Genetic diversity and relationships among Canavalia ensiformis (L.) DC. Accessions as revealed by sequence-related amplified polymorphism markers

Canavalia ensiformis is an under-exploited legume that has been used as forage, green manure, and a cover crop. Thus far, studies of the C. ensiformis germplasm have focused on morphological traits, which cannot be used to distinguish all known accessions or to evaluate their genetic diversity precisely. In this study, sequence-related amplified polymorphism (SRAP) markers were used to assess the genetic diversity and relationships among 29 C. ensiformis accessions originating from 16 countries. In total, 274 clear bands were amplified and 144 of them (52.6%) were polymorphic. The polymorphism information content values (PIC) ranged from 0.10 to 0.43, with an average of 0.27. An analysis of molecular variance (AMOVA) revealed that the most significant variation (92.0% of the total) occurred among accessions; the remaining 8.0% was attributed to variation within accessions. A cluster analysis and principal coordinates (PCoA) analysis produced similar results, whereby the 29 C. ensiformis accessions were divided into 5 clusters, each of which was composed of different accessions with different phenotypic traits. This study provides the theoretical basis for future biodiversity studies and breeding programs.     

Genetic diversity and phylogenetic relationships among five endemic Pinus taxa (Pinaceae) of China as revealed by SRAP markers

The genetic diversity and phylogenetic relationships among five endemic Pinus taxa of China (Pinus tabulaeformis, P. tabulaeformis var. mukdensis, P. tabulaeformis f. shekanensis, Pinus massoniana and Pinus henryi) were studied by SRAP markers. Using 10 SRAP primer pairs, 247 bands were generated. The percent of polymorphic bands (94.8%), Nei's genetic diversity (0.2134), and Shannon's information index (0.3426) revealed a high level of genetic diversity at the genus-level. At the taxon level, P. tabulaeformis f. shekanensis and P. henryi showed a higher genetic diversity than the others. The coefficient of genetic differentiation among taxa (0.3332) indicated a higher level of genetic diversity within taxon, rather than among taxa. An estimate of gene flow among taxa was 1.0004 and implied a certain amount of gene exchange among taxa. The results of neighbor-joining cluster analysis and principal co-ordinate analysis revealed that P. tabulaeformis, P. tabulaeformis var. mukdensis and P. tabulaeformis f. shekanensis were conspecific, which was in agreement with the traditional classification. Phylogenetic relationships analysis also indicated that P. henryi might be a distinct species closely related to P. tabulaeformis.     

Genetic diversity of Chinese common bean (Phaseolus vulgaris L.) landraces assessed with simple sequence repeat markers

Common beans were introduced from the Americas to China over 400 years ago and presently constitute an important export crop in many areas of the country. Evaluation of the genetic diversity present in Chinese accessions of common beans is essential for conservation, management and utilization of these genetic resources. The objective of this research was to evaluate a collection of 229 Chinese landraces with 30 microsatellite markers to evaluate the genetic variability, genepool identity and relationships within and between the groups identified among the genotypes. A total of 166 alleles were detected with an average of 5.5 alleles per locus for all microsatellites. The landraces were clustered into two genepools with two subgroups each. The level of diversity for Chinese landraces of Andean origin was higher than for the Chinese landraces of Mesoamerican origin due to the presence of more infrequent alleles in this first group. The range of marker prevalence indices was from 0.288 to 0.676 within the Andean group and from 0.426 to 0.754 within the Mesoamerican group. Two subgroups were identified in each genepool group with one of the Mesoamerican subgroups arising from introgression. Gene flow (N ( m )) was 0.86 or below between subgroups from different gene pools and 2.6 or above between subgroups within the genepools. We discuss the existence of a secondary center of diversity for common beans in China and the importance of inter genepool introgression.     

Genetic diversity and phylogenetic relationship of kenaf (Hibiscus cannabinus L.) accessions evaluated by SRAP and ISSR

Understanding genetic diversity and phylogenetic relationships is useful for plant breeding. In this study, we assessed the genetic diversity in a panel of 84 accessions of kenaf from 26 countries using SRAP and ISSR markers. The kenaf accessions could be divided into L1 (60 cultivated varieties) and L2 (24 wild accessions) at the level of 0.145 genetic dissimilarity coefficient by UPGMA. The L₂ group was further divided into two subgroups (16 relative-wide and 9 origin wide accessions) at the level of 0.207 genetic dissimilarity. Out of the 9 wild accessions in the L₂ group, 6 were from Tanzania and the remaining 3 lines were from Kenya. These results suggest that the center of origin for kenaf might be Tanzania and Kenya.     

Genetic diversity analysis of Pinellia ternata based on SRAP and TRAP markers

An assessment of the genetic diversity and variation of Pinellia ternata collected from 43 populations in China was undertaken using SRAP + TRAP markers. A total of 13 SRAP primers in addition to 3 TRAP primer combinations yielded 292 bands in total of which 286 were polymorphic (98.0%), with an average of 16 for each. The PIC value ranged from 0.88 to 0.95, with a mean polymorphic information content (PIC) of 0.92 over all the primers. A cluster analysis was conducted based on the unweighted pair group method with arithmetic average (UPGMA), and a principle coordinate analysis (PCA) was performed relying on Nei's genetic distance, both of which showed similar outcomes in that the results of clustering did not correlate to the geography locations but showed an association with morphology. An analysis of molecular variance (AMOVA) was performed to detect the source of variation; the results indicated that the main variation existed within populations (67.2%), whereas there was still 32.8% differentiation existing among the populations.     

黄麻种质资源遗传多样性的SRAP分析

为明确黄麻(Corchorus L.)种质资源的遗传多样性,采用SRAP分子标记方法,对来自13个国家的两个黄麻栽培种及野生种共96份黄麻种质资源进行了分析。研究结果如下:(1)供试黄麻种质资源之间的遗传距离在0.0169至0.9667之间,变幅较大,其中近缘野生种与其他种质的遗传距离最大,基本在0.8以上;圆果栽培黄麻与其他种质的遗传距离最小,平均<0.5。(2)当在聚类图上遗传距离为0.53处划切割线L₁时,96份黄麻种质资源被分为两个大类群(Ⅰ、Ⅱ)、一个小类群(Ⅲ)和5个独立个类。(3)当在遗传距离为0.33处作切割线L₂时,各大类群被分为不同的亚类群,并表现出按地域聚类的趋势。(4)供试黄麻种质资源基于SRAP分子标记的聚类与形态学上的表现并不完全一致。     

Genetic diversity of common bean (Phaseolus vulgaris L.) nodulating rhizobia in Nepal

Background and Aims

This study was conducted to reveal the genetic diversity of common bean (Phaseolus vulgaris L.) nodulating rhizobia in various agroecological regions in Nepal.

Method

A total of 63 strains were isolated from common bean grown in the soils collected from seven bean fields in Nepal and characterized based on the partial sequences of 16S–23S internal transcribed spacer (ITS) regions, 16S rDNA, nodC, and nifH. Symbiotic properties of some representative strains with host plants were examined to elucidate their characteristics in relation to genotype and their origin.

Results

The isolated strains belonged to Rhizobium leguminosarum, Rhizobium etli, Rhizobium phaseoli, and one unknown Rhizobium lineage, all belonging to a common symbiovar (sv.) phaseoli. Nine ITS genotypes were detected mainly corresponding to a single site, including a dominant group at three sites harboring highly diverse multiple ITS sequences. Three symbiotic genotypes corresponded to a geographical region, not to the ribosomal DNA group, suggesting horizontal transfer of symbiotic genes separately in each region. Great differences in nitrogenase activity and nodule forming ability among the strains irrespective of their species and origin were observed.

Conclusions

Nepalese Himalaya harbor phylogenetically highly diverse and site-specific strains of common bean rhizobia, some of which could have high potential of symbiotic nitrogen fixation.     

Genetic diversity and population structure of common bean (Phaseolus vulgaris) landraces from China revealed by a new set of EST-SSR markers

A new set of EST-SSR markers were developed and employed to analyze the genetic diversity and population structure of Phaseolus vulgaris in China. A total of 2452 microsatellites were identified in 2144 unigenes assembled from P. vulgaris ESTs, indicating that merely 6.9% of the 30,952 unigene sequences contained SSRs. Seventeen of 153 randomly designed EST-SSR primer pairs successfully amplified polymorphic products in 31 landraces from six major production provinces of China, with the mean number of alleles per locus of 2.700 and polymorphism information content of 0.378. The observed and expected heterozygosity ranged from 0.100 to 0.954 and 0.081 to 0.558, respectively. Using these markers, both an unrooted neighbor-joining tree and principal coordinates analysis showed that almost all of the landraces were separated according with their regional distribution. Moreover, population structure analysis revealed that all genotypes formed into three distinct clusters (k = 3), suggesting that geographic and climatic factors could provide diverse degrees of selection pressure. Accordingly, germplasm collection and cross breeding among different regions are suggested to accelerate the process of diverse germplasm creation and broaden germplasm resources of Chinese common bean.     

Description and analysis of genetic diversity between commercial bean lines (Phaseolus vulgaris L.)

The effectiveness of RFLP, DAMD-PCR, ISSR and RAPD markers in assessing polymorphism and relationships between 24 commercial lines of Phaseolus vulgaris L.was evaluated. We have used a Phaseolus-specific minisatellite sequence as a probe, which enabled 23 of the bean lines tested to be fingerprinted. Based on the sequence information obtained, primers corresponding to the bean-specific minisatellite core sequence were used in subsequent PCR amplifications. Our observations indicated that while the DAMD-PCR was sensitive in detecting genetic variation between bean species and between accessions of P. vulgaris, when used alone it may be limited in its ability to detect genetic variation among cultivated bean lines due to the low number of loci amplified. Only one out of the five ISSR primers tested was efficient in generating multiple band profiles, which was insufficient to distinguish all the different bean lines. Reproducible RAPD profiles were obtained, and these allowed us to differentiate all the genotypes tested with seven primers. We ultimately used only results from RFLP and RAPD markers to explore the genetic diversity among commercial bean lines. Both analyses led to the same clustering of the bean lines according to their geographical origins (United States or Europe). With respect to the European lines, the results obtained from RAPD data also enable the lines to be clustered according to their creators. Received: 15 January 2000 / Accepted: 21 March 2000     

Microsatellite marker diversity in common bean (Phaseolus vulgaris L.)

A diversity survey was used to estimate allelic diversity and heterozygosity of 129 microsatellite markers in a panel of 44 common bean (Phaseolus vulgaris L.) genotypes that have been used as parents of mapping populations. Two types of microsatellites were evaluated, based respectively on gene coding and genomic sequences. Genetic diversity was evaluated by estimating the polymorphism information content (PIC), as well as the distribution and range of alleles sizes. Gene-based microsatellites proved to be less polymorphic than genomic microsatellites in terms of both number of alleles (6.0 vs. 9.2) and PIC values (0.446 vs. 0.594) while greater size differences between the largest and the smallest allele were observed for the genomic microsatellites than for the gene-based microsatellites (31.4 vs. 19.1 bp). Markers that showed a high number of alleles were identified with a maximum of 28 alleles for the marker BMd1. The microsatellites were useful for distinguishing Andean and Mesoamerican genotypes, for uncovering the races within each genepool and for separating wild accessions from cultivars. Greater polymorphism and race structure was found within the Andean gene pool than within the Mesoamerican gene pool and polymorphism rate between genotypes was consistent with genepool and race identity. Comparisons between Andean genotypes had higher polymorphism (53.0%) on average than comparisons among Mesoamerican genotypes (33.4%). Within the Mesoamerican parental combinations, the intra-racial combinations between Mesoamerica and Durango or Jalisco race genotypes showed higher average rates of polymorphism (37.5%) than the within-race combinations between Mesoamerica race genotypes (31.7%). In multiple correspondance analysis we found two principal clusters of genotypes corresponding to the Mesoamerican and Andean gene pools and subgroups representing specific races especially for the Nueva Granada and Peru races of the Andean gene pool. Intra population diversity was higher within the Andean genepool than within the Mesoamerican genepool and this pattern was observed for both gene-based and genomic microsatellites. Furthermore, intra-population diversity within the Andean races (0.356 on average) was higher than within the Mesoamerican races (0.302). Within the Andean gene pool, race Peru had higher diversity compared to race Nueva Granada, while within the Mesoamerican gene pool, the races Durango, Guatemala and Jalisco had comparable levels of diversity which were below that of race Mesoamerica.     

Genetic diversity in Vicia amoena (Fabaceae) germplasm resource in China using SRAP and ISSR markers

The genetic diversity in 17 germplasms of Vicia amoena L. from north China was analyzed using SRAP and ISSR markers. Three hundred and sixty-eight (94.11%) polymorphic bands (211 and 157 obtained from 20 pairs of SRAP and ISSR primers, respectively) were scored. Although SRAP was more effective than ISSR markers with higher PIC, RP and larger variation range of genetic distance, both the markers were useful for assessing V. amoena genetic diversity. Cluster analysis showed that the 17 germplasms were clustered into 5 groups. The results of principal coordinate analysis supported UPGMA clustering. The germplasms from source areas where the annual average temperature ranged from −1.0 to 5 °C exhibited the highest level of genetic diversity with the highest PPI, I and H. These results have important implications in genome mapping, breeding purposes, and germplasm conservation.     

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。     

Analysis of the genetic diversity of garlic (Allium sativum L.) germplasm by SRAP

Cluster analysis and principal component analysis were used to investigate the genetic diversity of 40 garlic germplasms analyzed with 23 sequence-related amplified polymorphism (SRAP) primer combinations. A total of 130 polymorphic loci were detected among these germplasms, with an average of 5.65 polymorphic loci per SRAP primer combination. The percentage of polymorphic loci was 69.1%, whereas the mean effective number of alleles, the mean Nei's gene diversity, and the mean Shannon's information index were 1.4446, 0.2788, and 0.4365, respectively. Cluster analysis revealed that the 40 germplasms could be divided into 3 groups. The results of principal component analysis were consistent with those of unweighted pair-group method with arithmetic averages (UPGMA) clustering analysis. The Shannon-Weaver information index ranged from 0.2419 to 0.4202, indicating that the garlic germplasms had high genetic diversity.     

Genetic diversity of castor bean (Ricinus communis L.) in Northeast China revealed by ISSR markers

Inter-Simple Sequence Repeat (ISSR) markers were employed to analyze the genetic diversity of Ricinus communis L. in northeastern China plants. We selected ten primers that produced clear, reproducible and multiple bands for these experiments and 179 bands were obtained across 39 genotypes. Polymorphic band ratios ranged from 100% to a minimum of 78.9% with an average of 96.4% while band numbers were comprised between 13 (UBC823) and 23 (UBC856). The results obtained from UPGMA clustering dendrogram and PCoA lead to 39 distinct castor bean accessions belonging to four major groups. We found that all groups shared a common node with 66% similarity while Jaccard's similarity coefficient ranged from 0.58 to 0.92. Compatible inference was also observed from the high values of heterozygosity (Ht = 0.3378 ± 0.0218), Nei's genetic diversity (H = 0.1765 ± 0.2090), and Shannon's information index (I = 0.4942 ± 0.1872). In addition, our data reveal a Nei's genetic differentiation index (G_ST) of 0.3452 and estimated the gene flow (Nm) at 0.9482. These findings clearly suggest a genetic diversity in castor bean germplasms from various geographic origins and contribute to our understanding of breeding and conservation of castor beans.     

Race structure within the Mesoamerican gene pool of common bean (Phaseolus vulgaris L.) as determined by microsatellite markers

Common bean (Phaseolus vulgaris L.) cultivars are distinguished morphologically, agronomically and ecologically into specific races within each of the two gene pools found for the species (Andean and Mesoamerican). The objective of this study was to describe the race structure of the Mesoamerican gene pool using microsatellite markers. A total of 60 genotypes previously described as pertaining to specific Mesoamerican races as well as two Andean control genotypes were analyzed with 52 markers. A total of 267 bands were generated with an average of 5.1 alleles per marker and 0.297 heterozygosity across all microsatellites. Correspondence analysis identified two major groups equivalent to the Mesoamerica race and a group containing both Durango and Jalisco race genotypes. Two outlying individuals were classified as potentially of the Guatemala race although this race does not have a defined structure and previously classified members of this race were classified with other races. Population structure analysis with K = 1–4 agreed with this classification. The genetic diversity based on Nei’s index for the entire set of genotypes was 0.468 while this was highest for the Durango–Jalisco group (0.414), intermediate for race Mesoamerica (0.340) and low for race Guatemala (0.262). Genetic differentiation (G _ST) between the Mesoamerican races was 0.27 while genetic distance and identity showed race Durango and Jalisco individuals to be closely related with high gene flow (N _m) both between these two races (1.67) and between races Durango and Mesoamerica (1.58). Observed heterozygosity was low in all the races as would be expected for an inbreeding species. The analysis with microsatellite markers identified subgroups, which agreed well with commercial class divisions, and seed size was the main distinguishing factor between the two major groups identified.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

油莎豆SRAP指纹图谱构建及遗传多样性分析

利用SRAP分子标记构建了14份不同地理来源、表型具有差异的油莎豆品系的分子指纹图谱并进行遗传多样性分析。结果表明100对引物中共有多态性引物42对,扩增出多态性带328条,平均每对引物7.8条。28对引物在12个品系上具有特征谱带,除品系4和14外,均可用1对引物进行鉴定;采用引物组合法仅用Me2/Em6和Me8/Em11这2对引物就可将14份材料区分开,并利用这2对引物构建了上述品系的数字指纹图谱。UPGMA聚类分析表明,所有参试材料间的遗传距离在0.12～0.75之间,平均为0.42,表明我国不同地理来源的油莎豆品系遗传差异较大,具有较为丰富的遗传多样性。     

Genetic diversity analysis of Perinereis aibuhitensis based on ISSR and SRAP markers of Chinese coast populations

The objective of this study was to obtain an overview of the genetic relationships within Perinereis aibuhitensis using Inter-Simple Sequence Repeat (ISSR) and Sequence-Related Amplified Polymorphism (SRAP) markers that were derived from related populations residing in the Chinese coasts. The percentage of polymorphic bands, Nei's gene diversity and Shannon's information index revealed a high level of genetic diversity at the species level. The analysis of molecular variance revealed that 81.22% (ISSR) and 76.29% (SRAP) of variability were partitioned among individuals within populations, which indicated the coherent trend by Nei's genetic differentiation (Gst) (0.2568/0.2876). The gene flow number (Nm) was 1.4470/1.2385, which indicated that there was limited gene exchange between populations. The phylogenetic tree of the ten P. aibuhitensis populations was separated into four major clusters using the neighbor-joining (NJ) method. These results provide a simple and useful basis for P. aibuhitensis germplasm research and aquaculture breeding.     

Genetic diversity of endangered Manglietia patungensis assessed by inter simple sequence repeat and sequence-related amplified polymorphism markers

Manglietia patungensis Hu is an endangered plant native to China. Knowledge of its genetic diversity and structure would aid its conservation. This study assessed nine natural populations of M. patungensis using two methods: inter simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. Using 10 ISSR primer pairs, 334 bands were generated, and 10 SRAP primer pairs generated 276 bands. The percent of polymorphic bands (91.32% and 93.48%), Nei's genetic diversity (0.3448 and 0.3323), and Shannon's information index (0.5075 and 0.4935) revealed a high level of genetic diversity at the species level. Total heterozygosity was 0.3439 by ISSR and 0.3281 by SRAP. The mean heterozygosity was 0.2323 by ISSR and 0.2521 by SRAP. The coefficient of genetic differentiation among natural populations was 0.3245 by ISSR and 0.2316 by SRAP. These data indicated higher levels of genetic diversity of M. patungensis within, rather than among, populations. Estimates of gene flow among natural populations were 1.0411 and 1.0589, which implied a certain amount of gene exchange among populations. A Mantel test revealed no significant correlation between genetic and geographic distance. ISSR and SRAP markers are both effective for genetic diversity research in M. Patungensis. Based on these results, conservation of M. patungensis should be performed both in situ and ex situ.     

Genetic diversity assessment of a germplasm collection of Salvia miltiorrhiza Bunge. based on morphology,ISSR and SRAP markers

Salvia miltiorrhiza is one of the most important traditional Chinese medicinal plants for its therapeutic effects. In the present study, morphological traits, ISSR (inter-simple sequence related) and SRAP (sequence-related amplified polymorphism) markers were used to analyze the genetic diversity of 59 S. miltiorrhiza phenotypes. Out of the 100 ISSR primers and 100 SRAP primer combinations screened, 13 ISSRs and 7 SRAPs were exploited to evaluate the level of polymorphism and discriminating capacity. The results showed that the 13 ISSRs generated 190 repeatable amplified bands, of which 177 (93.2%) were polymorphic, with an average of 13.6 polymorphic fragments per primer. The 7 SRAPs produced 286 repeatable amplified bands, of which 266 (93.4%) were polymorphic, with an average of 38.1 polymorphic fragments per primer. Cluster analysis readily separated different morphological accessions, wild and cultivated controls based on morphological traits, ISSR and SRAP markers. The study indicated that morphological traits, ISSR and SRAP markers were reliable and effective for assessing the genetic diversity of phenotypic S. miltiorrhiza accessions. The overall results suggested that the introduction of genetic variation from morphology-based germplasms enlarged the genetic base for the collection, conservation and further breeding program of S. miltiorrhiza germplasm.     

Genetic diversity of common bean (Phaseolus vulgaris L.) ecotypes from Pakistan using Simple Sequence Repeats

Common bean (Phaseolus vulgaris L.) is a legume crop grown all over the world and is a very important food of mountain population of Pakistan for protein intake. The Western Himalayan Mountains are rich in biodiversity including unexplored landraces of the common bean crop. Unfortunately, very little attention has been given to this valuable crop in Pakistan, and it is being exported, majorly from Ethiopia, to meet the country’s requirements. The exploitation, utilization, preservation and multiplication of existing germplasm within the area are very important for sustainable production of the crop and enhancing the nutrition value for the local community in mountain regions. A research study was conducted for evaluation of biological diversity of common bean landraces from Azad Kashmir and Northern areas of Pakistan using morpho-physiological and molecular markers. Thirty-five common bean ecotypes along with one check variety were collected from different altitudes of Azad Kashmir and Northern Pakistan and screened for biological diversity. Morphological characterization revealed high genetic diversity in parameters including stem anthocyanin, growth type, days to flowering, pods/plant and 100 seeds weight. Genomic characterization using SSR markers, for allelic diversity evaluation among germplasm, also provided diverse profile with 83.3% polymorphism in banding pattern. The bulk of gene pool diversity evaluated within bean landraces may help to initiate breeding program for common bean improvement.