Extent and patterns of RAPD variation in landraces and cultivars of rye (Secale cereale L.) from northern Europe

Little is known about the extent and patterns of distribution of RAPD diversity in outcrossing species. This study is the first step in using RAPD markers to quantify the amount and distribution of genetic variation within and between accessions of 9 landraces and 3 cultivars of cultivated rye from Northern Europe. A high level of RAPD variation was detected, demonstrating the utility of RAPDs for genetic characterisation in rye. The results show that: (1) landraces and improved cultivars maintain roughly the same high levels of RAPD variation, (2) landraces from Norway, Germany and Finland showed the lowest level of variation, probably because of a small amount of seeds from the original samples, (3) most of the RAPD variation was found within rather than between the accessions, which is consistent with the pattern expected for a cross pollinated crop. Both the cluster and the principal coordinates analyses displayed the same pattern of genetic relationship among the accessions studied.     

Assessing the allozyme variation in cultivars and Swedish landraces of rye (Secale cereale L.)

Genetic interpretation and diversity of 9 isozyme loci have been estimated in 7 improved varieties and 19 landraces from Sweden by means of starch gel electrophoresis. The isozyme systems were ACO, DIA, GPI, MDH, PGD and PGM. For the statistic analysis we used the following measures: average number of alleles per locus, percentage of polymorphic loci, average heterozygosity direct count and average heterozygosity Hardy-Weinberg expected unbiased estimate. The measures were made on species and population levels. The distribution of the total genetic diversity among populations was also calculated. To illustrate the genetic relationships among populations, genetic distances were measured and principal component analysis performed. As expected in a cross-pollinated crop we found high genetic diversity and a larger variation within than among the populations. Somewhat unexpectedly, however, we found that the currently used varieties have the same high level of heterozygosity as the landraces but in the dendrogram the two groups are separated. The dendrogram showed three main clusters. The large cluster included 21 populations and the two small clusters were clearly distinguishable from the rest. The landrace spring-type could not be separated from the landraces winter-type, but we did detect a difference between different spring types. A few populations had unique alleles for certain loci.     

Genetic diversity of allozymes in turnip (Brassica rapa L. var. rapa) from the Nordic area

Genetic diversity and relationships based on isozymes were studied in 31 accessions of turnip (Brassica rapa L. var. rapa). The material included varieties, elite stocks, landraces and older turnip of slash-and-burn type from the Nordic area. A total of 9 isozyme loci and 26 alleles were studied. The isozyme systems were ACO, DIA, GPI, GOT, PGM, PGD and SKD. The level of heterozygosity was reduced in the landraces, but it was high for the variety group 'Ostersundom'. Turnip has a higher genetic variation than other crops within B. rapa and than in other species with the same breeding system. The genetic diversity showed that 18.7% of the genetic variation was within the accessions, and the total H tau value was 0.358. Gpi-I and Pgd-I showed the lowest variation compared with the other loci. The cluster analysis revealed five clusters, with one main cluster including 25 of the 31 accessions. The dendrogram indicated that the variety group 'Ostersundom' clustered together whereas the variety group 'Bortfelder' was associated with country of origin. The landraces were spread in different clusters. The 'slash-and-burn' type of turnip belonged to two groups.     

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.     

Genetic Diversity and Core Collection Evaluations in Common Wheat Germplasm from the Northwestern Spring Wheat Region in China

Fluorescence microsatellite markers were employed to reveal genetic diversity of 340 wheat accessions consisting of 229 landraces and 111 modern varieties from the Northwest Spring Wheat Region in China. The 340 accessions were chosen as candidate core collections for wheat germplasm in this region. A core collection representing the genetic diversity of these accessions was identified based on a cluster dendrogram of 78 SSR loci. A total of 967 alleles were detected with a mean of 13.6 alleles (5–32) per locus. Mean PIC was 0.64, ranged from 0.05 to 0.91. All loci were distributed relatively evenly in the A, B and D wheat genomes. Mean genetic richness of A, B and D genomes for both landraces and modern varieties was B > A > D. However, mean genetic diversity indices of landraces changed to B > D > A. As a whole, genetic diversity of the landraces was considerably higher than that of the modern varieties. The big difference of genetic diversity indices in the three genomes suggested that breeding has exerted greater selection pressure in the D than the A or B genomes in this region. Changes of allelic proportions represented in the proposed core collection at different sampling scales suggested that the sampling percentage of the core collection in the Northwest Spring Wheat Region should be greater than 4% of the base collection to ensure that more than 70% of the variation is represented by the core collection. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Genetic diversity and relationship of global faba bean (<Emphasis Type="Italic">Vicia faba</Emphasis> L.) germplasm revealed by ISSR markers

Genetic diversity and relationships of 802 faba bean (Vicia faba L.) landraces and varieties from different geographical locations of China and abroad were examined using ISSR markers. A total of 212 repeatable amplified bands were generated with 11 ISSR primers, of which 209 were polymorphic. Accessions from North China showed highest genetic diversity, while accessions from central China showed low level of diversity. Chinese spring faba bean germplasm was clearly separated from Chinese winter faba bean, based on principal component analysis and UPGMA clustering analysis. Winter accessions from Zhejiang (East China), Jiangxi (East China), Sichuan (Southwest China) and Guizhou (Southwest China) were quite distinct to that from other provinces in China. Great differentiation between Chinese accessions and those from rest of the world was shown with a UPGMA dendrogram. AMOVA analyses demonstrated large variation and differentiation within and among groups of accessions from China. As a continental geographic group, accessions from Europe were genetically closer to those from North Africa. Based on ISSR data, grouping results of accessions from Asia, Europe and Africa were obviously associated with their geographical origin. The overall results indicated that the genetic relationship of faba bean germplasm was closely associated with their geographical origin and their ecological habit.     

SSR标记揭示的云南地方稻品种遗传多样性及其保育意义

为了探索水稻(Oryza sativa L.)地方品种的遗传多样性及其有效保育方法,对采自云南省17个村寨的82个水稻地方品种和3个国际常用的典型籼稻和粳稻品种进行了微卫星(SSR)分子标记的分析.利用19对SSR引物在85个水稻品种中共扩增出了83个基因型,其分子量变异在100～500 bp之间.基于各品种SSR基因型遗传相似系数聚类分析而获得的UPGMA树状图表明各水稻品种之间存在较大的遗传多样性,其相似系数变异在0.15～0.90之间.但这些地方品种的遗传多样性并非呈均等的地理分布.这85个水稻品种在相似系数为0.52之处分为二组,其中一组包括几乎所有的籼稻品种,而另一组包括全部的粳稻品种,表明SSR标记能很好揭示水稻籼-粳分化.同时,有些来自不同采集地的同名品种表现出一定的遗传差异,说明同名异物的现象存在.云南水稻地方品种具有丰富的遗传多样性,对其有效保育十分重要和迫切,但只有根据遗传多样性的水平和分布特点,采用正确的保育对策和取样方法才能确保对云南水稻地方品种的有效保育.结果进一步表明,选用适当的微卫星引物,可以为准确鉴定籼稻和粳稻品种及研究其进化规律提供有效的分子标记方法,并有利于有目标的水稻遗传资源保育和育种创新.     

SSR标记揭示的云南地方稻品种遗传多样性及其保育意义

为了探索水稻(Oryza　sativa　L.)地方品种的遗传多样性及其有效保育方法,对采自云南省17个村寨的82个水稻地方品种和3个国际常用的典型籼稻和粳稻品种进行了微卫星(SSR)分子标记的分析。利用19对SSR引物在85个水稻品种中共扩增出了83个基因型,其分子量变异在100～500　bp之间。基于各品种SSR基因型遗传相似系数聚类分析而获得的UPGMA树状图表明各水稻品种之间存在较大的遗传多样性,其相似系数变异在0.15～0.90之间。但这些地方品种的遗传多样性并非呈均等的地理分布。这85个水稻品种在相似系数为0.52之处分为二组,其中一组包括几乎所有的籼稻品种,而另一组包括全部的粳稻品种,表明SSR标记能很好揭示水稻籼-粳分化。同时,有些来自不同采集地的同名品种表现出一定的遗传差异,说明同名异物的现象存在。云南水稻地方品种具有丰富的遗传多样性,对其有效保育十分重要和迫切,　但只有根据遗传多样性的水平和分布特点,采用正确的保育对策和取样方法才能确保对云南水稻地方品种的有效保育。结果进一步表明,选用适当的微卫星引物,可以为准确鉴定籼稻和粳稻品种及研究其进化规律提供有效的分子标记方法,并有利于有目标的水稻遗传资源保育和育种创新。     

Assessment of Genetic Diversity in <Emphasis Type="Italic">Secale cereale</Emphasis> Based on SSR Markers

The primary aim of this study was to estimate genetic diversity among Secale cereale L. accessions using 22 previously published simple sequence repeat (SSR) markers. The plant material included 367 rye accessions comprising historical and contemporary cultivars, cultivated materials, landraces, and breeding strains from the Polish breeding company Danko. The studied accessions represented a wide geographical diversity. Several methods were employed to analyze genetic diversity among the Secale cereale L. accessions and to determine population structure: principal coordinate analysis (PCoA), neighbor-joining (NJ), and Bayesian clustering. We also defined a core collection of 25 rye accessions representing over 93 % of SSR alleles. The results of these analyses showed that accessions from the rye gene bank are clearly divergent in comparison with materials received directly from European breeding companies. Our findings suggest also that the genetic pool of current rye cultivars is becoming narrower during breeding processes. The selected panel of SSR markers performed well in detection of genetic diversity patterns and can be recommended for future germplasm characterization studies in rye.     

Patterns of genetic diversity in the Andean gene pool of common bean reveal a candidate domestication gene

Most studies on the genetic diversity of common bean (Phaseolus vulgaris L.) have focussed on accessions from the Mesoamerican gene pool compared to the Andean gene pool. A deeper knowledge of the genetic structure of Argentinian germplasm would enable researchers to determine how the Andean domestication event affected patterns of genetic diversity in domesticated beans and to identify candidates for genes targeted by selection during the evolution of the cultivated common bean. A collection of 116 wild and domesticated accessions representing the diversity of the Andean bean in Argentina was genotyped by means of 114 simple sequence repeat (SSR) markers. Forty-seven Mesoamerican bean accessions and 16 Andean bean accessions representing the diversity of Andean landraces and wild accessions were also included. Using the Bayesian algorithm implemented in the software STRUCTURE we identified five major groups that correspond to Mesoamerican and Argentinian wild accessions and landraces and a group that corresponds to accessions from different Andean and Mesoamerican countries. The neighbour-joining algorithm and principal coordinate clustering analysis confirmed the genetic relationships among accessions observed with the STRUCTURE analysis. Argentinian accessions showed a substantial genetic variation with a considerable number of unique haplotypes and private alleles, suggesting that they may have played an important role in the evolution of the species. The results of statistical analyses aimed at identifying genomic regions with consistent patterns of variation were significant for 35 loci (~20 % of the SSRs used in the Argentinian accessions). One of these loci mapped in or near the genomic region of the glutamate decarboxylase gene. Our data characterize the population structure of the Argentinian germplasm. This information on its diversity will be very valuable for use in introgressing Argentinian genes into commercial varieties because the majority of present-day common bean varieties are of Andean origin.     

黔东南香禾糯AFLP遗传多样性分析与评价

香禾糯是我国侗族人民数百年来的传统主食,也是传统农业生态系统的重要组成部分。本文通过民族植物学调查与现代分子生物学试验相结合的方法,对黔东南侗族地区传统分类的香禾糯农家品种进行了评价,以便探讨香禾糯种质资源的遗传多样性变化。通过8对AFLP引物并基于遗传距离和遗传相似系数,对从黔东南侗族地区收集的95个香禾糯农家品种进行了分析。共检测到707个位点,其中多态性位点为619个,占87.55%,Shannon-Weiner多样性指数为0.3738,基因多样性指数为0.2446,遗传相似系数为0.7121~0.9958。当遗传相似系数为0.7546时,可划分为Ⅰ、Ⅱ两大类,外加1个特殊品种,其中Ⅰ类群有88个品种,Ⅱ类群有6个品种,来自相同和相邻侗寨或者形态性状相近的品种并没有完全聚在一起。结果表明黔东南地区香禾糯农家品种遗传多样性总体水平较高,特别是传统耕作文化保护较好的侗寨内,其遗传背景差异较大。香禾糯种质资源的多样性形成,在很大程度上与黔东南地区复杂多变的自然环境有关,还与该地区少数民族的传统耕作制度和民族传统文化延续密切相关。     

凉山州马铃薯栽培品种的遗传多样性分析

利用SSR分子标记技术对凉山州马铃薯地方品种、自育品种和各地育成品种共计60份进行了遗传多样性分析,筛选出16对有效SSR引物。采用筛选的16对引物在供试材料中共检测到68个位点,其中多态性位点42个占总扩增位点的61.76%,平均PIC值为0.4717。通过NTSYSpc 2.0对所有材料间的遗传距离进行计算,平均遗传距离在2.43~3.96之间。使用MEGA4分析软件将供试材料分成3大类,2个凉山州地方品种在聚类图中最先被分离出来。利用PoPGEN将凉山州地方种和其余材料分成两类,。上述结果表明凉山州地方种与试验中其他品种的遗传基础差异较大,是较好的资源材料。该研究为凉山州地方马铃薯品种在今后育种中的应用提供了部分参考依据。     

Genetic differentiation among Sri Lankan traditional rice (Oryza sativa) varieties and wild rice species by AFLP markers

Traditional rice varieties are one important component of the biodiversity of Sri Lanka. However, no proper studies have been performed on genetic diversity of the Sri Lankan traditional rice varieties used in our breeding programs. In the present study, the genetic diversity of 46 traditional rice (Oryza sativa) varieties and 5 wild rice species is assesed using Amplified Fragment Length Polymorphism (AFLP) markers. Ten primer combinations generated a total of 784 fragments. Of these, 772 fragments were polymorphic (98.4%). UPGMA analysis based on Jaccard's similarity separated the accessions into four major clusters. A cophenetic correlation with r=0.786 strongly supported the clustering pattern of UPGMA dendrogram. A principal coordinate analysis (PCoA) also confirmed the UPGMA clusters. Accessions referred to the same cluster showed similar morphological characteristics (e.g. height, grain colour etc.) while accessions which are known to be morphologically distinct appeared genetically separated. In addition, the clustering pattern distinctly separated lowland and upland rice varieties. This genetic diversity assessment at the molecular level provides reliable information for selection of germplasm in the development of new rice varieties and in conservation of traditional rice genetic resources.     

香稻资源遗传多样性的比较

利用60个水稻SSR标记, 对来自国内外的370份香稻材料的遗传多样性进行了比较分析。结果共检测到361个等位基因, 每个位点的等位基因变幅为2~10个, 平均Nei基因多样性指数(He)为0.663, 变幅为0.104(RM308)~0.885(RM2634)。籼粳亚种间的遗传多样性具有明显差异, 籼稻的等位基因数和Nei基因多样性指数均高于粳稻。地方品种的遗传多样性高于选育品种, 选育品种等位基因数仅为地方品种的86.5%。分子方差分析表明, 香稻材料中总变异的43.08%是由于亚种间的遗传差异引起的。不同稻区的遗传分化程度总体介于1.69%~14.40%之间。其中, 华南与西南、华中与西南地方品种间遗传差异的分化程度达显著水平。聚类分析将参试材料明显分为籼粳两大类, 同时地域相同(稻区)、相邻省份的香稻材料基本归为同一类群。     

Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers

The archipelago of Indonesia has a long history of rice production across a broad range of rice-growing environments resulting in a diverse array of local Indonesian rice varieties. Although some have been incorporated into modern breeding programs, the vast majority of these landraces remain untapped. To better understand this rich source of genetic diversity we have characterized 330 rice accessions, including 246 Indonesian landraces and 63 Indonesian improved cultivars, using 30 fluorescently-labeled microsatellite markers. The landraces were selected across 21 provinces and include representatives of the classical subpopulations of cere, bulu, and gundil rices. A total of 394 alleles were detected at the 30 simple sequence repeat loci, with an average number of 13 alleles per locus across all accessions, and an average polymorphism information content value of 0.66. Genetic diversity analysis characterized the Indonesian landraces as 68% indica and 32% tropical japonica, with an indica gene diversity of 0.53 and a tropical japonica gene diversity of 0.56, and a Fst of 0.38 between the two groups. All of the improved varieties sampled were indica, and had an average gene diversity of 0.46. A set of high quality Indonesian varieties, including Rojolele, formed a separate cluster within the tropical japonicas. This germplasm presents a valuable source of diversity for future breeding and association mapping efforts.     

Wheat gene bank accessions as a source of new alleles of the powdery mildew resistance gene <Emphasis Type="Italic">Pm3</Emphasis>: a large scale allele mining project

Background  

In the last hundred years, the development of improved wheat cultivars has led to the replacement of landraces and traditional varieties by modern cultivars. This has resulted in a decline in the genetic diversity of agriculturally used wheat. However, the diversity lost in the elite material is somewhat preserved in crop gene banks. Therefore, the gene bank accessions provide the basis for genetic improvement of crops for specific traits and and represent rich sources of novel allelic variation.     

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.     

Diversity of North European oat analyzed by SSR, AFLP and DArT markers

Oat is an important crop in Nordic countries both for feed and human consumption. Maintaining a high level of genetic diversity is essential for both breeding and agronomy. A panel of 94 oat accessions was used in this study, including 24 museum accessions over 100- to 120-year old and 70 genebank accessions from mainly Nordic countries and Germany, covering different breeding periods. Sixty-one polymorphic SSR, 201 AFLP and 1056 DArT markers were used to evaluate the past and present genetic diversity of the Nordic gene pool. Norwegian accessions showed the highest diversity, followed by Swedish and Finnish, with German accessions the least diverse. In addition, the Nordic accessions appeared to be highly interrelated and distinct from the German, reflecting a frequent germplasm exchange and interbreeding among Nordic countries. A significant loss of diversity happened at the transition from landraces and old cultivars to modern cultivars. Modern oat originated from only a segment of the landraces and left the remainder, especially black oat, unused. However, no significant overall diversity reduction was found during modern breeding periods, although fluctuation of diversity indices was observed. The narrow genetic basis of the modern Nordic gene pool calls for increasing genetic diversity through cultivar introduction and prebreeding based on neglected sources like the Nordic black oat.     

太湖粳稻同名地方品种的遗传差异

选用45个SSR标记分析太湖流域荔枝红、老来青、太湖青和老虎稻共4组粳稻同名地方品种的遗传差异。结果表明:同名地方品种平均Nei遗传距离为0.120~0.171,遗传同一性程度较高,其中有8对同名品种难以区别,但多数品种仍然存在一定的遗传变异,且个别品种差异较大;同名品种遗传差异与种质来源、品种名称的近似程度没有关系。     

Analysis of genetic diversity among indigenous landraces from sesame (Sesamum indicum L.) core collection in China as revealed by SRAP and SSR markers

The molecular genetic diversity of 404 indigenous landraces from sesame core collection in China were evaluated by 11 SRAP and 3 SSR markers, 175 fragments were generated, of which 126 were polymorphic with an average polymorphism rate of 72%. Jaccard’s genetic similarity coefficients (GS=0.7130), Nei’s gene diversity (h=0.2418) and Shannon’s Information index (I=0.3847) were calculated, a dendrogram of the 404 landraces was made, landraces from various zones were distributed throughout the dendrogram, accessions from different agro-ecological zones were indistinguishable by cluster analysis, geographical separation did not generally result in greater genetic distance, a similar pattern was obtained using principal coordinates (PCO) analysis. As to seven agro-ecological zones, the maximum Nei’s gene diversity (h = 0.2613) and Shannon index (I = 0.3980) values in zone VII indicated that they were genetically more diverse than those in other zones, while the least genetically diverse region was zone III (h = 0.1772, I = 0.2858). Nei’s genetic identity and genetic distance among landraces from seven agro-ecological zones were also analyzed, the genetic relationship of seven zones was inferred using the UPGMA method. This study demonstrated that SRAP and SSR markers were appropriate for evaluation of sesame genetic diversities. There existed extensive genetic diverse among indigenous landraces and the abundance of genetic diversity of landraces in different agro-ecological zones was various. Understanding of these characteristics of indigenous landraces in China can provide theoretical foundation for further collection, effective protection and reasonable utilization of these sesame landraces in breeding.