利用SSR技术研究花生属种间亲缘关系

用44对SSR特异引物对花生属不同区组的21份种质进行了分析,获得能稳定揭示花生属种间差异的SSR引物34对。34对引物在21份种质中共检测到190个等位基因变异,每个位点上检测的等位变异数为3~11个,平均为5.59个。21份材料间存在很大的遗传变异,平均遗传距离为0.63,变异范围为0.08~0.95。聚类分析表明,区组间的遗传分化大于区组内的遗传分化,匍匐区组的遗传分化大于其他区组的遗传分化,同一物种不同种质间也存在很大的差异。栽培种花生与花生区组材料的亲缘关系相对较近,与花生属的植物学分类一致,其中A基因组的A.duranensis和A.villosa及B基因组的A.bati-zocoi与栽培种花生的亲缘关系更近一些。     

用SSR和AFLP技术分析花生抗青枯病种质遗传多样性的比较

由Ralstonia solanacearum E.F.Smith引起的青枯病是若干亚洲和非洲国家花生生产的重要限制因子,利用抗病品种是防治这一病害最好的措施。虽然一大批抗青枯病花生种质资源材料已被鉴定出来,但对其遗传多样性没有足够的研究,限制了在育种中的有效利用。本研究以31份对青枯病具有不同抗性的栽培种花生种质为材料,通过简单序列重复(SSR)和扩增片段长度多态性(AFLP)技术分析了它们的遗传多样性。通过78对SSR引物和126对AFLP引物的鉴定,筛选出能显示抗青枯病种质多态性的SSR引物29对和AFLP引物32对。所选用的29对多态性SSR引物共扩增91条多态性带,平均每对引物扩增3.14条多态性带;32对多态性AFLP引物共扩增72条多态性带,平均扩增2.25条多态性带。在所筛选引物中,4对SSR引物(14H06,7G02,3A8,16C6)和1对AFLP引物(P1M62)检测花生多态性的效果优于其他引物。SSR分析获得的31个花生种质的遗传距离为0.12-0.94,平均为0.53,而AFLP分析获得的遗传距离为0.06～0.57,平均为0.25,基于SSR分析的遗传距离大于基于AFLP分析的遗传距离,疏枝亚种组的遗传分化相对大于密枝亚种组。基于两种分析方法所获得的聚类结果基本一致,但SSR数据聚类结果与栽培种花生的形态分类系统更为吻合。根据分析结果,对构建青枯病抗性遗传图谱群体的核心亲本和抗性育种策略提出了建议。     

基于SSR标记分析小豆及其近缘植物的遗传关系

本研究利用87对SSR引物分析了80份栽培小豆(Vigna angularis)、22份野生小豆(V.angularis var.nipponensis)以及10份豇豆属(共7个种)近缘植物,旨在比较豇豆属不同种的遗传多样性,并分析种间的遗传关系.结果显示87对SSR引物在112份小豆及其近缘植物资源中共检测到667个等位变异.其中有75个、71个和82个SSR位点分别在栽培小豆、野生小豆和近缘植物中表现为多态.随机抽样分析发现,平均每SSR位点检测到的等位变异数目为近缘植物>野生小豆>栽培小豆,与多态信息含量(PIC)值一致,说明近缘植物及野生小豆中蕴含着丰富的遗传变异,是栽培小豆育种的重要基因来源.聚类分析显示,栽培小豆、野生小豆和近缘植物间的遗传分化比较明显,分别聚为三大类,其中栽培小豆的遗传背景与其生态环境相对应;近缘植物又可以分为三个亚类,亚类间的遗传距离与其亲缘关系相对应.本研究结果也说明利用SSR标记辅助豇豆属的种间分类是可行的.     

基于全长转录组信息的枸杞SSR标记开发北大核心CSCD

枸杞是茄科枸杞属的重要经济植物,广泛分布于我国西北地区,环境适应性强。本研究分析了枸杞基因组中SSR的分布特征,并基于宁杞1号全长转录组开发SSR分子标记,对28个枸杞种质进行遗传多样性分析和亲缘关系分析。用MISA软件搜索全长转录组中SSR位点,设计并筛选多态性好的SSR引物,对206对引物经过毛细管电泳筛选后最终选出23对引物对28个不同分布区的枸杞种质进行遗传多样性分析,遗传相似系数用非加权组平均法(UPGMA)聚类。23对引物共扩增得到240个等位基因,每个位点的等位基因数范围为4~17,Shannon信息指数范围为1.177~2.487,期望杂合度和观测杂合度的范围分别为0.635~0.909和0.250~0.964,PIC的范围是0.580~0.902。遗传距离聚类分析显示28份枸杞种质在遗传相似系数为0.71时被分为4类,宁夏枸杞为Ⅰ类,中国枸杞为Ⅱ类,黑果枸杞为Ⅲ类,Ⅳ类中只有中国枸杞种的枸杞岛种质。利用全长转录组序列可以高质量实现枸杞SSR标记开发,新开发的23对引物后续可用于枸杞种质遗传多样性分析和分子标记辅助育种工作。     

白及种质资源及其近缘种的SSR指纹图谱研究

白及(Bletilla striata Rchb.)为中国珍稀濒危药用植物,野生资源枯竭,混伪种繁多。该研究基于SSR标记技术对16个地区48份白及(Bletilla striata Rchb.)样品和4份黄花白及(Bletilla ochracea Schltr.)、4份小白及(Bletilla formosana(Hayata)Schltr.)、4份华白及(Bletilla sinensis(Rolfe)Schltr.)样品进行遗传多样性分析,构建白及种质资源的SSR指纹图谱,并对60份白及样品进行种质资源鉴定,分析白及属种内及其种间的遗传分化特征。结果表明:(1)20对白及SSR引物均能在4个白及属植物中成功扩增,条带清晰且多态性丰富,每对引物的复等位基因数(Na)在4~9之间,等位基因数(Na)总和为127,平均为6.35。(2)筛选出基因型丰富、多态性信息含量(PIC)高的7对白及SSR引物(BJSSR01、BJSSR14、BJSSR15、BJSSR16、BJSSR18、BJSSR19、BJSSR22)构建的白及SSR指纹图谱能将白及属各种质资源清楚分开。(3)白及属在种间水平均有较高的遗传多样性(Na=6.35,I=1.429 1,h=0.706 8),物种间遗传分化强烈(Gst=0.44),物种间的基因流较弱(Nm=0.475 3)。(4)UPGMA聚类分析表明,60份供试样品明显聚为4大支,同一物种的个体首先聚在一起,这与形态学分类基本一致;不同来源地的样品种内和种间的亲缘关系有明显差异,地理距离较近的白及样品具有较近的遗传关系。     

基于SSR分子标记分析云南月季种质资源亲缘关系(英文)

利用简单重复序列SSR(simple sequence repeat)标记技术对48份月季种质资源(包括14份野生种、20份古老月季品种和14份栽培品种)的遗传多样性和亲缘关系进行了分析.结果表明,(1)18对SSR引物在18个SSR位点上共检测到160个等位基因,每一位点的等位基因变幅为6～13个,平均8.9个,材料间遗传相似系数变化范围为0.157 8～0.754 9,表明在分子水平上云南月季种质资源具有丰富的遗传多样性.(2)聚类分析结果显示,在相似系数为0.44处,可将 14个野生种明显分为6个组,这与植物形态学分类结果上基本一致;在遗传相似系数为0.40水平上将48份供试材料分为八大组群.(3)亲缘关系分析结果显示,5个野生种和所有古老月季品种与大多数栽培品种的亲缘关系较近.     

辣椒种质遗传多样性的RAPD和ISSR及其表型数据分析

用RAPDI、SSR分子标记及28个表型性状数据对辣椒属5个栽培种的13份材料进行了分析,结果表明:23条RAPD引物共扩增出209条带,平均每个引物扩增出9.09条,多态性位点比率为83.73%;16条ISSR引物共扩增出94条带,平均每个引物扩增出5.88条,多态性位点比率为79.79%.与RAPD相比,ISSR标记检测到的有效等位基因数(Ne)及Shannon多样性指数(I)、遗传离散度(Ht)和遗传分化系数(Gst)等遗传多样性参数都较大,多态性位点比例在亲缘关系较近的一年生辣椒(Capsicum annuum)种内较高,说明ISSR有更高的多态性检测效率,并且适合亲缘关系较近的种群间遗传多样性分析.基于RAPDI、SSR的聚类与基于表型数据的聚类之间存在极显著正相关,且都能将C.annuum与其它栽培种区分开来.     

基于SSR标记的花椰菜和青花菜遗传多样性分析

选用30对SSR引物,利用毛细管电泳荧光检测技术对收集和引进的花椰菜、青花菜、宝塔菜(又叫罗马花椰菜)和近缘野生种及地方种共计187份材料的遗传多样性进行分析,进一步明确了花椰菜、青花菜、地方种和近缘野生种与如今栽培种间的遗传差异和亲缘关系,可为优异种质创新和新品种选育提供参考。研究结果表明:30对SSR引物在187份材料的DNA样品中共扩增出313个等位位点,平均每对引物为10.4333个。依据材料的花球性状,将其分为4个类群即花椰菜(类群1,P1～P81)、青花菜(类群2,P82～P147)、宝塔菜(类群3,P148～P154)、近缘野生种及地方种(类群4,P155～P187)。总体来说,类群1、2和3之间的遗传多样性差异较小,类群4的遗传多样性最丰富。系统发育树和群体结构分析较为统一的将187份材料分为了3大组,花椰菜(G1)和青花菜(G2)被清晰地分到了两个极端,而宝塔菜与野生种聚在了一起,和地方种一起归为第3组(G3)。     

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。     

新疆甜瓜地方种质资源遗传多样性的SRAP分析

为研究我国新疆甜瓜地方种质资源亲缘关系及其分类,充分高效的利用种质资源,利用SRAP(sequence-related amplified polymorphism technique)标记对117份中国新疆甜瓜地方品种和28份国内外对照材料进行亲缘关系和遗传多样性分析。结果表明,20对SRAP引物共扩增出224个带,其中多态性谱带216个,多态性比率达96%,平均每对引物扩增的带数和多态性带数分别为11.2个和10.8个,每对引物的多态性信息含量PIC值为0.73~0.94,平均为0.85;不同生态区域供试材料的Nei's基因多样性指数(H)和Shannon's信息指数(I)分别为0.1075~0.2560和0.1569~0.4061,中国新疆的南疆、东疆和北疆均高于其他生态区域供试材料,且以南疆最高,具有非常丰富的遗传多样性;不同生态区域甜瓜种质资源的遗传一致度和遗传距离分别为0.6384~0.9919和0.0081~0.4488,其中南疆、东疆和北疆两两之间的遗传一致度均在0.95以上,遗传距离均在0.04以下,三者之间遗传分化较小;中国新疆甜瓜与印度、西亚、西班牙的甜瓜种质资源亲缘关系较近,与韩国、日本、美国和前苏联的甜瓜种质资源亲缘关系较远。聚类分析结果表明,以遗传相似系数0.548为阈值,145份种质材料可分为3大类群;厚皮甜瓜与薄皮甜瓜间在分子水平上没有严格的界限,两者之间亲缘关系的远近在不同的种质材料间差异很大;117份中国新疆甜瓜地方种质资源可分为A(Ⅰ-1)、B(Ⅰ-2、Ⅰ-3、Ⅰ-5)、C(Ⅰ-6)、D(Ⅱ)等4大类6个亚类群,与传统4个变种10个品种群分类结果不同,但在每个大类或亚类群中属于同一变种或品种群的材料倾向于聚在一起。     

RAPD and ISSR fingerprints as useful genetic markers for analysis of genetic diversity, varietal identification, and phylogenetic relationships in peanut (Arachis hypogaea) cultivars and wild species.

Abstract: Twenty-one random and 29 SSR primers were used to assess genetic variation and interrelationships among subspecies and botanical varieties of cultivated peanut, Arachis hypogaea (2n = 4x = 40), and phylogenetic relationships among cultivated peanut and wild species of the genus Arachis. In contrast with the previous generalization that peanut accessions lack genetic variation, both random and SSR primers revealed 42.7 and 54.4% polymorphism, respectively, among 220 and 124 genetic loci amplified from 13 accessions. Moreover, the dendrograms based on RAPD, ISSR, and RAPD + ISSR data precisely organized the five botanical varieties of the two subspecies into five clusters. One SSR primer was identified that could distinguish all the accessions analysed within a variety. Although the polymorphic index content varied from 0.1 to 0.5 for both ISSR and RAPD markers, primer index values were substantially higher for RAPD primers (0.35-4.65) than for SSR primers (0.35-1.73). It was possible to identify accessions, particularly those of divergent origins, by RAPD and (or) ISSR fingerprints. Based on these results, marker-based genetic improvement in A. hypogaea appears possible. None of the 486 RAPD and 330 ISSR amplification products were found to be commonly shared among 13 species of section Arachis and one species each of sections Heteranthae, Rhizomatosae, and Procumbentes. Dendrograms constructed from RAPD, ISSR, and RAPD + ISSR data showed overall similar topologies. They could be resolved into four groups corresponding to the species grouped in four taxonomic sections. The present results strongly support the view that Arachis monticola (2n = 4x = 40) and A. hypogaea are very closely related, and indicate that A. villosa and A. ipaensis are the diploid wild progenitors of these tetraploid species.     

Abundant Microsatellite Diversity and Oil Content in Wild Arachis Species

The peanut (Arachis hypogaea) is an important oil crop. Breeding for high oil content is becoming increasingly important. Wild Arachis species have been reported to harbor genes for many valuable traits that may enable the improvement of cultivated Arachis hypogaea, such as resistance to pests and disease. However, only limited information is available on variation in oil content. In the present study, a collection of 72 wild Arachis accessions representing 19 species and 3 cultivated peanut accessions were genotyped using 136 genome-wide SSR markers and phenotyped for oil content over three growing seasons. The wild Arachis accessions showed abundant diversity across the 19 species. A. duranensis exhibited the highest diversity, with a Shannon-Weaver diversity index of 0.35. A total of 129 unique alleles were detected in the species studied. A. rigonii exhibited the largest number of unique alleles (75), indicating that this species is highly differentiated. AMOVA and genetic distance analyses confirmed the genetic differentiation between the wild Arachis species. The majority of SSR alleles were detected exclusively in the wild species and not in A. hypogaea, indicating that directional selection or the hitchhiking effect has played an important role in the domestication of the cultivated peanut. The 75 accessions were grouped into three clusters based on population structure and phylogenic analysis, consistent with their taxonomic sections, species and genome types. A. villosa and A. batizocoi were grouped with A. hypogaea, suggesting the close relationship between these two diploid wild species and the cultivated peanut. Considerable phenotypic variation in oil content was observed among different sections and species. Nine alleles were identified as associated with oil content based on association analysis, of these, three alleles were associated with higher oil content but were absent in the cultivated peanut. The results demonstrated that there is great potential to increase the oil content in A. hypogaea by using the wild Arachis germplasm.     

Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut

With the aim to increase the number of functional markers in resource poor crop like cultivated peanut (Arachis hypogaea), large numbers of available expressed sequence tags (ESTs) in the public databases, were employed for the development of novel EST derived simple sequence repeat (SSR) markers. From 16424 unigenes, 2784 (16.95%) SSRs containing unigenes having 3373 SSR motifs were identified. Of these, 2027 (72.81%) sequences were annotated and 4124 gene ontology terms were assigned. Among different SSR motif-classes, tri-nucleotide repeats (33.86%) were the most abundant followed by di-nucleotide repeats (27.51%) while AG/CT (20.7%) and AAG/CTT (13.25%) were the most abundant repeat-motifs. A total of 2456 EST-SSR novel primer pairs were designed, of which 366 unigenes having relevance to various stresses and other functions, were PCR validated using a set of 11 diverse peanut genotypes. Of these, 340 (92.62%) primer pairs yielded clear and scorable PCR products and 39 (10.66%) primer pairs exhibited polymorphisms. Overall, the number of alleles per marker ranged from 1-12 with an average of 3.77 and the PIC ranged from 0.028 to 0.375 with an average of 0.325. The identified EST-SSRs not only enriched the existing molecular markers kitty, but would also facilitate the targeted research in marker-trait association for various stresses, inter-specific studies and genetic diversity analysis in peanut.     

Identification of simple sequence repeats (SSRs) in olive ( Olea europaea L.)

A small insert genomic library of Olea europaea L., highly enriched in (GA/CT)n repeats, was obtained using the procedure of Kandpal et al. (1994). The sequencing of 103 clones randomly extracted from this library allowed the identification of 56 unique genomic inserts containing simple sequence repeat regions made by at least three single repeats. A sample of 20 primer pairs out of the 42 available were tested for functionality using the six olive varieties whose DNA served for library construction. All primer pairs succeeded in amplifying at least one product from the six DNA samples, and ten pairs detecting more than one allele were used for the genetic characterisation of a panel of 20 olive accessions belonging to 16 distinct varieties. A total of 57 alleles were detected among the 20 genotypes at the ten polymorphic SSR loci. The remaining primer pair allowed the amplification of a single SSR allele for all accessions plus a longer fragment for some genotypes. Considering the simple sequence repeat polymorphism, 5.7 alleles were scored on average for each of the ten SSR loci. A genetic dissimilarity matrix, based on the proportion of shared alleles among all the pair-wise combinations of genotypes, was constructed and used to disentangle the genetic relationships among varieties by means of the UPGMA clustering algorithm. Graphical representation of the results showed the presence of two distinct clusters of varieties. The first cluster grouped the varieties cultivated on the Ionian Sea coasts. The second cluster showed two subdivisions: the first sub-cluster agglomerated the varieties from some inland areas of Calabria; the second grouped the remaining varieties from Basilicata and Apulia cultivated in nearby areas. Results of cluster analysis showed a significant relationship between the multilocus genetic similarities and the geographic origin of the cultivars. Received: 2 February 2001 / Accepted: 1 June 2001     

Taxonomic relationships among Arachis sect. Arachis species as revealed by AFLP markers.

Cultivated peanut, Arachis hypogaea L., is a tetraploid (2n = 4x = 40) species thought to be of allopolyploid origin. Its closest relatives are the diploid (2n = 2x = 20) annual and perennial species included with it in Arachis sect. Arachis. Species in section Arachis represent an important source of novel alleles for improvement of cultivated peanut. A better understanding of the level of speciation and taxonomic relationships between taxa within section Arachis is a prerequisite to the effective use of this secondary gene pool in peanut breeding programs. The AFLP technique was used to determine intra- and interspecific relationships among and within 108 accessions of 26 species of this section. A total of 1328 fragments were generated with 8 primer combinations. From those, 239 bands ranging in size from 65 to 760 bp were scored as binary data. Genetic distances among accessions ranged from 0 to 0.50. Average distances among diploid species (0.30) were much higher than that detected between tetraploid species (0.05). Cluster analysis using different methods and principal component analysis were performed. The resulting grouping of accessions and species supports previous taxonomic classifications and genome designations. Based on genetic distances and cluster analysis, A-genome accessions KG 30029 (Arachis helodes) and KSSc 36009 (Arachis simpsonii) and B-genome accession KGBSPSc 30076 (A. ipaensis) were the most closely related to both Arachis hypogaea and Arachis monticola. This finding suggests their involvement in the evolution of the tetraploid peanut species.     

SSR分子标记检测出的花生类型内遗传变异

花生是我国重要的食用油和蛋白质来源作物,鉴定其DNA分子多态性对品种改良和资源评价具有重要的意义。从已公布的花生Genomic-SSR和EST-SSR引物中筛选出34对引物,用来分别鉴定花生4大类型各24份共96份品种资源的分子变异,其中龙生型资源全部来自广西,普通型资源中有11份从国外引进,有13份来自广西和国内其他省市,多粒型资源只有两份来自中国,其他22份分别来自印度、美国和非洲等地,珍珠豆型资源中有22份是来自中国各地的育成品种或农家品种,有2份来自国外。研究结果为:分别有10～16对SSR引物能在4大类型花生资源中扩增出多态性DNA片段;这些多态性SSR引物都具有多位点特性;首次为SSR分子标记设立了一个新的评价指标——区别指数,多态性SSR引物的区别指数最高达0.992;资源间的平均遗传距离,多粒型为0.59,普通型为0.48,珍珠豆型为0.38,龙生型为0.17。根据遗传距离采用最长距离法对4大类型花生资源分别进行了聚类分析,构建了资源间的遗传关系图,花生4大类型可进一步分成不同类群,资源间的亲缘关系与其来源相关。观察到PM15和PMc297的扩增产物具有类型特异性,PM15能在龙生型、普通型和多粒型花生资源中扩增出多态性条带,而在珍珠豆型花生中扩增条带完全相同,PMc297也有相似的扩增结果。由于在多粒型花生资源中检测出的遗传多样性最丰富,研究结果支持西班牙专家Krapovickas 1994年公布的花生栽培种分类系统。总之在花生4大类型内资源中能检测出丰富的SSR分子标记,开发出更多的SSR分子标记将能充分揭示花生分子水平的变异,从而使花生遗传图谱构建、分子标记辅助育种成为可能。     

Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp.

Large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed in peanut (Arachis hypogaea L.) to obtain more informative genetic markers. A total of 10,102 potential non-redundant EST sequences, including 3,445 contigs and 6,657 singletons, were generated from cDNA libraries of the gynophore, roots, leaves and seedlings. A total of 3,187 primer pairs were designed on flanking regions of SSRs, some of which allowed one and two base mismatches. Among the 3,187 markers generated, 2,540 (80%) were trinucleotide repeats, 302 (9%) were dinucleotide repeats, and 345 (11%) were tetranucleotide repeats. Pre-polymorphic analyses of 24 Arachis accessions were performed using 10% polyacrylamide gels. A total of 1,571 EST-SSR markers showing clear polymorphisms were selected for further polymorphic analysis with a Fluoro-fragment Analyzer. The 16 Arachis accessions examined included cultivated peanut varieties as well as diploid species with the A or B genome. Altogether 1,281 (81.5%) of the 1,571 markers were polymorphic among the 16 accessions, and 366 (23.3%) were polymorphic among the 12 cultivated varieties. Diversity analysis was performed and the genotypes of all 16 Arachis accessions showed similarity coefficients ranging from 0.37 to 0.97. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9604-8) contains supplementary material, which is available to authorized users.     

Genomic diversity among sorghum genotypes with resistance to sorghum shoot fly, Atherigona soccata

Host plant resistance is one of the important components for management of sorghum shoot fly, Atherigona soccata. The levels of resistance in cultivated germplasm are low to moderate, and therefore, it is important to identify sorghum genotypes with diverse mechanisms of resistance based on physico-chemical and or molecular markers. We assessed the genetic diversity of 15 sorghum genotypes with different levels of resistance/susceptibility to shoot fly, A. soccata using 93 sorghum simple sequence repeat (SSR) primer pairs and simultaneously characterized for 15 morpho-biochemical traits associated with shoot fly resistance. Of these 93 SSR primer pairs, amplification products from 79, thought to correspond to single-copy loci distributed across all ten sorghum chromosome pairs, showed good polymorphism across the 15 sorghum genotypes. The polymorphic information content (PIC) values of these 79 SSR markers ranged from 0.06 to 0.86. The Principal Coordinate Analyses (PCoA) and cluster analyses based on dissimilarity matrices derived from SSR based allelic variation (Neighbor-Joining distance) and variation in 15 morpho-biochemical traits (based on Gower??s distance), revealed grouping of most susceptible genotypes in single cluster. The improved breeding lines grouped with resistant or susceptible genotypes, based on shared pedigree. Based on these results, three resistant accessions viz., IS 1054, IS 1057 and IS 4664 were found diverse to IS 18551, which is widely used as shoot fly resistance donor. These diverse sources, after further characterization for resistance mechanisms, can be used in breeding programs for improving shoot fly resistance.