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Genetic diversity of grasspea and its relative species revealed by SSR markers.

ABSTRACT: The study of genetic diversity between Lathyrus sativus L. and its relative species may yield fundamental insights into evolutionary history and provide options to meet the challenge of climate changes. 30 SSR loci were employed to assess the genetic diversity and population structure of 283 individuals from wild and domesticated populations from Africa, Europe, Asia and ICARDA. The allele number per loci ranged from 3 to 14. The average gene diversity index and average polymorphism information content (PIC) was 0.5340 and 0.4817, respectively. A model based population structure analysis divided the germplasm resources into three subgroups: the relative species, the grasspea from Asia, and the grasspea from Europe and Africa. The UPGMA dendrogram and PCA cluster also demonstrated that Asian group was convincingly separated from the other group. The AMOVA result showed that the cultivated species was quite distinct from its relative species, however a low level of differentiation was revealed among their geographic origins. In all, these results provided a molecular basis for understanding genetic diversity of L. sativus and its relatives.

SUBMITTER: Wang F

PROVIDER: S-EPMC4368647 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Genetic diversity of grasspea and its relative species revealed by SSR markers.

Wang Fang F Yang Tao T Burlyaeva Marina M Li Ling L Jiang Junye J Fang Li L Redden Robert R Zong Xuxiao X

PloS one 20150320 3

The study of genetic diversity between Lathyrus sativus L. and its relative species may yield fundamental insights into evolutionary history and provide options to meet the challenge of climate changes. 30 SSR loci were employed to assess the genetic diversity and population structure of 283 individuals from wild and domesticated populations from Africa, Europe, Asia and ICARDA. The allele number per loci ranged from 3 to 14. The average gene diversity index and average polymorphism information ...[more]

PMID: 25793712

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Project description:Twenty-five primer pairs developed from genomic simple sequence repeats (SSR) were compared with 25 expressed sequence tags (EST) SSRs to evaluate the efficiency of these two sets of primers using 59 sugarcane genetic stocks. The mean polymorphism information content (PIC) of genomic SSR was higher (0.72) compared to the PIC value recorded by EST-SSR marker (0.62). The relatively low level of polymorphism in EST-SSR markers may be due to the location of these markers in more conserved and expressed sequences compared to genomic sequences which are spread throughout the genome. Dendrogram based on the genomic SSR and EST-SSR marker data showed differences in grouping of genotypes. A total of 59 sugarcane accessions were grouped into 6 and 4 clusters using genomic SSR and EST-SSR, respectively. The highly efficient genomic SSR could subcluster the genotypes of some of the clusters formed by EST-SSR markers. The difference in dendrogram observed was probably due to the variation in number of markers produced by genomic SSR and EST-SSR and different portion of genome amplified by both the markers. The combined dendrogram (genomic SSR and EST-SSR) more clearly showed the genetic relationship among the sugarcane genotypes by forming four clusters. The mean genetic similarity (GS) value obtained using EST-SSR among 59 sugarcane accessions was 0.70, whereas the mean GS obtained using genomic SSR was 0.63. Although relatively lower level of polymorphism was displayed by the EST-SSR markers, genetic diversity shown by the EST-SSR was found to be promising as they were functional marker. High level of PIC and low genetic similarity values of genomic SSR may be more useful in DNA fingerprinting, selection of true hybrids, identification of variety specific markers and genetic diversity analysis. Identification of diverse parents based on cluster analysis can be effectively done with EST-SSR as the genetic similarity estimates are based on functional attributes related to morphological/agronomical traits.

Project description:Cocoyam (Xanthosoma sagittifolium (L.) Schott) is an exotic species from tropical America that is widely cultivated in Ethiopia for its edible cormels and leaves. There is a dearth of information on the genetic diversity of Ethiopian cocoyam. In order to evaluate and select cocoyam germplasm for breeding and conservation, genetic diversity of 100 Ethiopian cocoyam accessions (65 green- and 35 purple- cocoyam) were analyzed using 29 morphological traits (16 qualitative and 13 quantitative) and 12 SSR loci. Two classes of qualitative traits were observed. ANOVA revealed significant variation in 11 (84.6%) of the 13 studied quantitative traits. The SSR marker analysis showed high genetic diversity. A total of 36 alleles were detected with a range of 2 to 5 (average of 3.273) alleles per locus. The average observed heterozygosity (Ho) and expected heterozygosity (He) values across populations were 0.503 and 0.443, respectively. The analysis of molecular variance showed that the variation among populations, among individuals within populations, and within individuals explained 14%, 18%, and 68% of the total variation, respectively. Cluster analysis grouped the accessions irrespective of the collection sites. A dendrogram based on Nei's standard genetic distance grouped the green cocoyam accessions together while the purple cocoyam accessions occupied a separate position within the dendrogram. Significant variation in quantitative traits and the high level of genetic diversity revealed by the SSR markers suggest that diverse cocoyam accessions, probably with multiple lineage, were introduced multiple times, through multiple routes and probably by multiple agents, an hypothesis that needs futher testing and analyis. The crop, therefore, needs more research efforts commensurate with its economic and social values than it has been accorded thus far. Further study is recommended to clarify the taxonomic status of Ethiopian cocoyam accesions and to trace their evolutionary relationships with Xanthosoma species elsewhere.

Dataset Information

Genetic diversity of grasspea and its relative species revealed by SSR markers.

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Genetic diversity of grasspea and its relative species revealed by SSR markers.

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