Genetic Diversity and Population Structure of Tetraploid Wheats (Triticum turgidum L.) Estimated by SSR,DArT and Pedigree Data

Levels of genetic diversity and population genetic structure of a collection of 230 accessions of seven tetraploid Triticum turgidum L. subspecies were investigated using six morphological, nine seed storage protein loci, 26 SSRs and 970 DArT markers. The genetic diversity of the morphological traits and seed storage proteins was always lower in the durum wheat compared to the wild and domesticated emmer. Using Bayesian clustering (K = 2), both of the sets of molecular markers distinguished the durum wheat cultivars from the other tetraploid subspecies, and two distinct subgroups were detected within the durum wheat subspecies, which is in agreement with their origin and year of release. The genetic diversity of morphological traits and seed storage proteins was always lower in the improved durum cultivars registered after 1990, than in the intermediate and older ones. This marked effect on diversity was not observed for molecular markers, where there was only a weak reduction. At K >2, the SSR markers showed a greater degree of resolution than for DArT, with their identification of a greater number of groups within each subspecies. Analysis of DArT marker differentiation between the wheat subspecies indicated outlier loci that are potentially linked to genes controlling some important agronomic traits. Among the 211 loci identified under selection, 109 markers were recently mapped, and some of these markers were clustered into specific regions on chromosome arms 2BL, 3BS and 4AL, where several genes/quantitative trait loci (QTLs) are involved in the domestication of tetraploid wheats, such as the tenacious glumes (Tg) and brittle rachis (Br) characteristics. On the basis of these results, it can be assumed that the population structure of the tetraploid wheat collection partially reflects the evolutionary history of Triticum turgidum L. subspecies and the genetic potential of landraces and wild accessions for the detection of unexplored alleles.     

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.     

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.     

豌豆种质表型性状SSR标记关联分析

关联分析是以连锁不平衡原理为基础,鉴定某一群体内表型性状与遗传标记或候选基因间关系的遗传分析方法。本研究利用59个多态性SSR标记,对192份豌豆种质进行全基因组扫描,以分析SSR位点遗传多样性,寻找其连锁不平衡位点;采用TASSEL软件的一般线性模型,利用59个SSR标记对19个形态性状进行关联分析。结果显示SSR位点间有较高的多态性和一定程度的连锁不平衡,共检测出32个SSR标记位点与14个表形性状相关联,一些SSR标记与2个或多个形态性状相关联。     

Genetic structure and a selected core set of Brazilian soybean cultivars

Soybean is one of the most valuable and profitable oil crop species and a thorough knowledge of the genetic structure of this crop is necessary for developing the best breeding strategies. In this study, a representative collection of soybean cultivars recommended for farming in all Brazilian regions was genotyped using 27 simple sequence repeat (SSR) loci. A total of 130 alleles were detected, with an average allelic number of 4.81 per locus. These alleles determined the core set that best represented this soybean germplasm. The Bayesian analysis revealed the presence of two clusters or subgroups within the whole collection (435 soybean cultivars) and the core set (31 entries). Cultivars of similar origin (ancestral) were clustered into the same groups in both analyses. The genetic diversity parameters, based on the SSR loci, revealed high similarity between the whole collection and core set. Differences between the two clusters detected in the core set were attributed more to the frequency of their ancestors than to their genetic base. In terms of ancestry, divergent groups were presented and a panel is shown which may foster efficient breeding programs and aid soybean breeders in planning reliable crossings in the development of new varieties.     

Comparison of different methods to construct a core germplasm collection in woody perennial species with simple sequence repeat markers. A case study in cherimoya (Annona cherimola, Annonaceae), an underutilised subtropical fruit tree species

Although molecular markers are becoming the tool of choice to develop core collections in plants, the examples of their use in woody perennial species are very scarce. In this work, we used simple sequence repeat (SSR) marker data to develop a core collection in an underutilised subtropical fruit tree species, cherimoya ( Annona cherimola , Annonaceae), from an initial collection of 279 genotypes from different countries. We compared six alternative allocation methods to construct the core collection, four not based upon the similarity dendrogram [random sampling, maximisation strategy (M strategy) and simulated annealing algorithm maximising both genetic diversity and number of SSR alleles] and two based on dendrogram data (logarithmic strategy and stepwise clustering). The diversity maintained in each subset was compared with that present in the entire collection. The results obtained indicate that the use of SSRs together with the M strategy is the most efficient method to develop a core collection in cherimoya. In the best subset, with 40 accessions, all the SSR alleles present in the whole collection were recovered and no significant differences in frequency distribution of alleles for any of the loci studied or in variability parameters ( H _O, H _E) were recorded between the core and the whole collection.     

Simple Sequence Repeat Analysis of Genetic Diversity in Primary Core Collection of Peach （Prunus persica）

In this study, the genetic diversity of 51 cultivars in the primary core collection of peach （Prunus persica （L.） Batsch） was evaluated by using simple sequence repeats （SSRs）. The phylogenetic relationships and the evolutionary history among different cultivars were determined on the basis of SSR data. Twenty-two polymorphic SSR primer pairs were selected, and a total of 111 alleles were identified in the 51 cultivars, with an average of 5 alleles per locus. According to traditional Chinese classification of peach cultivars, the 51 cultivars in the peach primary core collection belong to six variety groups. The SSR analysis revealed that the levels of the genetic diversity within each variety group were ranked as Sweet peach 〉 Crisp peach 〉 Flat peach 〉 Nectarine 〉 Honey Peach 〉 Yellow fleshed peach. The genetic diversity among the Chinese cultivars was higher than that among the introduced cultivars. Cluster analysis by the unweighted pair group method with arithmetic averaging （UPGMA） placed the 51 cultivars into five linkage clusters. Cultivar members from the same variety group were distributed in different UPGMA clusters and some members from different variety groups were placed under the same cluster. Different variety groups could not be differentiated in accordance with SSR markers. The SSR analysis revealed rich genetic diversity in the peach primary core collection, representative of genetic resources of peach.     

Genetic diversity and association mapping in a collection of selected Chinese soybean accessions based on SSR marker analysis

For broadening the narrow genetic base of modern soybean cultivars, 159 accessions were selected from the Chinese soybean collection which contained at least one of seven important agronomic traits: resistance to soybean cyst nematode (SCN) or soybean mosaic virus (SMV), tolerance to salt, cold, or drought, high seed oil content or high protein content. Genetic diversity evaluation using 55 microsatellite loci distributed across the genome indicated that a large amount of genetic diversity (0.806) and allelic variation (781) were conserved in this selected set, which captured 65.6% of the alleles present in Chinese soybean collection (1,863 accessions). On average, 9.4 rare alleles (frequency <5%) per locus were present, which were highly informative. Using model-based Bayesian clustering in STRUCTURE we distinguished four main clusters and a set of accessions with admixed ancestry. The four clusters reflected different geographic regions of origin of the accessions. Since the clusters were also clearly different with respect to the seven agronomic traits, the inferred population structure was introduced when association analysis was conducted. A total of 21 SSR markers on 16 chromosomes were identified as significantly (P < 0.01) associated with high oil content (6), high protein content (1), drought tolerance (5), SCN resistance (6) and SMV resistance (3). Twelve of these markers were located in or near previously identified quantitative trait loci (QTL). The results for both genetic relationship and trait-related markers will be useful for effective conservation and utilization of soybean germplasm.     

利用分子标记和数量性状基因型值构建作物核心种质库的研究

提出了一种基于分子标记数据及数量性状基因型值构建作物种质资源核心种质库的方法.采用包括基因型与环境互作的遗传模型及相应的混合线性模型统计分析方法,无偏预测各材料的基因型值,分别用基因型值和分子标记数据计算个体间的相似系数,加权得到最终的相似距离.采用不加权类平均法（UPGMA）进行系统聚类,用多次聚类随机取样法构建核心种质库.以水稻DH群体111个基因型8个农艺性状、175个分子标记位点的数据为实例,按四种抽样比率（25%,20%,15%,10%）构建了四个核心种质库,比较了核心种质库与整个群体的分子标记多样性及数量性状的遗传变异,评价了所用方法的有效性。     

SSR-based genetic diversity and structure of garlic accessions from Brazil

Garlic is a spice and a medicinal plant; hence, there is an increasing interest in ‘developing’ new varieties with different culinary properties or with high content of nutraceutical compounds. Phenotypic traits and dominant molecular markers are predominantly used to evaluate the genetic diversity of garlic clones. However, 24 SSR markers (codominant) specific for garlic are available in the literature, fostering germplasm researches. In this study, we genotyped 130 garlic accessions from Brazil and abroad using 17 polymorphic SSR markers to assess the genetic diversity and structure. This is the first attempt to evaluate a large set of accessions maintained by Brazilian institutions. A high level of redundancy was detected in the collection (50 % of the accessions represented eight haplotypes). However, non-redundant accessions presented high genetic diversity. We detected on average five alleles per locus, Shannon index of 1.2, H_O of 0.5, and H_E of 0.6. A core collection was set with 17 accessions, covering 100 % of the alleles with minimum redundancy. Overall F_ST and D values indicate a strong genetic structure within accessions. Two major groups identified by both model-based (Bayesian approach) and hierarchical clustering (UPGMA dendrogram) techniques were coherent with the classification of accessions according to maturity time (growth cycle): early-late and midseason accessions. Assessing genetic diversity and structure of garlic collections is the first step towards an efficient management and conservation of accessions in genebanks, as well as to advance future genetic studies and improvement of garlic worldwide.     

Genetic diversity analysis of 60 ginger germplasm core accessions using ISSR and SSR markers

Molecular techniques play a critical role in studies of phylogeny and, thus, have been applied to understand the distribution and extent of genetic variation within and between species. In the present study, a genetic analysis was undertaken using molecular markers (9 ISSR and 13 SSR) on 60 ginger cultivars from different regions of the eastern coast of India (Odisha). The data obtained with 22 polymorphic markers revealed moderate to high diversity in the collection. Both ISSR and SSR markers were efficient in distinguishing all the 60 ginger cultivars. A total of 42 and 160 polymorphic bands were observed with ISSR and SSR markers, respectively. However, SSR markers were observed to be better at displaying average polymorphism (63.29%) than ISSR markers (55%). Analysis of molecular variance results showed that 52 and 66% of the variation occurred among different ginger populations, whereas 48 and 34% of the variation was found within populations, respectively, using ISSR and SSR markers, indicating that ginger cultivars display significant genetic diversity at the population level. Principal coordinates analysis and the dendrogram constructed out of combined data of both markers showed grouping of ginger accessions to their respective area of collection, indicating geographical closeness due to genetic similarity irrespective of the relationship that exists at the morphological level.     

Evaluation of Genetic Diversity and Development of a Core Collection of Wild Rice (Oryza rufipogon Griff.) Populations in China

Common wild rice (Oryza rufipogon Griff.), the progenitor of Asian cultivated rice (O. sativa L.), is endangered due to habitat loss. The objectives of this research were to evaluate the genetic diversity of wild rice species in isolated populations and to develop a core collection of representative genotypes for ex situ conservation. We collected 885 wild rice accessions from eight geographically distinct regions and transplanted these accessions in a protected conservation garden over a period of almost two decades. We evaluated these accessions for 13 morphological or phenological traits and genotyped them for 36 DNA markers evenly distributed on the 12 chromosomes. The coefficient of variation of quantitative traits was 0.56 and ranged from 0.37 to 1.06. SSR markers detected 206 different alleles with an average of 6 alleles per locus. The mean polymorphism information content (PIC) was 0.64 in all populations, indicating that the marker loci have a high level of polymorphism and genetic diversity in all populations. Phylogenetic analyses based on morphological and molecular data revealed remarkable differences in the genetic diversity of common wild rice populations. The results showed that the Zengcheng, Gaozhou, and Suixi populations possess higher levels of genetic diversity, whereas the Huilai and Boluo populations have lower levels of genetic diversity than do the other populations. Based on their genetic distance, 130 accessions were selected as a core collection that retained over 90% of the alleles at the 36 marker loci. This genetically diverse core collection will be a useful resource for genomic studies of rice and for initiatives aimed at developing rice with improved agronomic traits.     

Molecular and Cytogenetic Characterization of Wild Musa Species

The production of bananas is threatened by rapid spreading of various diseases and adverse environmental conditions. The preservation and characterization of banana diversity is essential for the purposes of crop improvement. The world''s largest banana germplasm collection maintained at the Bioversity International Transit Centre (ITC) in Belgium is continuously expanded by new accessions of edible cultivars and wild species. Detailed morphological and molecular characterization of the accessions is necessary for efficient management of the collection and utilization of banana diversity. In this work, nuclear DNA content and genomic distribution of 45S and 5S rDNA were examined in 21 diploid accessions recently added to ITC collection, representing both sections of the genus Musa. 2C DNA content in the section Musa ranged from 1.217 to 1.315 pg. Species belonging to section Callimusa had 2C DNA contents ranging from 1.390 to 1.772 pg. While the number of 45S rDNA loci was conserved in the section Musa, it was highly variable in Callimusa species. 5S rRNA gene clusters were found on two to eight chromosomes per diploid cell. The accessions were genotyped using a set of 19 microsatellite markers to establish their relationships with the remaining accessions held at ITC. Genetic diversity done by SSR genotyping platform was extended by phylogenetic analysis of ITS region. ITS sequence data supported the clustering obtained by SSR analysis for most of the accessions. High level of nucleotide diversity and presence of more than two types of ITS sequences in eight wild diploids pointed to their origin by hybridization of different genotypes. This study significantly expands the number of wild Musa species where nuclear genome size and genomic distribution of rDNA loci is known. SSR genotyping identified Musa species that are closely related to the previously characterized accessions and provided data to aid in their classification. Sequence analysis of ITS region provided further information about evolutionary relationships between individual accessions and suggested that some of analyzed accessions were interspecific hybrids and/or backcross progeny.     

Establishment of a Core Collection of Traditional Cuban <Emphasis Type="Italic">Theobroma cacao</Emphasis> Plants for Conservation and Utilization Purposes

Presently, Theobroma cacao L. (cacao) in Cuba is mainly cultivated in the eastern region where plantations comprise a mixture of clonal varieties, hybrids, progeny of Trinidad Selected Hybrids, and traditional—also known as ancient—cacao. The ancient genetic resources, probably the plants most closely related to the original introductions, are endangered by their progressive replacement by modern clones. To promote the conservation and utilization of these genetic resources, a representative sample of 537 traditional Cuban cacao plants was used to develop a core collection. Core collections based on 15 simple sequence repeat (SSR) markers were generated using five different sampling algorithms: random sampling, simulated annealing, stepwise clustering with random sampling, the M strategy, and maximum genetic diversity. The five core collections were designed to capture 95 % of the SSR alleles in the complete collection. The genetic, morphological, and geographical diversity of each core collection was compared with that of the entire collection. The entire collection contained 139 alleles, including 104 rare ones, with the 95 % allelic coverage threshold achieved with 133 alleles. The core collection generated by the maximum genetic diversity algorithm had the lowest number of accessions (185), the highest mean genetic distance (0.486), the lowest morphological character redundancy, and the highest diversity as assessed by the mean Shannon-Weaver diversity index (0.757). This core collection can thus serve as the basis of future improvement programs based on local genetic resources.     

Evaluation of genetic diversity and chemical profile of ginger cultivars in north-western Himalayas

Eighteen ginger cultivars from Northwest Himalayan region, showing significant differences in rhizome size, texture and pungency, were selected and characterized both by chemical and genetic analyses. The genetic analysis was undertaken utilizing molecular markers (ISSR and SSR) while chemical characterization was done through HPLC of four chemical markers (gingerol homologues and shogaol). The data revealed moderate to high diversity in the collection, clustering them broadly into two groups. Both ISSR and SSR techniques were efficient in distinguishing all the 18 ginger cultivars, however, SSR markers were observed to be better in displaying average polymorphism (77.8%) than ISSR (66.7%). Based on statistical analysis, one ISSR and two SSR primers could be identified which effectively distinguished closely related ginger cultivars. Chemical profiling and subsequent multivariate analysis distinguished five lines which were distinct from rest of the collection. The study has contributed in understanding the genetic and chemical diversity of the region, characterization of lines for commercial exploitation and ginger gene pool conservation.     

Genetic diversity and trait genomic prediction in a pea diversity panel

Background

Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection.

Results

A collection of diverse pea accessions, including landraces and cultivars of garden, field or fodder peas as well as wild peas was characterised at the molecular level using newly developed SNP markers, as well as SSR markers and RBIP markers. The three types of markers were used to describe the structure of the collection and revealed different pictures of the genetic diversity among the collection. SSR showed the fastest rate of evolution and RBIP the slowest rate of evolution, pointing to their contrasted mode of evolution. SNP markers were then used to predict phenotypes -the date of flowering (BegFlo), the number of seeds per plant (Nseed) and thousand seed weight (TSW)- that were recorded for the collection. Different statistical methods were tested including the LASSO (Least Absolute Shrinkage ans Selection Operator), PLS (Partial Least Squares), SPLS (Sparse Partial Least Squares), Bayes A, Bayes B and GBLUP (Genomic Best Linear Unbiased Prediction) methods and the structure of the collection was taken into account in the prediction. Despite a limited number of 331 markers used for prediction, TSW was reliably predicted.

Conclusion

The development of marker assisted selection has not reached its full potential in pea until now. This paper shows that the high-throughput SNP arrays that are being developed will most probably allow for a more efficient selection in this species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1266-1) contains supplementary material, which is available to authorized users.     

Genetic diversity in a collection of old and new bread wheat cultivars from Iran as revealed by simple sequence repeat-based analysis

Genetic diversity in a collection of 70 bread wheat ( Triticum aestivum ) genotypes was studied using 73 microsatellite [simple sequence repeat (SSR)] loci evenly spaced on wheat chromosomes. A total of 592 alleles with an average of 8.53 allele/locus were detected, of which 185 (31.25%) occurred only in a specific group of genotypes. A set of SSR markers consisted of 22 loci with polymorphic information content values of 0.80 or higher were selected for rapid fingerprinting of many genotypes. Average of gene diversity was 0.74 ± 0.017, and significant difference between observed and maximum theoretical values of gene diversity in the analysed SSR loci was obtained using a paired t -test. Genetic distance-based clustering methods including unweighted pair group method with arithmetic average and neighbour joining (NJ) were used for grouping of genotypes. The resulted dendrogram based on NJ and number of differences coefficient hinted of the existence of three groups. This grouping was in agreement with the pedigree information and confirmed by high within-group bootstrap value. A comparatively higher genetic diversity in the studied wheat collection as revealed by presence of high allelic diversity and large number of specific alleles could be utilised in development of new cultivars with desired characteristics.