吻合,说明SSR纯度检测的准确度较高,可以作为进行快速检测棉花种质资源纯度的方法。共扩增出85种多态性基因型,每个标记检测到的基因型数在2-5,平均为3.27个,引物多态性信息量(PIC)介于0.073 7-0.928 1,平均为0.363 9。并利用NTsys-pc 2.10软件进行聚类分析,结果表明,58份种质资源的遗传相似系数(GS)变化范围为0.305 1-0.898 3,变幅为0.593 2,在GS=0.63水平上,将供试材料分为5大类,且这些资源材料的DNA聚类与其地理生态来源无关,而与材料的亲缘关系相关性较高,其聚类结果能更真实地反映种质资源间的遗传差异。     

用SSR标记分析辣椒属种质资源的遗传多样性

利用21对引物在33个辣椒材料中共检测到54个等位基因,每对SSR引物检测到2~4个等位基因变异,平均为2.6个,说明辣椒种质资源的遗传多样性相对较少。通过MVSP3.13f软件对SSR数据进行聚类分析,把33个辣椒材料分为五类,同个种的辣椒种质资源基本聚在一起,说明用SSR标记来区分辣椒种质是可行的,是研究辣椒种质资源遗传多样性的有效手段。     

转基因抗虫棉SSR和AFLP遗传变异研究

利用SSR和AFLP两种分子标记技术,分析了52份转基因抗虫棉品种（系）的遗传多样性。结果表明：在61对SSR引物中,有4对引物在供试材料中表现出多态性,共扩增出102个标记,其中多态性标记25个,多态性百分率为24．51％,每对引物的扩增带数变化在17～30之间;在100对AFLP引物中,有9对引物在供试材料中产生多态性,共扩增出618个标记,多态性标记33个,占总数的5．34％,每对引物组合扩增的标记数分布于47～81之间。成对品种的欧式距离变化在2．00～5．57之间,平均值为4．21,单一品种欧氏距离的平均值分布在3．73～4．75之间,表明不同品种之间遗传差异不大。基于SSRs和AFLPs多态性数据的聚类分析,可以将供试材料划分为3个类群（SAGs）,但类群划分与品种地理来源不十分吻合。     

茄子EST-SSR分子标记的鉴定及多态性分析

为了加快茄子(Solanumm elongena L.)分子遗传学研究和分子标记辅助育种,对其开展转录组测序,采用软件MISA(MicroSAtellite)对茄子转录组中的SSR位点进行搜索,共检测出5 562个SSR位点,分布于3 438条Unigene中,出现频率为13.23%,平均分布距离为9.73 Kb。三核苷酸和二核苷酸重复出现频率占优势,分别有3 546个和1 270个,分别占总SSR的63.75%和22.83%。利用Primer 3.0设计引物,随机选择其中20 bp以上SSR序列的100对引物进行合成,92对引物实现有效扩增,占100对SSR引物的92%,从有效扩增引物随机选取30对引物对29份茄子材料进行扩增及多态性评价,30对均有多态性差异。通过UPGMA作图,供试的29份不同的茄子材料被划分为2类。基于茄子转录组测序开发的EST-SSR标记具有较高的可用性,为茄子种质鉴定、亲缘关系分析及遗传图谱构建等提供更丰富的标记来源。     

38份晾晒烟种质资源遗传关系的SSR分析

利用SSR标记技术对38份晾晒烟种质资源的遗传关系进行了分析。从自己开发的近3000对烟草SSR引物中随机选出30对引物,在38份供试材料中共检测出173个等位基因,每对SSR引物可检测的等位基因数为2~11个,平均为5.77个。38份材料间遗传相似系数（GS）的变化范围为0.165-0.928,平均GS 为0.546。表明38份晾晒烟的遗传多样性丰富,遗传差异较大,亲缘关系较远。聚类分析表明,在L1（GS-0.165）处可将38个品种分为2大类,即晾晒烟类群和美国从烟草起源地收集的烟草（TI：Tobacco Instruction）类群;晾晒烟类群又可进一步分为4组,其聚类结果与所期望的结果基本一致。表明SSR是一种有效、稳定和可靠的分子标记,能较好地从分子水平上揭示烟草(尤其是晾晒烟)种质资源的遗传背景和亲缘关系。     

Genetic diversity in basmati rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) germplasm as revealed by microsatellite (SSR) markers

Genetic diversity among rice genotypes, including 15 indica basmati advance lines and 5 basmati improved varieties were investigated by 28 SSR markers including one indel marker. The SSRs covered all the 12 chromosomes that distributed across the rice genomes. The mean number of alleles per locus was 3.60, showing average number of polymorphism information content was 0.48. A total of 101 alleles were also identified from the microsatellite marker loci. A number of SSR markers were also identified that could be utilized to differentiate between rice genotypes. Pair wise Nei’s genetic distance between rice genotypes ranged from 0.07 to 0.95. The dendrogram based on cluster analysis by using SSR polymorphism that grouped the 20 genotypes of rice in to five clusters based on their genetic similarity. The result could be useful for the identification and selection of the diverse genotypes for the future cross breeding program and development of new rice varieties.     

Genetic diversity in basmati rice (Oryza sativa L.) germplasm as revealed by microsatellite (SSR) markers

Genetic diversity among rice genotypes, including 15 indica basmati advance lines and 5 basmati improved varieties were investigated by 28 SSR markets including one indel marker. The SSRs covered all the 12 chromosomes that distributed across the rice genomes. The mean number of alleles per locus was 3.60, showing average number of polymorphism information content was 0.48. A total of 101 alleles were also identified from the microsatellite marker loci. A number of SSR markers were also identified that could be utilized to differentiate between rice genotypes. Pair wise Nei,s genetic distance between rice genotypes ranged from 0.07 to 0.95. The dendrogram based on cluster analysis by using SSR polymorphism that grouped the 20 genotypes of rice in to five clusters based on their genetic similarity. The result could be useful for the identification and selection of the diverse genotypes for the future cross breeding program and development of new rice varieties.     

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.     

陕西省有色稻资源的SSR多态性分析

从水稻12条染色体上筛选出22对有效引物,对陕西省17个有色稻品种的遗传多样性进行分析,共检测到128个等位基因,平均每个标记检测到5.8个等位基因,每个SSR位点的遗传多态性信息含量在0.49-0.89之间,平均值为0.73。聚类分析表明,陕西省17个有色稻品种的遗传相似系数集中在0.24-0.88之间。     

Analysis of genetic diversity and population structure of rice cultivars from Korea, China and Japan using SSR markers

A total of 29 simple sequence repeat (SSR) markers were used to analyze the genetic diversity of 150 accessions of cultivated rice (Oryza sativa L.) from Korea, China, and Japan. A total of 375 alleles were detected with an average of 12.9 per locus. The averaged values of gene diversity and polymorphism information content (PIC) for each SSR locus were 0.7001 and 0.6683, respectively. Alleles per locus in Korean rice were 8.8, whereas 8.1 and 7.2 alleles per locus were found in Chinese and Japanese rice, respectively. The mean gene diversity in Korean, Chinese, and Japanese rice was 0.6058, 0.6457, and 0.5174, respectively, whereas the mean PIC values for each SSR locus were 0.5759, 0.6138, and 0.4881, respectively. The genetic diversity of the Korean and Chinese cultivars was higher than that of the Japanese cultivars, and the genetic diversity ofjaponica was higher than that ofindica. The model-based structure analysis revealed the presence of three subpopulations, which was basically consistent with clustering based on genetic distance. An AMOVA analysis showed that the between-population component of genetic variance was less than 22% in contrast to 78% for the within-population component. The overallFST value was 0.2180, indicating a moderate differentiation among groups. The results could be used for designing effective breeding programs aimed at broadening the genetic bases of commercially grown varieties.     

New microsatellite markers for bananas (Musa spp)

Thirty-four microsatellite markers (SSRs) were identified in EST and BAC clones from Musa acuminata burmannicoides var. Calcutta 4 and validated in 22 Musa genotypes from the Banana Germplasm Bank of Embrapa-CNPMF, which includes wild and improved diploids. The number of alleles per locus ranged from 2 to 14. The markers were considered highly informative based on their polymorphism information content values; more than 50% were above 0.5. These SSRs will be useful for banana breeding programs, for studies of genetic diversity, germplasm characterization and selection, development of saturated genetic linkage maps, and marker assisted selection.     

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。     

从CIMMYT引进的人工合成六倍体小麦D染色体组微卫星分子标记的遗传差异

采用微卫星（SSR）分子标记技术,选用23个D染色体组特异性引的对来自CIMMYT的26份人工合成六倍体小麦D染色体组的遗传多样性进行了分析。研究发现,26份材料在D染色体组上存在丰富的等位基因变异（92个）,平均每个基因座为4个。遗传距离计算结果也显示,26份材料D染色体组之间具有较大的遗传差异,平均遗传距离高达0．4955。因此,人工合成六倍体小麦D染色体组中存在丰富的遗传多样性,可以作为拓宽普通小麦遗传基础的新的遗传变异来源。研究还发现,由同一个粗山羊草基因型与不同硬粒小麦杂交合成的人工合成六倍体小麦（如合成种17和18）在所用检测的23个基因座中有3个存在差异,说明小麦在多倍化后,供体基因组在重复序列区域会发生遗传分化。     

Population structure and genetic diversity analysis of Indian and exotic rice (Oryza sativa L.) accessions using SSR markers

In order to understand the population structure and genetic diversity among a set of 82 rice genotypes collected from different parts of the Asian countries including India were characterized using 39 microsatellite loci. The Population structure analysis suggested that the optimum number of subpopulations was four (K = 4) among the rice genotypes, whereas phylogenetic analysis grouped them into three populations. The results obtained from phylogenetic and STRUCTURE analysis proved to be very powerful for the differentiation of rice genotypes based on their place of origin. The genetic diversity analysis using 39 SSR loci yielded 183 scorable alleles, out of which 182 alleles were observed to be polymorphic with an average of 4.8 alleles per locus. The Polymorphism Information Content (PIC) values for all the polymorphic primers across 82 rice genotypes varied from 0.02 to 0.77, with an average of 0.50. Gene diversity (He) was found to be in the range of 0.02 (RM484) to 0.80 (OSR13) with an average value of 0.55, while heterozygosity (Ho) was observed with an average of 0.07, ranging from 0.01 (RM334) to 0.31 (RM316). The present study resulted in identification of seven highly polymorphic SSR loci viz., OSR13, RM152, RM144, RM536, RM489, RM259 and RM271 based on the parameters like PIC value (≥0.70), gene diversity (≥0.71), and polymorphic alleles (≥6). These seven polymorphic primers can effectively be used in further molecular breeding programs and QTL mapping studies of rice since they exhibited very high polymorphism over other loci. SSR analysis resulted in a more definitive separation of clustering of genotypes indicating a higher level of efficiency of SSR markers for the accurate determination of relationships between accessions.     

Microsatellite marker-mediated analysis of the EMBRAPA Rice Core Collection genetic diversity

The objectives of this study were to determine the genetic structure of 242 accessions from the EMBRAPA Rice Core Collection (ERiCC), to create a mini-core collection and to develop a multiplex panel of fluorescent labeled simple sequence repeats (SSRs). Eighty-six SSRs were used to identify 1,066 alleles, with an average number of 12.4 alleles/locus and average polymorphism information content (PIC)/locus of 0.75. A model-based clustering method recognized the structure of the accessions on two levels, according to their cultivation system and origin. The most divergent subgroup identified was the worldwide lowland accessions, with the highest values for gene diversity (0.75), average Rogers distance modified by Wright (0.80), average number of alleles/locus (11.7) and private alleles (132). A mini-core was assembled with the most divergent 24 lowland and upland accessions. This mini-core displayed an average distance of 0.86, an average number of alleles/locus of 8.4 and an average PIC/locus of 0.8. From the 86 SSRs, 24 were selected to compose six multiplex panels in order to optimize the process of rice genotyping. This set of markers distinguished all 242 accessions, and showed an average PIC of 0.80 and an average number of alleles/locus of 15.4, higher than the entire set of 86 SSRs. Since the heterogeneity found in lines and cultivars of ERiCC was higher than expected, it is necessary to analyze pooled DNA samples to get a better estimate of genetic variability. The SSR characterization of ERiCC clearly indicates that there is high genetic variability in rice accessions stored in genebanks worldwide which can be promptly explored by rice pre-breeding programs.