新疆甜高粱种质资源遗传多样性的SSR分析

选用50对SSR引物对新疆现有72份甜高粱种质资源进行遗传多样性分析。结果表明:有20对引物在72份甜高粱种质资源中表现为多态性。共检测到91个等位基因,每对引物可检测到的等位基因数目为2～5个,平均为3.45个。多态性信息量(PIC)的变动范围为0.2859～0.6652,平均为0.5057。72份甜高粱种质间的遗传相似系数变化范围为0.2001～1.000,平均值为0.5599。UPGMA聚类分析将72份材料划分为A、B两大类群,A群包括69份材料,而A群又被分成从Ⅰ到Ⅺ共11个亚群,B群包括3份材料,农艺性状近似的大多被聚到同一类群。     

Molecular characterization and genetic diversity analysis of soybean (Glycine max (L.) Merr.) germplasm accessions in India

Molecular characterization and genetic diversity among 82 soybean accessions was carried out by using 44 simple sequence repeat (SSR) markers. Of the 44 SSR markers used, 40 markers were found polymorphic among 82 soybean accessions. These 40 polymorphic markers produced a total of 119 alleles, of which five were unique alleles and four alleles were rare. The allele number for each SSR locus varied between two to four with an average of 2.97 alleles per marker. Polymorphic information content values of SSRs ranged from 0.101 to 0.742 with an average of 0.477. Jaccard’s similarity coefficient was employed to study the molecular diversity of 82 soybean accessions. The pairwise genetic similarity among 82 soybean accessions varied from 0.28 to 0.90. The dendrogram constructed based on genetic similarities among 82 soybean accessions identified three major clusters. The majority of genotypes including four improved cultivars were grouped in a single subcluster IIIa of cluster III, indicating high genetic resemblance among soybean germplasm collection in India.

Electronic supplementary material

The online version of this article (doi:10.1007/s12298-014-0266-y) contains supplementary material, which is available to authorized users.     

Identification of unique alleles and assessment of genetic diversity of rabi sorghum accessions using simple sequence repeat markers

Genetic diversity among 42 sorghum accessions representing landraces (19), advanced breeding lines (16), local cultivars (2) and release varieties (5) with 30 simple sequence repeat (SSR) markers revealed 7.6 mean number of alleles per locus showing 93.3% polymorphism and an average polymorphism information content of 0.78 which range from 0.22 (Xtxp12) and 0.91(Xtxp321). The average heterozygosity and effective number of alleles per locus were 0.8 and 6.65 respectively. Cluster analysis based on microsatellite allelic diversity clearly demarcated the accessions into ten clusters. A total of 24 unique alleles were obtained from seven SSR loci in 23 accessions in a size range of 110–380 bp; these unique alleles may serve as diagnostic tools for particular region of the genome of respective genotypes. Selected SSR markers from different linkage groups provided an accurate way of determining genetic diversity at the molecular level.     

Genetic diversity and population structure analysis of accessions in the US historic sweet sorghum collection

Sweet sorghum has the potential to become a versatile feedstock for large-scale bioenergy production given its sugar from stem juice, cellulose/hemicellulose from stalks, and starch from grain. However, for researchers to maximize its feedstock potential a first step includes additional evaluations of the 2,180 accessions with varied origins in the US historic sweet sorghum collection. To assess genetic diversity of this collection for bioenergy breeding and population structure for association mapping, we selected 96 accessions and genotyped them with 95 simple sequence repeat markers. Subsequent genetic diversity and population structure analysis methods identified four subpopulations in this panel, which correlated well with the geographic locations where these accessions originated or were collected. Model comparisons for three quantitative traits revealed different levels of population structure effects on flowering time, plant height, and brix. Our results suggest that diverse germplasm accessions curated from different geographical regions should be considered for plant breeding programs to develop sweet sorghum cultivars or hybrids, and that this sweet sorghum panel can be further explored for association mapping.     

利用RAPD标记分析大麦种质资源的遗传多样性

利用RAPD标记对19份西藏近缘野生大麦材料、33份我国不同省市的地方品种以及8份国外引进大麦品种共60份大麦种质资源的遗传多样性进行检测.结果表明材料间遗传差异明显.32个RAPD引物中,有25个引物(占78.13%)可扩增出清晰且具多态性的条带,另外7个引物能扩增出1～3条清晰但无多态性的条带.每个引物可扩增出1～8条多态性带,平均为3.72条.32个引物共产生119条DNA片段,其中87条具有多态性,多态性比率(PPB)为73.11%,平均多态信息量(PIC)为0.434;每个位点平均有效等位基因数(Ne)为2.304;材料间遗传相似系数GS变化范围为0.757～0.981,平均值为0.871.19份来源于西藏的近缘野生大麦材料间GS值变幅为0.818～0.969,平均为0.892;33份我国栽培大麦地方品种间的GS值变化范围为0.783～0.981,平均为0.879;8份分别来自8个国家的栽培大麦品种间的GS值变幅为0.820～0.956,平均为0.882.根据RAPD标记分析的结果,对60份大麦种质资源进行聚类分析,在平均GS值0.871水平上60份大麦材料可聚为5类,聚类结果能在一定程度上反应材料的地理分布关系,但某些相同地理来源的材料也较分散地分布在整个聚类树中.本研究从分子水平上进一步证明了我国栽培大麦丰富的遗传多样性,是世界栽培大麦的遗传多样性中心之一.     

Genetic diversity changes in Indian lentils over the times

The genetic diversity of 96 genotypes of lentil comprising 34 cultivars, 46 advanced breeding lines, and 16 germplasm lines were studied using 260 SSR markers. These markers generated a total of 749 alleles. The alleles/locus ranged from 2 to 16 with an average value of 2.87. Polymorphic information content varied from 0.02 to 0.91 with a mean of 0.30. Major allelic frequency ranged from 0.14 to 0.99 with a mean of 0.77. Studied genotypes were clustered into two groups according to their breeding history. Advanced breeding lines derived from exotic lines were clustered in one group, while another group accommodated most of the cultivars and advanced breeding lines with common cultivars in parentage. The germplasm lines were sub-clustered within first group. Cumulatively, first three principal components contributed 21.2% to the total variability. Advanced breeding lines showed higher number of alleles/locus and gene diversity (He) than other sets of genetic materials. In present study, no significant differences were observed between cultivars developed in different decadal groups for both NA and He. Moreover, genetic diversity changes between small and large seeded lentil cultivars were also found non-significant in this study. These findings showed that the use of alien genes can help to diversify active gene pool for developing improved new cultivars in lentil.     

Genetic diversity in watermelon (Citrullus lanatus) landraces from Zimbabwe revealed by RAPD and SSR markers

Low polymorphism in cultivated watermelon has been reported in previous studies, based mainly on US Plant Introductions and watermelon cultivars, most of which were linked to breeding programmes associated with disease resistance. Since germplasm sampled in a putative centre of origin in southern Africa may harbour considerably higher variability, DNA marker-based diversity was estimated among 81 seedlings from eight accessions of watermelon collected in Zimbabwe; five accessions of cow-melons (Citrullus lanatus var. citroides) and three of sweet watermelons (C. lanatus var. lanatus). Two molecular marker methods were used, random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) also known as microsatellite DNA. Ten RAPD primers produced 138 markers of which 122 were polymorphic. Nine SSR primer pairs detected a total of 43 alleles with an average of 4.8 alleles per locus. The polymorphic information content (PIC) ranged from 0.47 to 0.77 for the RAPD primers and from 0.39 to 0.97 for the SSR loci. Similarity matrices obtained with SSR and RAPD, respectively, were highly correlated but only RAPD was able to provide each sample with an individual-specific DNA profile. Dendrograms and multidimensional scaling (MDS) produced two major clusters; one with the five cow-melon accessions and the other with the three sweet watermelon accessions. One of the most variable cow-melon accessions took an intermediate position in the MDS analysis, indicating the occurrence of gene flow between the two subspecies. Analysis of molecular variation (AMOVA) attributed most of the variability to within-accessions, and contrary to previous reports, sweet watermelon accessions apparently contain diversity of the same magnitude as the cow-melons.     

Restriction fragment variation in the nuclear and chloroplast genomes of cultivated and wild Sorghum bicolor

Summary Fifty-six accessions of cultivated and wild sorghum were surveyed for genetic diversity using 50 low-copy-number nuclear DNA sequence probes to detect restriction fragment length polymorphisms (RFLPs). These probes revealed greater genetic diversity in wild sorghum than in cultivated sorghum, including a larger number of alleles per locus and a greater portion of polymorphic loci in wild sorghum. In comparison to previously published isozyme analyses of the same accessions, RFLP analysis reveals a greater number of alleles per locus. Furthermore, many RFLP alleles have frequencies between 0.25–0.75, while the vast majority of isozyme alleles are either rare (< 0.25) or near fixation (> 0.75). Correlations between genetic and geographic distances among the accessions were stronger when calculated with RFLP than with isozyme data. Systematic relationships revealed by nuclear and chloroplast restriction site analysis indicate that cultivated sorghum is derived from the wild ssp. arundinaceum. The portion of the wild gene pool most genetically similar to the cultivars is from central-northeastern Africa. Previous published data also suggested that this is most likely the principal area of domestication of sorghum. Introgression between wild and cultivated sorghum was inferred from disconcordant relationships shown by nuclear and chloroplast DNA markers. Introgression apparently occurs infrequently enough that the crop and its wild relatives maintain distinct genetic constitutions.     

基于SSR标记的贵州薏苡种质资源遗传多样性?分析

利用SSR标记研究了22份薏苡种质的遗传多样性,用11对扩增带型稳定的SSR引物从供试材料中检测出105个等位基因变异,每对引物检测等位基因4～20个,平均9.55个。SSR引物的PIC介于0.3048～0.9238,平均多态性信息量为0.8255。利用UPGMA聚类分系法将供试自交系划分为4类,该划分结果与根据地理来源、种质系谱的分类结果基本一致。SSR分子标记辅助的种质改良是薏苡品种改良的重要途径。     

Genetic diversity among Chinese Hami melon and its relationship with melon germplasm of diverse origins revealed by microsatellite markers

Thick-skinned melon called Hami melon is the most widely cultivated and exported type of melon in China, and mainly grown in Xinjiang province. Here the genetic variation of 64 melon genotypes including 43 Xinjiang Hami melon accessions was analyzed using 36 simple sequence repeat (SSR) markers yielding 145 alleles. The polymorphic information content of SSR markers ranged from 0.09 to 0.83 (average 0.45). Based on the SSR markers, the melon accessions were clustered into 2 major groups (thick and thin-skinned melons). In addition, the sub-cluster analysis based on SSR markers partitioned different botanical groups, even separating similar agronomic trait groups (Xinjiang landraces var. ameri and var. inodorus). SSR analysis showed that 4 SSR markers (CMBR150, CMCTT144, CMBR84 and CMBR12) produced polymorphic bands of different sizes between these two botanical groups. Those four molecular markers might be related to melon fruit maturing time. A considerably low level of genetic diversity was detected in Xinjiang melon accessions. Genetic distances indicated the relatively narrower genetic base but specific taxonomic status of Xinjiang landraces compared with foreign reference accessions.     

Genetic diversity in Indian cucumber based on microsatellite and morphological markers

Genetic variation among 44 cucumber accessions was assessed using morphological and SSR markers. High genetic variability was observed for days to 50% female flowering (37–46 days from sowing), number of fruits per plant (1.4–6.0), individual fruit weight (0.04–0.552 kg) and root length (14.25–32.8 cm). The pair-wise Jaccard similarity coefficient ranged between 0.25 and 0.85 indicating that the accessions represent genetically diverse populations. The allelic diversity of polymorphic markers ranged from 0.001 to 0.9396 with an average of 0.31 based on polymorphic information content. The clustering pattern of SSR markers was not in consonance with the groupings based on quantitative traits. The accession of Indian state i.e.; Madhya Pradesh and Uttar Pradesh were diverged from the accessions of other parts of India. The study provides information for future exploration and collection of cucumber germplasm in India and utilization of diverse germplasm for developing cultivars/hybrids for specific traits.     

Diversification of indigenous gene- pool by using exotic germplasm in lentil (Lens culinaris Medikus subsp. culinaris)

Genetic diversity was studied among 21 accessions of lentil using SSR markers and morphological traits in order to assess the diversification of Indian gene-pool of lentil through introgression of exotic genes and introduction of germplasm. Among these , 16 genotypes either had ‘Precoz’ gene, an Argentine line in their pedigree or genes from introduced lines from ICARDA. Sixty five SSR markers and eight phenotypic traits were used to analyse the level of genetic diversity in these genotypes. Forty three SSR markers (66 %) were polymorphic and generated a total of 177 alleles with an average of 4.1 alleles per SSR marker. Alleles per marker ranged from 2 to 6. The polymorphic information content ranged 0.33 to 0.80 with an average of 0.57, suggesting that SSR markers are highly polymorphic among the studied genotypes. Genetic dissimilarity based a dendrogram grouped these accessions into two main clusters (cluster I and cluster II) and it ranged 33 % to 71 %, suggesting high level of genetic diversity among the genotypes. First three components of PCA based morphological traits explained higher variance (95.6 %) compared to PCA components based on SSR markers (42.7 %) of total genetic variance. Thus, more diversity was observed for morphological traits and genotypes in each cluster and sub-cluster showed a range of variability for seed size, earliness, pods/plant and plant height. Molecular and phenotypic diversity analysis thus suggested that use of germplasm of exotic lines have diversified the genetic base of lentil germplasm in India. This diversified gene-pool will be very useful in the development of improved varieties of lentil in order to address the effect of climate change, to adapt in new cropping systems niches such as mixed cropping, relay cropping, etc. and to meet consumers’ preference.     

Analysis of genetic diversity and relationships among waxy maize inbred lines in Korea using SSR markers

Information regarding the genetic diversity and genetic relationships among elite inbred lines is necessary to improve new cultivars in maize breeding programs. In this study, genetic diversity and genetic relationships were investigated among 84 waxy maize inbred lines using 50 SSR markers. A total of 269 alleles were identified at all the loci with an average of 5.38 and a range between 2 and 13 alleles per locus. The gene diversity values varied from 0.383 to 0.923 with an average of 0.641. The cluster tree generated using the described SSR markers recognized two major groups at 32% genetic similarity. Group I included 33 inbred lines while group II included 51 inbred lines. The clustering patterns of most of the waxy maize inbred lines did not clearly agree with their source, pedigree or geographic location. The average GS among all inbred lines was 35.7 ± 10.8. Analysis of waxy maize inbred lines collected from Korea and China at 50 SSR loci revealed higher values of average number of alleles (4.9) and gene diversity (0.638) in Korean inbred lines as compared to Chinese inbred lines (3.5 and 0.563, respectively). The information obtained from the present studies would be very useful for maize breeding programs in Korea.     

Genetic Diversity Analysis of Nelumbo Accessions Based on EST SSR Markers

EST-SSR markers were applied to estimate the genetic diversity for 30 accessions of Nelumbo nucifera, 6 accessions of Nelumbo lutea and 14 hybrids between these two species. The 52 of 123 EST SSR markers (423%) were screened and then applied to amplify the 50 Nelumbo accessions. A total of 177 alleles were identified, and the number of alleles per locus and Polymorphic Information Content (PIC) value varied from 2 to 8 with an average of 34 alleles and from 063 (NNFB 1059) to 091 (NNFB 750) with an average value of 079, respectively. Jaccard similarity coefficients of the amplification results were analyzed by NTSYS pc2.11 software and the genetic similarity coefficient was from 024 to 086. The clustering dendrogram constructed by UPGMA method indicated that 50 accessions of Nelumbo could be divided into four major groups at the similarity coefficient of 037. Group I and group II included Nnucifera; group III included the majority of Asian American lotus hybrids; and group IV included Nlutea. In addition, the Asian American hybrids were closer to Nnucifera based on genetic relationship, which is consistent with the traditional classification result and the previous reports.     

Genetic diversity analysis in sorghum germplasm as estimated by AFLP, SSR and morpho-agronomical markers

A comparison of the different methods of the estimation of genetic diversity is important to evaluate their utility as a tool in germplasm conservation and plant breeding. Amplified fragment length polymorphism (AFLP), microsatellites or SSR and morphological traits markers were used to evaluate 45 sorghum germplasm for genetic diversity assessment and discrimination power. The mean polymorphism information content (PIC) values were 0.65 (AFLPs) and 0.46 (SSRs). The average pairwise genetic distance estimates were 0.57 (morphological traits), 0.62 (AFLPs) and 0.60 (SSRs) markers data sets. The Shannon diversity index was higher for morphological traits (0.678) than AFLP (0.487) and SSR (0.539). The correlation coefficients obtained by the Mantel matrix correspondence test, which was used to compare the cophenetic matrices for the different markers, showed that estimated values of genetic relationship given for AFLP and SSR markers, as well as for morphological and SSR markers were significantly related (p <0.001). However, morphological and AFLP data showed non-significant correlation (p >0.05). Both data sets from AFLP and SSR allowed all accessions to be uniquely identified; two accessions could not be distinguished by the morphological data. In summary, AFLP and SSR markers proved to be efficient tools in assessing the genetic variability among sorghum genotypes. The patterns of variation appeared to be consistent for the three marker systems, and they can be used for designing breeding programmes, conservation of germplasm and management of sorghum genetic resources.     

The pattern of genetic diversity of Guinea-race Sorghum bicolor (L.) Moench landraces as revealed with SSR markers

The Guinea-race of sorghum [Sorghum bicolor (L.) Moench] is a predominantly inbreeding, diploid cereal crop. It originated from West Africa and appears to have spread throughout Africa and South Asia, where it is now the dominant sorghum race, via ancient trade routes. To elucidate the genetic diversity and differentiation among Guinea-race sorghum landraces, we selected 100 accessions from the ICRISAT sorghum Guinea-race Core Collection and genotyped these using 21 simple sequence repeat (SSR) markers. The 21 SSR markers revealed a total of 123 alleles with an average Dice similarity coefficient of 0.37 across 4,950 pairs of accessions, with nearly 50% of the alleles being rare among the accessions analysed. Stratification of the accessions into 11 countries and five eco-regional groups confirmed earlier reports on the spread of Guinea-race sorghum across Africa and South Asia: most of the variation was found among the accessions from semi-arid and Sahelian Africa and the least among accessions from South Asia. In addition, accessions from South Asia most closely resembled those from southern and eastern Africa, supporting earlier suggestions that sorghum germplasm might have reached South Asia via ancient trade routes along the Arabian Sea coasts of eastern Africa, Arabia and South Asia. Stratification of the accessions according to their Snowden classification indicated clear genetic variation between margeritiferum, conspicuum and Roxburghii accessions, whereas the gambicum and guineënse accessions were genetically similar. The implications of these findings for sorghum Guinea-race plant breeding activities are discussed.     

Genetic diversity and geographical differentiation of Iranian landrace,cultivars, and exotic chickpea lines as revealed by morphological and microsatellite markers

Assessment of the extent of genetic variability within chickpea is fundamental for chickpea breeding and conservation of genetic resources and is particularly useful as a general guide in the choice of parents for breeding hybrids. To establish genetic diversity among 60 accessions of chickpea comprising landraces, internationally developed improved lines, and cultivars, genetic distances were evaluated using 14 simple sequence repeat markers. These markers showed a high level of polymorphism; a total of 59 different alleles were detected, with a mean of 4.2 alleles per locus. The polymorphic information content (PIC) value ranged from 0.31 to 0.89. All the markers, with the exception of TAA170, TA110, GA34, and Ts35, were considered to be informative (PIC > 0.5), indicating their potential usefulness for cultivar identification. Based on the UNJ clustering method, all accessions were clustered in five groups, which indicated the probable origin and region similarity of Iranian landraces over the other cultivars. It also represents a wide diversity among available germplasm. The result has firmly established that introduction of genetic materials from exotic sources has broadened the genetic base of the national chickpea breeding program. As further implications of the findings, this study can be useful for selective breeding for specific traits and in enhancing the genetic base of breeding programs.     

用SSR标记分析抗疫霉根腐病大豆品种(系)的遗传多样性

利用50对SSR引物对抗疫霉根腐病大豆品种(系)进行遗传多样性分析。在166份品种(系)中,50个SSR座位共产生265个等位变异,平均每个座位5.3个。采用NTSYS-pc2.10计算品种(系)间遗传相似系数,平均相似系数为0.3124,表明抗疫霉根腐病大豆品种(系)间的遗传差异较大。用UPMGA进行聚类分析,166个品种(系)在相似系数为0.33时被聚为6类,地理来源相同的品种(系)大多聚类在一起。一些具有相同或相近抗病反应型的品种(系)被聚类在同一个类群中,表明这些抗病品种(系)的遗传关系较近,应有选择地利用。W illiam s和C lark抗疫霉根腐病近等基因系构成明显不同于中国大豆的基因源,可以用于拓宽我国大豆品种的遗传基础。     

高粱抗旱种质筛选及遗传多样性的SSR分析

对61份高粱育种材料进行了抗旱性鉴定,旨在筛选既有较好抗旱性能又具较高丰产性能的高粱种质供育种利用。本研究筛选出抗旱性3级以上的材料14份,其中1级抗旱材料2份。选用109对SSR引物对61份高粱种质进行了遗传多样性分析,结果表明51对引物有较好的多态性,共扩增到508个等位变异片段,平均每个标记获得10个等位基因,多态性信息量(PIC)值平均为0.6615,变幅0.0322~0.9134。聚类分析结果表明,61份高粱材料聚成4类,聚类结果与根据地理来源、遗传背景的分类结果基本一致。中国高粱恢复系之间的遗传距离较近,说明我国目前的恢复系材料遗传基础狭窄,应在育种中拓宽恢复系的遗传基础。     

Genetic diversity in sorghum (Sorghum bicolor (L.) Moench) accessions of Zambia as revealed by simple sequence repeats (SSR)

Twenty seven accessions of sorghum conserved in the national gene bank of Zambia, representing two of the three agroecological regions of the country, were investigated using simple sequence repeats (SSR) markers in order to determine the extent and distribution of its genetic diversity. We used 10 microsatellite primer-pairs, which generated 2-9 alleles per locus and a total of 44 alleles across the 27 accessions. The observed heterozygosity (Ho(P) ) among the accessions ranged from 0 to 0.19 with an average of 0.04 whereas the average expected heterozygosity (He(P) ) among accessions was 0.07 in line with the fact that sorghum is predominately inbreeder. The analysis of molecular variance (AMOVA) revealed that 82% of the total genetic variation was attributable to the genetic variation among accessions (F(ST) = 0.824; p < 0.001) whereas the genetic variation within accessions accounted for 18% of the total genetic variation. AMOVA on sorghum accessions grouped based on four ethnic groups (Soli, Chikunda, Lozi and Tonga) associated with collection sites revealed a highly significant variation among groups (23%; p < 0.001). Although cluster analysis grouped most accessions according to their sites of collection, some accessions that originated from the same site were placed under different clusters. In addition to the extent and pattern of genetic diversity, consideration should also be given to other factors such as ecogeographic and ethnic differences when sampling sorghum genetic resources for rational and efficient conservation and utilization in the breeding program.