利用SSR技术分析我国16种甜玉米的遗传特性

利用SSR分子标记研究16个甜玉米品种的遗传变异。从200对SSR引物中筛选出10对具有稳定多态性的引物,它们在供试材料中共检测出254个位点,每对引物检测位点5-38个,平均为25.4个,得出的平均多态性信息量为0.920 8;据此进行了聚类分析,将16个品种分为3大类。研究表明,SSR分子标记技术可以用于品种间的遗传分析,方便杂交育种品种的选择。     

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。     

中国35个苦荞审定品种EST-SSR指纹图谱构建与遗传多样性分析

核心引物对种质资源遗传多样性分析、品种鉴定、指纹图谱构建等研究具有重要价值。本研究以35个苦荞（Fagopyrum tataricum（L.） Gaertn）审定品种为材料,从91对苦荞EST-SSR引物中筛选出50对多态性引物。综合考虑引物多态性信息量（PIC）大小、鉴别力（DP）,筛选出等位变异位点数在2~4,PIC值在0.60~0.78之间的6对引物（SSR9007、SSR6873、SSR7642、SSR2234、SSR6789、SSR68216）构建了供试品种的分子指纹图谱。遗传多样性聚类分析结果表明,供试品种的相似系数为0.50~0.99。当遗传相似系数为0.60时,可将供试品种分为4大类群,其中54.3%的供试品种被聚为一类,表明苦荞审定品种遗传组成差异较小,遗传基础狭窄。聚类结果表明各类群间没有明显的地域分布趋势,但能较好的反映供试品种间的亲缘关系。     

甘蓝型特高含油量油菜种质资源及主栽品种指纹图谱构建

本研究选择特高含油量资源7份,与中国各油菜主产区具有代表性的主栽品种16份,利用SSR多引物组合法开展指纹图谱构建研究。选择多态丰富、图谱清晰稳定且来自不同连锁群的引物28对,对所有材料进行指纹图谱分析,共获SSR指纹条带302条,其中多态性条带为279条,每引物所获条带6-16条,平均10.79条,平均多态率92. 38%,通过指纹图谱将所有材料有效地区别开来。用非加权类平均法（UPGAM）聚类分析显示：高油材料之间以及高油材料与主栽品种之间遗传距离均有较大差异,在遗传距离0.171处可将23份材料分成9个类群,其中7份高油材料分处4个类群,遗传距离差异显著;而其他8份主栽品种被分别聚类在另外5个类群中;所有材料间皆具有丰富的遗传多样性,其中高油材料与主栽品种间遗传差异更大。     

利用SSR标记鉴定番茄种质资源

采用SSR技术,从32对番茄引物中筛选出9对多态性较高的引物,分析了24份番茄种质材料的遗传多态性。9对引物共检测到64条带,其中在每个位点上检测到3～12条带,平均为7．1条。供试材料间遗传距离介于0．031～0．437之间,平均遗传距离为0．198。UPGMA分类结果将24份材料分为抗病毒材料和易感病毒材料两大类,每大类进一步又分为小果型和中大果型两亚类。归类有较明显的遗传类型的趋同性,而与来源地没有相关性。     

SSR分子标记在山茶属观赏资源遗传多样性研究中的应用

采用微卫星(SSR)分子标记的方法,利用20对SSR引物对33份山茶属资源(含种和品种)的DNA样品进行了PCR扩增,从中筛选出10对扩增效果较好的SSR引物,并对33份资源进行了遗传多样性分析。结果显示:10对引物在33个植物材料中共检测出123个等位基因,每个SSR位点的等位基因数为3~22个,SSR2引物检测到的等位基因数量最多,达22个,平均每对引物含有12.3个等位基因,平均多态性信息量为0.74,变化范围为0.06~0.96。利用遗传距离矩阵按UPGMA方法进行聚类,结果表明33份植物材料可分为9个分支,很好的区分了品种间的亲缘关系,可为杂交育种的组合选择提供理论基础。不同花型的山茶属植物在10个微卫星位点上共发现42个特异等位基因,可能与不同的花型性状有关。     

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。     

利用SSR标记研究茄子种质资源遗传多样性

本研究利用105个SSR分子标记分析了50份茄子种质资源遗传多样性。105对SSR引物中筛选出的20对多态性含量较高的引物,在50份茄子品种组成的群体中共检测出91个等位基因,平均每个基因位点检测到4.55个等位基因。PIC的变幅为0.202 1~0.735 6,平均为0.401 2。根据遗传距离并结合UPGMA聚类分析可将50份种质分为10个类群。SSR分子标记与品种资源性状聚类分析基本一致。     

冀鲁豫花生育成品种的遗传多样性分析

以冀鲁豫三省不同地域的41个花生育成品种为材料,利用SSR分子标记结合田间表型鉴定、聚类分析等方法对其遗传多样性进行了研究。结果表明,21对SSR引物对41个花生育成品种进行了扫描,共检测到52个等位变异,每个位点2～4个,平均2.5个,Shannon信息指数变幅为0.21～1.40,平均为0.73,聚类分析显示在阈值为5.54可将供试品种分为3大类群7个亚类。不同品种9个农艺性状变异系数在13.16%～186.49%之间,基于农艺性状的聚类分析结果显示在阈值为5.48时可以将供试品种分为6大类群11个亚类,各大类群间品种的农艺性状表现各具特点。     

基于SSR标记的彩色马铃薯亲缘关系分析及指纹图谱构建

为了探究彩色马铃薯种质资源的遗传背景,该试验共选用22对SSR标记引物,对33份彩色马铃薯品种(系)进行遗传多样性分析以及指纹图谱构建。结果表明:(1)22对引物可扩增得到95个等位位点,其中82个为多态性位点,多态性比率达到86.31%;多态信息量(PIC)从0.168 7(STM1053)到0.991 9(STI033),平均为0.8411。(2)UPGMA聚类分析表明,在相似系数0.71处,33份供试材料分为4个主要聚类群,不同聚类群之间具有较大的遗传差异。(3)利用STM0031、STM0030、STI014、STM1029、STI001共5对SSR标记引物构建了33份彩色马铃薯材料的分子标记指纹图谱。该研究结果为彩色马铃薯育种亲本组配奠定了理论基础,有助于彩色马铃薯种质资源的快速鉴定。     

我国茶树主要骨干亲本及其衍生品种(系)的SSR分析

铁观音、黄棪和福鼎大白茶分别是我国乌龙茶和红绿茶育种中的骨干亲本,由他们衍生出了一系列的优良品种,研究他们的遗传多样性及构建指纹图谱将有助于今后茶树育种工作中骨干亲本的合理利用和品种权的保护。本研究利用40对SSR引物对我国乌龙茶骨干亲本铁观音、黄棪及其衍生品种(系)和红绿茶骨干亲本福鼎大白茶及衍生品种进行了研究。结果表明,34份供试品种(系)的基因多样性指数（H）为0.54,平均遗传距离0.58,表明我国茶树主要骨干亲本及其衍生品种(系)具有较高的遗传多样性水平和较大的遗传变异,且90%的遗传多样性来自品种之间的遗传差异。聚类结果表明两套品种(系)各自聚为一类,遗传结构分析也显示两套品种(系)之间存在明显的差异。利用其中5对引物组合构建了供试材料的数码指纹图谱。     

Assessment of genetic variation among commercial tomato (Solanum lycopersicum L) varieties using SSR markers and morphological characteristics

Simple sequence repeats (SSR) is one of the most suitable markers for variety identification as it has great discrimination power for varieties with limited genetic variation. Genetic characterization of commercial tomato varieties was investigated using 33 SSR markers and 22 morphological traits. Thirty three SSR primer pairs were screened for 63 tomato varieties. A total of 132 polymorphic amplified fragments were obtained by using 33 SSR markers. The average polymorphism information content (PIC) was 0.628 ranging from 0.210 to 0.880. One hundred thirty two SSR loci were used to calculate Jaccard's distance coefficients for UPGMA cluster analysis. A clustering group of varieties, based on the results of SSR analysis, were categorized into cherry and classic fruit type varieties. Almost all of the varieties were discriminated by SSR marker genotypes. The relationship between morphological and molecular data for 33 varieties out of 63 varieties was analyzed using Mantel matrix correspondence test. The correlation value between two methods was 0.644. However, SSR based dendrogram topology showed some similar form with morphological traits at the two main groups. Therefore, these markers may be used wide range of practical application in variety identification and pre-screening for distinctiveness test of tomato varieties.     

苜蓿SSR遗传距离与杂种优势的相关性分析

利用SSR标记技术对40份苜蓿材料（6个雄性不育株系和34个苜蓿品种）的遗传距离进行分析,并利用其中的6个不育株系与14个苜蓿品种测交,进一步对遗传距离(GD)、产量配合力与杂种优势效应进行相关性分析。结果表明,25对SSR引物共扩增出189条谱带,其中多态性条带136条,平均多态性位点百分率为69.23%;40份苜蓿材料的遗传距离为0.1818～0.9091,平均0.4544;各亲本一般配合力及GD均与杂种优势效应存在显著正相关,其中亲本一般配合力与杂种优势的相关性要高于GD.因此,仅以SSR遗传距离还不足以准确的组配强优势组合,需结合各性状配合力的分析,以充分发挥杂种优势效应。     

Diversity in commercial varieties and landraces of black eggplants and implications for broadening the breeders' gene pool

Black‐coloured eggplants (Solanum melongena) represent the commercially most important group of eggplants in Europe and North America. Most of the modern varieties of black eggplants correspond to F₁ hybrids, which at the same time constitute an elite gene pool for the development of new varieties. However, there are many black landraces and old varieties, which could be useful as sources of variation for black eggplant breeding programmes as well as for the broadening of the genetic diversity of the breeders’ gene pool. We have studied the morphological and molecular [amplified fragment length polymorphism and simple sequence repeat (SSR)] diversity in a collection of 38 black eggplant accessions, including commercial (modern F₁ hybrid and old nonhybrid) varieties and landraces as well as in six nonblack control eggplants, from different origins. The results show that black eggplants contain a considerable morphological and molecular diversity, but commercial varieties, and in particular F₁ hybrids, display a reduced morphological and molecular diversity when compared with landraces. The principal components analysis morphological and principal coordinates analysis molecular analyses show that commercial F₁ hybrids group together, indicating that they share a common and narrow gene pool. Commercial F₁ hybrids present a series of productive advantages, like early production, intense black colour (low L*, a* and b*) values and absence of fruit calyx prickles. However, several of the landraces and old nonhybrid varieties studied present a high yield as well as other traits of interest for eggplant breeding. Furthermore, given the low genetic diversity of F₁ hybrids and the moderate level of SSR heterozygosity found in these materials (0.382), introduction of black landraces and old varieties in the present breeding programmes could contribute to broadening the gene pool used by breeders and this could help increase the heterosis for yield of F₁ hybrids, which is greatly favoured by high heterozygosity levels.     

Identifying loci influencing 1,000-kernel weight in wheat by microsatellite screening for evidence of selection during breeding

Chinese wheat mini core collection (262 accessions) was genotyped at 531 microsatellite loci representing a mean marker density of 5.1 cM. One-thousand-kernel weights (TKW) of lines were measured in five trials (three environments in four growing seasons). Structure analysis based on 42 unlinked SSR loci indicated that the materials formed two sub-populations, viz., landraces and modern varieties. A large difference in TKW (7.08 g, P<0.001) was found between the two sub-groups. Therefore, TKW is a major yield component that was improved in the past 6 decades; it increased from a mean 31.5 g in the 1940s to 44.64 g in the 2000s, representing a 2.19 g increase in each decade. Analyses based on a mixed linear model (MLM), population structure (Q) and relative kinship (K) revealed 22 SSR loci that were significantly associated with mean TKW (MTKW) of the five trials estimated by the best linear unbiased predictor (BLUP) method. They were mainly distributed on chromosomes of homoeologous groups 1, 2, 3, 5 and 7. Six loci, cfa2234-3A, gwm156-3B, barc56-5A, gwm234-5B, wmc17-7A and cfa2257-7A individually explained more than 11.84% of the total phenotypic variation. Favored alleles for breeding at the 22 loci were inferred according to their estimated effects on MTKW based on mean difference of varieties grouped by genotypes. Statistical simulation showed that these favored alleles have additive genetic effects. Frequency changes of alleles at loci associated with TKW are much more dramatic than those at neutral loci between the sub-groups. The numbers of favored alleles in modern varieties indicate there is still considerable genetic potential for their use as markers for genome selection of TKW in wheat breeding. Alleles that can be used globally to increase TKW were inferred according to their distribution by latitude and frequency of changes between landraces and the modern varieties.     

An estimation of the minimum number of SSR loci needed to reveal genetic relationships in wheat varieties: Information from 96 random accessions with maximized genetic diversity

Genetic relationships among common wheat varieties from the 10 wheat growing regions of China were assessed using SSR markers. The wheat varieties included 33 modern varieties and 63 landraces selected from the national gene bank collection of China. One hundred and four pairs of selected primers detected a total of 802 alleles, of which 234 were specific to A genome, 309 to B genome, and 221 to D genome. The average genetic richness per locus (A _ij /loci) for A, B and D genomes were 6.88, 7.92 and 7.62, respectively. Their average genetic dispersion indices (H _t ) were 0.637, 0.694 and 0.656, respectively. The B genome showed the highest genetic diversity among the three wheat genomes. The landraces had a higher genetic diversity than the modern varieties, and the major difference between the landraces and the modern varieties in China existed in the D genome, followed by B and A genomes. The majority of the accessions (65.6%) had heterogeneity at the 112 loci detected. The highest heterogeneity locus percentages were 9.09 and 12.73 in the modern varieties and the landraces, respectively. SSR data were analyzed with NTSYS-pc software. The genetic similarities between accessions were estimated with the DICE coefficient. The accessions clustered into two groups, the modern varieties and the landraces by the un-weighted pair-group method using arithmetic average (UPGMA). The trend of correlation coefficients between genetic similarity matrices based on different numbers of random alleles and that of 802 alleles showed that 550 alleles were sufficient to construct a robust dendrogram. The separated simulations from six sub-samples revealed that 550 alleles were the minimum number required to confidently determine the genetic relationships. It was shown that the number of alleles (loci) needed do not have a strong association with the number of wheat lines in the sample size. These data suggested that 73 loci with good polymorphism are needed to reflect genetic relationships among accessions with more than 90% certainty. In the dendrogram, most accessions from the same wheat region were clustered together, and those from geographically adjacent regions usually appeared in the same small group. This indicated that genetic diversity of Chinese common wheat has a close association with their geographic distribution and ecological environment.     

甘、青两省春小麦遗传多样性演变

对甘、青两省自20世纪40年代以来生产上曾大面积应用的200多个春小麦地方品种和育成品种资料进行了分析,结果表明,19个形态性状,5个农艺性状和2个品质性状都存在着广泛的遗传多样性,虽然育成品种农艺性状和品质性状的遗传多样性总体上大于地方品种,但是从20世纪60年代开展春小麦杂交育种工作之后,育成品种形态性状,农艺性状和品质性状遗传多样性呈下降趋势,评价育种对小麦遗传多样性的影响,不能足将地方品种和育成品种的遗传多样性作一简单比较就得出结论,而是应该在遗传多样性演变的动态过程中去研究。     

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。     

SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato

Background

The tomato (Solanum lycopersium L.) is the most widely grown vegetable in the world. It was domesticated in Latin America and Italy and Spain are considered secondary centers of diversification. This food crop has experienced severe genetic bottlenecks and modern breeding activities have been characterized by trait introgression from wild species and divergence in different market classes.

Results

With the aim to examine patterns of polymorphism, characterize population structure and identify putative loci under positive selection, we genotyped 214 tomato accessions (which include cultivated landraces, commercial varieties and wild relatives) using a custom-made Illumina SNP-panel. Most of the 175 successfully scored SNP loci were found to be polymorphic. Population structure analysis and estimates of genetic differentiation indicated that landraces constitute distinct sub-populations. Furthermore, contemporary varieties could be separated in groups (processing, fresh and cherry) that are consistent with the recent breeding aimed at market-class specialization. In addition, at the 95% confidence level, we identified 30, 34 and 37 loci under positive selection between landraces and each of the groups of commercial variety (cherry, processing and fresh market, respectively). Their number and genomic locations imply the presence of some extended regions with high genetic variation between landraces and contemporary varieties.

Conclusions

Our work provides knowledge concerning the level and distribution of genetic variation within cultivated tomato landraces and increases our understanding of the genetic subdivision of contemporary varieties. The data indicate that adaptation and selection have led to a genomic signature in cultivated landraces and that the subpopulation structure of contemporary varieties is shaped by directed breeding and largely of recent origin. The genomic characterization presented here is an essential step towards a future exploitation of the available tomato genetic resources in research and breeding programs.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-835) contains supplementary material, which is available to authorized users.     

Genetic diversity in Chinese modern wheat varieties revealed by microsatellite markers

Genetic diversity of 1680 modern varieties in Chinese candidate core collections was analyzed at 78 SSR loci by fluorescence detection system. A total of 1336 alleles were detected, of which 1253 alleles could be annotated into 71 loci. For these 71 loci, the alleles ranged from 4 to 44 with an average of 17.6, and the PIC values changed from 0.19 to 0.89 with an average of 0.69. (1) In the three genomes of wheat, the average genetic richness was B>A>D, and the genetic diversity indexes were B>D>A. (2) Among the seven homoeologous groups, the average genetic richness was 2=7>3>4>6>5>1, and the genetic diversity indexes were 7>3>2>4>6>5>1. As a whole, group 7 possessed the highest genetic diversity, while groups 1 and 5 were the lowest. (3) In the 21 wheat chromosomes, 7A, 3B and 2D possessed much higher genetic diversity, while 2A, 1B, 4D, 5D and 1D were the lowest. (4) The highest average genetic diversity index existed in varieties bred in the 1950s, and then it declined continually. However, the change tendency of genetic diversity among decades was not greatly sharp. This was further illustrated by changes of the average genetic distance between varieties. In the 1950s it was the largest (0.731). Since the 1960s, it has decreased gradually (0.711, 0.706, 0.696, 0.695). The genetic base of modern varieties is becoming narrower and narrower. This should be given enough attention by breeders and policy makers.