Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers

A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 landraces derived from natural interspecific crosses. Out of 106 SSR markers, 25 polymorphic SSR markers (24 %) detected a total of 76 alleles (average, 3.04; range, 2–5). The average polymorphic information content (PIC) was 0.69 (range, 0.29–0.92). Seventeen RAMPO markers produced 87 polymorphic fragments with average PIC of 0.63 (range, 0.44–0.81). Dendrograms based on SSRs and RAMPOs generated two clusters. All 38 Capsicum annuum genotypes and an interspecific landrace clustered together, whereas nine non-annuum (three Capsicum frutescens, one Capsicum chinense, one Capsicum baccatum and four interspecific landraces) genotypes clustered separately. Genetic variation within non-annuum genotypes was greater than the C. annuum genotypes. Distinctness of interspecific derivative landraces grown in northeast India was validated; natural crossing between sympatric Capsicum species has been proposed as the mechanism of their origin.     

应用SSR标记分析中国糯大麦种质的遗传多样性

利用SSR标记对来自中国不同省市的76份糯大麦种质的遗传多样性进行分析,并以遗传相似系数为基础进行聚类分析。SSR标记分析表明,50对大麦SSR引物在76份糯大麦中共扩增出203个等位基因,属于高度多态性位点范畴。当遗传相似系数为0.70时可将76个糯大麦品种划分为5个类群,在一定程度上反映了与材料的地理来源和皮裸性。糯大麦资源平均Shan-non多样性指数显示,来自云南和西藏的糯大麦品种遗传多样性略高。SSR标记分析表明,中国糯大麦具有丰富的遗传多样性,对揭示糯大麦的起源与传播以及对资源的有效利用具有现实意义。     

Assessment of genetic diversity in Brazilian barley using SSR markers

Barley is a major cereal grown widely and used in several food products, beverage production and animal fodder. Genetic diversity is a key component in breeding programs. We have analyzed the genetic diversity of barley accessions using microsatellite markers. The accessions were composed of wild and domesticated barley representing genotypes from six countries and three breeding programs in Brazil. A total of 280 alleles were detected, 36 unique to Brazilian barley. The marker Bmag120 showed the greatest polymorphism information content (PIC), with the highest mean value found on chromosome three, and the lowest on chromosomes four and six. The wild accessions presented the highest diversity followed by the foreign genotypes. Genetic analysis was performed using Principal Coordinates Analysis, UPGMA clustering, and Bayesian clustering analysis implemented in Structure. All results obtained by the different methods were similar. Loss of genetic diversity has occurred in Brazilian genotypes. The number of alleles detected in genotypes released in 1980s was higher, whereas most of the cultivars released thereafter showed lower PIC and clustered in separate subgroups from the older cultivars. The use of a more diverse panel of genotypes should be considered in order to exploit novel alleles in Brazilian barley breeding programs.     

Genetic diversity analysis of common beans based on molecular markers

A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.     

Genetic diversity among cultivars, landraces and wild relatives of rice as revealed by microsatellite markers

Genetic diversity among 35 rice accessions, which included 19 landraces, 9 cultivars and 7 wild relatives, was investigated by using microsatellite (SSR) markers distributed across the rice genome. The mean number of alleles per locus was 4.86, showing 95.2% polymorphism and an average polymorphism information content of 0.707. Cluster analysis based on microsatellite allelic diversity clearly demarcated the landraces, cultivars and wild relatives into different groups. The allelic richness computed for the clusters indicated that genetic diversity was the highest among wild relatives (0.436), followed by landraces (0.356), and the lowest for cultivars. Allelic variability among the SSR markers was high enough to categorize cultivars, landraces and wild relatives of the rice germplasm, and to catalogue the genetic variability observed for future use. The results also suggested the necessity to introgress genes from landraces and wild relatives into cultivars, for cultivar improvement.     

Comparison of RAMP and SSR markers for the study of wild barley genetic diversity

Two molecular marker technologies, random amplified microsatellite polymorphism (RAMP) and simple sequence repeats (SSR), were used to determine genetic diversity of 27 accessions of the wild barley Hordeum vulgare ssp. spontaneum. 19 primer combinations were used to generate RAMP fragments and 16 SSR loci were analysed. A high level of polymorphism was found with both kind of markers as revealed by the mean polymorphism information content (PIC) values obtained: 0.838 and 0.855 for RAMP and SSR, respectively. Genetic dissimilarities between genotypes were estimated from RAMP and SSR data. A lack of correlation was found between both sets of data. This was reflected in the two dendrograms obtained which presented accessions clustered differently. The results suggest that both sets of markers reveal genetic variation induced by different mechanisms. The dendrogram produced from the RAMP dissimilarity estimates showed most of the groups related to the geographic origin of the accessions.     

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 among East Asian accessions of the barley core collection as revealed by six isozyme loci

 Studies of allelic variations at six isozyme loci revealed genetic diversity of 380 East Asian accessions of the Barley Core Collection. Genetic variation was found in both cultivars and landraces in different regions. Allelic variations at the Aco-1 and Aco-2 loci were detected for East Asian barley for the first time. Moreover, the Aco-1 locus displayed the highest genetic diversity among the six loci assayed. Indian cultivars showed the highest diversity, followed by Korean and Chinese cultivars. Landraces from Bhutan and Nepal showed the lowest diversity. Cultivars had generally higher diversity than landraces within as well as among regions. The cluster analysis of genetic identity showed that all landraces from different countries can be placed in one group; the cultivars from Japan, India and Korea each form independent groups. Gpi-1 Gu, Pgd-1 Tj, Aco-1 Si, Ndh-2 D and Aco-2 A were rare alleles found in only a few accessions of 6-rowed barley. The Pgd-2 Tn allele was very rare in East Asian accessions. Received: 29 July 1998 / Accepted: 2 November 1998     

Morphological and molecular diversity reveal wide variability among sorghum Maldandi landraces from India

Maldandi is a popular sorghum variety for post-rainy or rabi cultivation in southern and central states of India, which is predominantly used for food purpose. Over time many landraces have been collected from these states which have vernacular connection with Maldandi. Genetic diversity among 82 Maldandi landraces, collected from such geographical regions was evaluated using both morphological (quantitative and qualitative) and SSR markers. In general, both morphological and SSR diversity revealed wide variability among the accessions studied. Euclidean distances based on 17 quantitative traits classified the accessions into two major clusters with two out groups, while the 19 qualitative traits clustered the accessions in one major cluster with six out groups. Sixteen out of 20 (80%) SSR markers detected polymorphism among the accessions with average PIC value of 0.36. Un-weighted neighbor joining clustering grouped the accessions into three clusters with 46, 16 and 17 accessions, respectively throwing three outliers. Average similarity coefficients of 0.62 and 0.34 based on morphological (qualitative) and SSR data indicated presence of wide variability among the Maldandi landraces. The standard check, M 35?C1 (a selection from the original Maldandi) could not be differentiated from EP 98, LG 2, LG 10, IS 4509 and IS 40791 based on qualitative data alone, while EP 54 and IS 33839 were indistinguishable from M 35?C1 solely using SSR markers. Either of the dendrogram threw unique grouping patterns with some identity. Thirteen promising Maldandi accessions selected based on field performance as well as morphological and molecular diversity could be used in the rabi improvement programme. SSR markers combined with morphological traits may effectively be used for designing breeding strategy and management of biodiversity and conservation of Maldandi genetic resources.     

RAPD Analysis and the Probable Evolutionary Route of Wild Relatives of Barley from China

he genetic relationships among 12 wild relatives and cultivar of barley ( Hordeum vulgare L.) as well as 1 perennial wild barley grass (H. brevisubulatum (Trin.) Link) from China were investigated by RAPD analysis. 36 out of 63 arbitrary primers produced 285 distinctive bands in total, 219 of which were polymorphic. Clearly resolved bands were treated as independent characters and scored for their presence or absence in a binary data matrix. Simple matching coefficients and Nei's similarity coefficients were calculated respectively. Dendrograms were generated by using the PHYLIP 3.5c software. The results revealed that the cultivated barley and their wild relatives from China were clustered into one group, among which, the two-rowed wild relatives of barley ( H. vulgare L. ssp. spontaneum (Koch) Hsü) and the six-rowed wild forms (H. vulgare L. ssp. agriocrithon (Aberg) Hsü) were respectively clustered into different subgroups. It was considered that wild relatives of barley from China were subspecies of H.vulgare. And it was proposed that the cultivated barley was originally evolved from the two-rowed wild barley. The retrogressive two-rowed wild barley and the bottle-shaped wild forms (H. vulgare L. ssp. agriocrithon var. lagunculiforme Bakht Hsü) were the intermediate types in the evolutionary route from the two-rowed wild barley to the six-rowed wild forms and eventually evolved to the cultivated barley.     

应用微卫星标记研究西藏野生大麦的遗传多样性

以西藏不同地区的106份野生大麦为材料,其中包括50份野生二棱大麦（HS）,27份野生瓶形大麦（HL）和29份野生六棱大麦（HA）,用Liu等（1996）发表的SSR连锁图的每个连锁群的两个臂的不同位置上选取3～5个共30个SSR标记,研究了西藏3类野生大麦的遗传多样性。结果表明,这3类野生大麦在遗传组成及等位变异频率分布上存在着明显的遗传分化。在总样本中,共检测到229个等位变异,平均每个SSR位点检测到7．6个等位变异,其中70个为这3类野生大麦间共同的等位变异,等位变异数在这3类野生大麦间有明显的差异,亚种问的遗传多样性明显高于亚种内的遗传多样性。其遗传多样性大小顺序为HS〉HL〉HA。聚类分析表明,野生二棱大麦、野生六棱大麦分别聚在不同的两类,而野生瓶形大麦中各有约50％的材料分别聚在这两类。根据本研究及前人研究结果,我们认为中国栽培大麦是从野生二棱大麦经野生瓶形大麦向野生六棱大麦进化的。该结果支持了栽培大麦起源的“野生二棱大麦单系起源论”的观点。     

Genetic Diversity and Population Structure Among Oat Cultivars and Landraces

In this study, genetic diversity among 177 oat (Avena sativa L.) accessions including both white and red oat landraces and 36 commercial cultivars was studied for simple sequence repeat (SSR) loci. Thirty-one genomic and expressed sequence tags (EST)-derived primer pairs were selected according to high polymorphism from an initial 66 SSR batch. Markers revealed a high level of polymorphism, detecting a total of 454 alleles. The average gene diversity for the whole sample was 0.29. Genetic similarity, calculated using the Dice coefficient, was used for cluster analysis, and principal component analysis was also applied. In addition, population structure using a Bayesian clustering approach identified discrete subpopulation based on allele frequency and showed similar clustering of oat genotypes in four groups. Accessions could be classified into four main clusters that clearly separated the commercial cultivars, the red oat landraces and two clusters of white oat landraces. Cultivars showed less diversity than the landraces indicating a reduction of genetic diversity during breeding, whereas white oat landraces showed higher diversity than red ones. The average polymorphic information content of 0.80 for the SSR loci indicated the usefulness of many of the SSR for genotype identification. In particular, two markers, MAMA5 and AM04, with a total of 50 alleles and a high discrimination power (>0.90), were sufficient to discriminate among all commercial cultivars studied highlighting their potential use for variety identification.     

云南栽培稻种SSR 遗传多样性比较

采用64个SSR标记对96份云南水稻(Oryz a sativa)地方品种和选育品种的遗传多样性进行比较分析。结果发现64个标记都具有多态性, 共检测到741个等位基因, 每个多态性位点检测到的等位基因数为2-29个, 平均11.57个; Nei基因多样性指数(He)范围在0.345(RM321)-0.932(RM1)之间, 平均为0.56。水稻品种的遗传多样性并非按地理位置均匀分布, 而是在相 似系数为0.17的水平上明显分为2个不同类群, 即籼稻类群和粳稻类群, 且籼粳亚种间的SSR多样性差异不明显, 籼稻平均等位基因数(Ap)和Nei基因多样性指数(Ap=10.6, He=0.46)与粳稻品种(Ap=10.7, He=0.48)十分接近, 可能与这些品种间存在一定频率的基因交流有关。糯稻和非糯稻在籼稻群和粳稻群中都有表现, 没有特别的分布规律。云南栽培稻选育品种与地方稻亲缘关系较近, 其遗传基础可能来源于云南水稻地方品种。本研究结果表明, SSR标记能较好地区分云南栽培稻品种, 且云南水稻地方品种遗传多样性丰富, 存在大量的优质性状可供育种实践选择。     

Genetic diversity in cultivars and landraces of Oryza sativa subsp. indica as revealed by AFLP markers.

Genetic diversity among 49 Indian accessions of rice (Oryza sativa subsp. indica), including 29 landraces from Jeypore, 12 modern cultivars, and 8 traditional cultivars from Tamil Nadu, was investigated using AFLP markers. In total, nine primer combinations revealed 664 AFLPs, 408 of which were found to be polymorphic. The percentage of polymorphic AFLPs was approximately the same within the cultivars and landraces. Similar results were obtained when genetic diversity values were estimated using the Shannon-Weiner index of diversity. Genetic diversity was slightly higher in the modern cultivars than in the traditional cultivars from Tamil Nadu. Among the landraces from Jeypore, the lowland landraces showed the highest diversity. The present study showed that the process of breeding modern cultivars did not appear to cause significant genetic erosion in rice. Cluster analysis and the first component of principle component analysis (PCA) both showed a clear demarcation between the cultivars and landraces as separate groups, although the genetic distance between them was narrow. The modern cultivars were positioned between the landraces from Jeypore and the traditional cultivars from Tamil Nadu. The second component of PCA further separated medium and upland landraces from lowland landraces, with the lowland landraces found closest to the traditional and modern cultivars.     

Functional Genetic Diversity Analysis and Identification of Associated Simple Sequence Repeats and Amplified Fragment Length Polymorphism Markers to Drought Tolerance in Lentil (<Emphasis Type="Italic">Lens culinaris</Emphasis> ssp. <Emphasis Type="Italic">culinaris</Emphasis> Medicus) Landraces

Genetic diversity of 70 Mediterranean lentil (Lens culinaris ssp. culinaris Medicus) landraces was assessed using simple sequence repeats (SSRs) and amplified fragment length polymorphisms (AFLPs). These landraces were also assessed for variation in root and shoot traits and drought tolerance as estimated by relative water content (RWC), water losing rate (WLR) and wilting score (WS). Genetic diversity and clear differentiation of Moroccan landraces from those from northern Mediterranean regions (Italy, Turkey and Greece) were found. High genetic variation in root and shoot traits and traits related to drought tolerance was also observed. No relationship was found between drought tolerance of landraces and their geographic origin. Landraces with higher dry root biomass, chlorophyll content and root–shoot ratio were drought tolerant as evidenced by higher RWC and lower WLR and wilting severity. Kruskal–Wallis non-parametric test (K-W) was used to find SSRs and AFLPs associated with RWC, WLR and WS. Regression analysis showed six SSR and AFLP alleles explaining the highest phenotypic variation of RWC, WLR and WS (ranging from 21 to 50 % for SSRs and from 14 to 33 % for AFLPs). Functional genetic diversity analysis showed relationships between drought response of landraces and linked SSR and AFLP alleles to RWC, WLR and WS according to K-W test using canonical discriminant analysis. Our results confirm the feasibility of using association mapping to find DNA markers associated with drought tolerance in larger numbers of lentil landraces.     

Population Structure and Genetic Diversity in Popular Rice Varieties of India as Evidenced from SSR Analysis

We report here on the phylogenetic analysis, population substructure, and identification of molecular tags of 25 popular rice varieties and four landraces from different ecological belts of India employing a set of 52 simple sequence repeat (SSR) markers. Genetic analysis using the SSR markers categorized the genotypes into two major clusters, distributed according to their pedigree. Population structure analysis suggested that the optimum number of subpopulations was three (K?=?3) in the popular varieties and landraces. At K?=?5 the allelic distribution was much more similar to the phylogenetic dendrogram. The molecular diversity and population structure analysis indicated that there is not much variation among the popular rice cultivars of India. The study has identified SSR markers producing unique alleles, which should aid in the precise identification, maintenance, and genetic purity analysis of rice varieties.     

Patterns of genetic and eco-geographical diversity in Spanish barleys

The pool of Western Mediterranean landraces has been under-utilised for barley breeding so far. The objectives of this study were to assess genetic diversity in a core collection of inbred lines derived from Spanish barley landraces to establish its relationship to barleys from other origins, and to correlate the distribution of diversity with geographical and climatic factors. To this end, 64 SSR were used to evaluate the polymorphism among 225 barley (Hordeum vulgare ssp. vulgare) genotypes, comprising two-row and six-row types. These included 159 landraces from the Spanish barley core collection (SBCC) plus 66 cultivars, mainly from European countries, as a reference set. Out of the 669 alleles generated, a large proportion of them were unique to the six-row Spanish barleys. An analysis of molecular variance revealed a clear genetic divergence between the six-row Spanish barleys and the reference cultivars, whereas this was not evident for the two-row barleys. A model-based clustering analysis identified an underlying population structure, consisting of four main populations for the whole genotype set, and suggested further possible subdivision within two of these populations. Most of the six-row Spanish landraces clustered into two groups that corresponded to geographic regions with contrasting environmental conditions. The existence of wide genetic diversity in Spanish germplasm, possibly related to adaptation to a broad range of environmental conditions, and its divergence from current European cultivars confirm its potential as a new resource for barley breeders, and make the SBCC a valuable tool for the study of adaptation in barley. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic differentiation analysis of African cassava (Manihot esculenta) landraces and elite germplasm using amplified fragment length polymorphism and simple sequence repeat markers

Molecular‐marker‐aided evaluation of germplasm plays an important role in defining the genetic diversity of plant genotypes for genetic and population improvement studies. A collection of African cassava landraces and elite cultivars was analysed for genetic diversity using 20 amplified fragment length polymorphic (AFLP) DNA primer combinations and 50 simple sequence repeat (SSR) markers. Within‐population diversity estimates obtained with both markers were correlated, showing little variation in their fixation index. The amount of within‐population variation was higher for landraces as illustrated by both markers, allowing discrimination among accessions along their geographical origins, with some overlap indicating the pattern of germplasm movement between countries. Elite cultivars were grouped in most cases in agreement with their pedigree and showed a narrow genetic variation. Both SSR and AFLP markers showed some similarity in results for the landraces, although SSR provided better genetic differentiation estimates. Genetic differentiation (Fst) in the landrace population was 0.746 for SSR and 0.656 for AFLP. The molecular variance among cultivars in both populations accounted for up to 83% of the overall variation, while 17% was found within populations. Gene diversity (H_e) estimated within each population varied with an average value of 0.607 for the landraces and 0.594 for the elite lines. Analyses of SSR data using ordination techniques identified additional cluster groups not detected by AFLP and also captured maximum variation within and between both populations. Our results indicate the importance of SSR and AFLP as efficient markers for the analysis of genetic diversity and population structure in cassava. Genetic differentiation analysis of the evaluated populations provides high prospects for identifying diverse parental combinations for the development of segregating populations for genetic studies and the introgression of desirable genes from diverse sources into the existing genetic base.     

Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.)

A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley ( Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3'-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5'-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 +/- 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity.