Investigating the genetic diversity of several varieties of Iranian tomato (Solanum lycopersicum) using RAPD and ISSR molecular markers

Background:Numerous studies have demonstrated the existence of approximately 7,500 genetic tomato varieties worldwide.Hence,it is crucial to assess the genetic diversity among tomato cultivars.This study aimed to investigate the genetic diversity of selected Iranian tomato cultivars(Solanum lycopersicum)using RAPD and ISSR molecular markers.Method:Ten RAPD primers and ten ISSR primers were employed to assess the genetic diversity among 10 tomato cultivars:Matin,RFT 112,Hirad,Golsar,Raha,Hengam,Hedah,Fasa,JS12,and Emerald.Data analysis involved the UPGMA algorithm and NTYSYSpc software.Results:RAPD analysis revealed close genetic proximity between Fasa and JS12,as well as between Raha and Hadieh.Conversely,the RFT 112,Hengam,Hirad,and Emerald cultivars exhibited significant genetic diversity within this group.ISSR primer analysis identified Hengam as the most diverse variety,while Matin,Emerald,and Vibrid,as well as Raha and JS12,displayed genetic similarities with minimal observed diversity.Furthermore,the overall analysis of the cultivars using RAPD and ISSR markers indicated that Hengam exhibited the highest diversity among all the varieties.Notably,Raha and JS12 demonstrated limited diversity in this analysis.Conclusion:This research demonstrates substantial genetic diversity among the investigated tomato varieties,with Hengam displaying the highest diversity within this group.Furthermore,ISSR markers proved more effective in determining genetic diversity in tomato plants.

Analysis of Genetic Diversity in Cultivated and Wild Tomato Varieties in Chinese Market by RAPD and SSR

RAPD and SSR were applied to assess genetic diversity in 61 tomato varieties from different species （Solanum lycopersicum L., hirsutum. Humb L., pimpinellifolium Miller L., chilense Dun. L., chmielenskii L., peruvianum Miller L., parvuflorum Miller L.）. 2 062 and 869 clear fragments were amplified by RAPD and SSR, respectively. On the other hand, more polymorphic products were found by SSR as compared to RAPD, i.e., 100 and 43.84%, respectively. In addition, a higher value of the average similarity coefficient and lower PIC value were reflected in RAPD （0.79, 0.407） compared to SSR （0.56, 0.687）. It can be inferred that SSR was a higher effective marker than RAPD to assess genetic diversity in tomato accessions. Similarly, the genetic base of tomato varieties in Chinese market was narrow. It is suggested that wild tomato varieties should be used to enrich the genetic base of the cultivated tomato varieties.

Genetic diversity of Ustilago hordei in Tibetan areas as revealed by RAPD and SSR

Covered smut, which is caused by Ustilago hordei（Pers.） Lagerh., is one of the most damaging diseases of highland barley（Hordeum vulgare Linn. var. nudum Hook. f） in Tibetan areas of China. To understand the molecular diversity of U. hordei, a total of 27 isolates, which were collected from highland barley plants from Tibet, Sichuan, Qinghai, and Gansu provinces/autonomous region, were analyzed using random amplified polymorphic DNA（RAPD） and simple sequence repeat（SSR） markers. Among the 100 RAPD primers used, 24 primers exhibited polymorphism. A total of 111 fragments were amplified, of which 103 were polymorphic with a polymorphic rate of 92.79%. The average observed number of alleles（Na）, effective number of alleles（Ne）, Nei＇s genetic diversity（H）, Shannon＇s information index（I） and polymorphism information content（PIC） value in the RAPD markers were 1.9279, 1.5016, 0.2974, 0.4503 and 0.6428, respectively. For the SSR markers, 40 of the 111 primer pairs exhibited polymorphism and provided a total of 119 bands, of which 109 were polymorphic and accounted for 91.60% of the total bands. The Na, Ne, H, I and PIC values of the SSR markers were 1.9160, 1.4639, 0.2757, 0.4211 and 0.4340, respectively. The similarity coefficients ranged from 0.4957 to 0.9261 with an average of 0.7028 among all the 27 isolates used. The dendrogram, which was developed based on the RAPD and SSR combined marker dataset showed that the 27 U. hordei isolates were divided into 3 clusters at similarity coefficient of 0.7314. We determined that RAPD and SSR markers can be successfully used to assess the genetic variation among U. hordei isolates. The RAPD markers revealed higher levels of genetic polymorphism than did the SSR markers in this study. There existed a moderate genetic difference among isolates. The molecular variation and differentiation was somewhat associated with geographical origin but not for all of the isolates.

Research Progress of Molecular Markers in Genetic Diversity of Rapeseed

In recent years,with the continuous improvement and development of molecular technology in the application process,different types of DNA molecular markers have made rapid progress in the study of genetic diversity of rapeseed. The study of genetic diversity is conducive to the correct formulation of the strategy of collecting and in situ preservation of genetic resources of rapeseed,and it is the genetic basis for the improvement of rapeseed varieties. This article mainly starts with the three DNA molecular markers( SSR,RAPD,AFLP) widely used in the study of genetic diversity of rapeseed. By introducing the application principles and characteristics of SSR,RFPD and AFLP molecular markers,research progress of these three marker technologies in genetic diversity of rapeseed is briefly described.

A Comprehensive Analysis of Genetic Diversity and Relationships of 13 Sweet Sorghum Varieties as Energy Sources

To investigate the genetic diversity and relationships among the sweet sorghum varieties as energy sources currently bred in China, 13 sweet sorghum varieties were selected for comprehensive analysis through observations of 31 biological traits and examinations of RAPD and SSR molecular markers. The numerical analysis showed that the differences in biological traits existed among 13 varieties, and the genetic distance (DIST) ranged from 0.787 to 2.221, and the two varieties from Inner Mongolia and Xinjiang were distinctly separated from all other varieties. A total of 22 polymorphism primers were obtained from the screening using RAPD marker analysis. The polymorphism rate was 58.33%, and the genetic similarity (GS) coefficients among the studied cultivars ranged from 0.694 to 0.896. Cluster analysis results indicated that the three varieties from Inner Mongolia, Xinjiang and Heilongjiang exhibited significant genetic differences from the other varieties. SSR marker analysis using 31 selected pairs of polymorphic primers showed that the polymorphism rate of amplified fragments was 78.64%, and GS coefficients among the tested cultivars were 0.534 to 0.971. Cluster analysis showed that variety No. 12 from Xinjiang and variety No. 7 from Inner Mongolia clustered into one group, and variety No. 6 from Heilongjiang was in a single group. The other ten varieties were grouped into another separate cluster. The results based on combined data displayed a similar trend with results from the three individual data analyses, but could more comprehensively and objectively reflect the fundamental genetic differences among these varieties. In summary, certain genetic differences exist among the varieties tested from different regions or different breeding institutions. However, varieties from the same region, especially those from the same breeding institution, exhibited small genetic variations and high genetic similarities. At present, more attention should be paid to discovery and innovation in the breeding of sweet sorghum varieties.

37份洋葱遗传多样性的RAPD和SSR分析

利用RAPD和SSR方法研究了37份洋葱种质资源间的遗传多样性,并对这2种分子标记方法进行了比较。结果表明,从15个RAPD引物中,检测到61条有多态性的带;利用筛选出的8对SSR引物,检测到41条多态性带;RAPD和SSR标记均有很高的多态性,RAPD多态性带所占比例为84.7%,SSR位点检测出的平均有效等位基因数为3.75;SSR标记的有效等位基因数、Nei's基因多样性指数及Shannon信息指数的平均值均高于RAPD标记。UPGMA聚类分析表明,2种标记均可将37份洋葱种质资源划分为四大类,聚类结果相似。RAPD和SSR标记均适于洋葱种质的遗传多样性研究,但SSR标记效果较好。

SSR和RAPD 2种分子标记对昆明西山野生蘡薁葡萄资源遗传多样性分析比较

本研究分别应用SSR和RAPD 2种分子标记技术对来自云南昆明西山5个近距离群体的41份野生蘡薁葡萄(Vitis bryoni-aegoliaBge)样品进行遗传结构分析,以比较2种方法评价同种野葡萄各群体间遗传多样性的差异。结果发现,2种分子标记得到的基因分化系数(Gst)均小于0.5,基因流较大(Nm>1),表明在较小的地理范围内,同一物种不同群体间存在的遗传分化小,遗传变异发生在群体内的概率远大于在群体间。但RAPD分子标记能更灵敏的体现各个近距离群体间的差异,得到的遗传距离与实际群体间的物理距离呈正相关(r=0.981,P=0.019<0.05)。对远距离的同种野生葡萄以及栽培葡萄进行研究后,发现SSR和RAPD标记均能有效地把不同品种的葡萄资源分开,表现为同种野生葡萄处于遗传距离较近的位置上,聚类为总的一枝,而人工栽培品种处于聚类树状图的另一分枝,遗传距离较远。

EST-SSR和RAPD标记检测油菜(Brassica napus)遗传多样性

亲本选配是杂种优势利用中强优势组合配制的关键环节，遗传距离决定优势强弱。本文采用EST—SSR和RAPD两种分子标记技术检测甘蓝型油菜4份不育系、3份保持系、10份恢复系和11份常规品种共35个材料的遗传多样性及与杂种优势的关系。结果共检测到399个等位位点，其中130个等位变异，占总检测位点的32．57％。NTSYS软件聚类分析结果表明：35份材料遗传距离范围为0．0280～0．2801，在遗传距离（GD）0．1401下分为6类，3个不育系Ogu、Polima和陕2A聚在第V类，Xin1 CMS（新1号不育系）遗传距离较远；不育系之间的遗传差异比不育系与保持系、恢复系及常规品种之间小，基本反映了品种（系）的遗传基础和系谱来源。

不同地理种群马铃薯甲虫SSR、RAPD遗传多样性分析

【目的】对哈萨克斯坦共和国毗邻的中国新疆伊犁河谷地区马铃薯甲虫发生区进行遗传多样性分析,研究不同地理种群的遗传分化状况,反演发生区马铃薯甲虫的传播路径。【方法】利用SSR、RAPD分子标记方法对不同地理种群的马铃薯甲虫进行遗传多样性分析。【结果】通过筛选8对有效引物进行SSR扩增得到的Shannon’s信息指数和平均基因多样性分别为(1.422 6±0.396 7)和(0.543 8±0.083 5),Nei's基因分化系数Fst为0.206 8,即20.68%、79.32%的遗传变异存在于种群内。运用RAPD分子标记方法扩增出28个条带,其中特异性条带14个,多态位点百分率为50%,Shannon’s信息指数和平均基因多样性为(0.215 9±0.129 2)和(0.113 8±0.084 2),RAPD分子标记得出的Gst值为0.163 7,即16.37%的遗传变异存在于种群间,83.67%的遗传多样性存在于种群内。运用UPGMA聚类分析得知SSR分子标记方法中,中国东北与西北地区分为两支,乌昌地区与塔城地区聚类;RAPD聚类分析得到的结果与SSR基本一致,个别地理种群聚类结果与地理位置存在一定偏差。【结论】SSR分子标记方法重复性好且较为高效,供试马铃薯甲虫样本遗传变异性较低,RAPD方法与SSR方法研究结果也进一步验证了马铃薯甲虫在中国新疆的传播路径,即马铃薯甲虫从哈萨克斯坦共和国的塔尔巴哈台地区传入中国新疆塔城市,之后沿天山北坡逐步向东扩散。

洮湖日本沼虾遗传多样性的RAPD和SSR分析

利用RAPD技术和微卫星(SSR)技术对洮湖日本沼虾群体的遗传多样性进行了分析。RAPD分析结果表明,每个随机引物扩增出3～8条带,片段大小在100～1 000 bp之间,17个引物共扩增出95条清晰条带;其中48条表现为多态,多态位点比例为16.67%～66.67%,群体遗传杂合度为0.196 0,Shannon多样性指数为0.257 6。微卫星分析结果表明,5个微卫星基因座共检测到50个等位基因,群体平均观测杂合度为0.742 5,平均期望杂合度为0.776 6,平均多态信息含量为0.574 0。2种研究结果表明,洮湖日本沼虾种质资源状况良好,遗传多样性较丰富。

不同产地人参种质资源RAPD和SSR分析

以15个产地人参种质资源为试材,采用RAPD和SSR分子标记技术对其遗传多样性进行分析。结果表明：2种分子标记均能揭示不同地区人参种质间的遗传多样性。共筛选出11条RAPD随机引物,平均每条引物可扩增出3~17条DNA片段,共扩增出104条清晰条带,多态性条带100条,多态性百分率为96.15%,揭示供试材料间遗传相似系数（GS）为0.505 3~0.989 5,平均值为0.760 4。筛选出5对SSR引物,平均每对引物可扩增出1~8条DNA片段,共扩增出38条清晰条带,多态性条带35条,多态性百分率为92.11%,揭示供试材料间遗传相似系数（GS）为0.400 0~0.960 0,平均值为0.742 1。RAPD和SSR标记的聚类分析在分类上稍有差异,但总体趋势一致,RAPD、SSR及RAPD＋SSR均将样品聚为三大类,均能揭示它们之间的亲缘关系,为人参种质资源的收集与利用奠定了基础。

落叶松杂种F_1代群体遗传多样性的RAPD、SSR分析

为给落叶松杂种F1代进化潜力的研究提供资料,利用RAPD、SSR标记分析了日本落叶松×兴安落叶松杂种F1代147个个体的遗传多样性。RAPD遗传多样性分析结果为,有效等位基因数平均值1.669 1,Nei遗传多样度平均值为0.395 5,Shannon多样性指数平均值为0.583 1;SSR遗传多样性分析结果为,有效等位基因数平均值1.689 2,Nei遗传多样度平均值为0.399 8,SSR标记的Shannon多样性指数平均值0.587 0。SSR标记和RAPD标记所揭示的杂种F1群体遗传多样性水平各指数值基本一致,且都表明与日本落叶松杂交后,杂种F1群体在遗传多样性上高出兴安落叶松。

引种粗皮桉种源遗传多样性的RAPD与SSR分析

利用RAPD和SSR分子标记对粗皮桉7个种源遗传多样性进行分析,10条RAPD引物共扩增出157个位点,其中多态位点145个,多态性百分率92.34%,遗传一致度范围0.906 1~0.971 4;21对SSR引物共检测到252个等位变异,平均等位基因数为12个,平均有效等位基因数为4.6个,遗传一致度范围0.727 1~0.908 0。2种标记遗传一致度相关分析表明呈显著相关,说明2种标记分析粗皮桉遗传多样性具有较高一致性。聚类分析显示,RAPD标记将粗皮桉7个种源被划分为4个类群,SSR标记将粗皮桉7个种源被划分为3个类群,SSR标记聚类结果与粗皮桉种源地理分布密切相关。RAPD和SSR分子标记均适合粗皮桉遗传多样性分析,SSR标记更具可靠性。

RAPD和SSR标记在玉米遗传多样性分析中的应用

利用RAPD和SSR两种标记方法研究了16个玉米自交系的遗传多样性,并对这两种分子标记系统进行了比较。结果表明,利用15条RAPD引物,检测到了126条有多态性的带。用筛选出的20对SSR引物,检测到69个等位基因。RAPD和SSR分子标记均有很高的多态性,RAPD多态性带比例数86%,SSR位点检测出的平均等位基因数3. 4个。RAPD分子标记结果将16个玉米自交系划分为4组,SSR分子标记将其划分为5组。与系谱分析基本一致,两种分子标记划分的结果也相似。研究认为,RAPD、SSR两种分子标记系统均适合于玉米种质的遗传多样性研究。

加工番茄种质资源的SSR分析

为探明加工番茄种质资源间的亲缘关系，利用SSR标记对20份加工番茄品种及育种材料进行了多样性分析。结果表明：从49对SSR引物中筛选出12对扩增稳定、条带清晰且多态性丰富的引物进行分析，共获得43个位点，多态性位点为37个，多态位点比率86％；供试材料间的遗传相似系数介于0．419～1．000之间，说明加工番茄种质资源间存在一定的遗传差异；通过UPGMA法聚类分析，将20份材料分为3大类群，其中亲缘关系较远的不同类群间及亚类间的种质资源可作为杂交育种的亲本。

利用SSR分子标记分析番茄的遗传多样性

简单重复序列(SSR)是进行遗传多样性研究的一种有效分子标记。选用来自国内外的番茄材料共36份,利用番茄的SSR引物进行扩增,采用聚类分析方法对供试材料进行了遗传多样性分析。从400对SSR引物中筛选到24对多态性高、扩增稳定、重复性好的引物,利用NTSYS软件进行聚类分析结果显示,36份材料被聚成7大类。

番茄SSR遗传多样性及其品质性状的关联分析

【目的】本文旨在分析番茄资源材料的亲缘关系及它们的遗传多样性,挖掘与番茄品质性状相关的分子标记。【方法】选用37对SSR多态性引物对30份番茄资源材料进行聚类分析,在此基础上采用Tassel3.0GLM方法进行标记位点与品质性状的关联分析。【结果】SSR结果显示,37对SSR引物共检测到102个等位变异位点,各种质遗传相似系数为0.61~0.97。关联分析结果表明与品种性状显著相关的位点有9个。供试材料之间有一定的遗传差异,但遗传背景较狭窄。【结论】利用SSR标记分析了30份番茄资源材料的遗传多样性,30份番茄资源材料在遗传相似系数0.71处被划分为4大类,并通过关联分析模型,找到了9个与总酸、成熟前果色、成熟果色、果面棱沟、番茄红素相关联的标记。

新疆加工番茄品种遗传多样性的SSR分析

选用已筛选出带型稳定的44对SSR引物,对新疆主栽以及美国引进的加工番茄品种进行遗传多样性分析,结果表明:在24个品种间共扩增了283个等位基因,每对引物的等位基因数变化范围在2～17之间,平均为4.422个;有效等位基因为189.638,平均为4.310;每个SSR位点的多态性信息量变化范围为0.140～0.915,平均为0.662;基因型多样性变化范围为0.325～2.620,平均值为1.438;24个品种间的遗传相似系数变幅为0.715～0.924,平均值为0.820,且95%的供试品种其遗传相似系数在0.715～0.800之间,亲缘关系较近。以遗传相似系数为原始数据,按UPGMA方法将供试品种划分为4大类群,结合系谱分析结果表明,新疆的加工番茄品种遗传多样不够丰富,多数品种间的亲缘关系较近,欲进一步提高新疆加工番茄的产量及品质性状还需拓宽亲本选择范围,扩大遗传背景。

马铃薯和番茄晚疫病菌全基因组DNA的RAPD多态性分析

对采集自云南省元谋等9个县的35个马铃薯和番茄晚疫病菌株用RAPD的方法进行了分子指纹的研究。马铃薯晚疫病菌和番茄晚疫病菌全基因组DNA指纹研究结果表明,两类晚疫病菌有丰富的遗传多态性,在不同的相似水平上可以划分为许多不同的遗传组群。来自不同寄主的菌株间有一定的遗传差异,但马铃薯晚疫病菌和番茄晚疫病菌不能完全划分为两个不同的组群,而是交叉分布在不同的遗传组群中。

番茄种质资源遗传多样性的RAPD分析

利用RAPD分子标记技术,对63份番茄种质资源进行了遗传多样性研究。结果表明:从180个RAPD引物当中,筛选出22条稳定性好、多态性强的RAPD引物,共扩增出多态性带207条,多态性条带比率为86.96%,63份番茄栽培品种或品系间的相似系数介于0.28～0.99之间,说明RAPD能很好的对番茄野生种、近缘野生种和栽培种进行多态性分析。采用UPGMA进行聚类分析,得到与生物学分类地位基本一致的结果。