Genetic diversity and population structure analysis of chickpea (Cicer arietinum L.) advanced breeding lines using whole-genome DArTseq-generated SilicoDArT markers

Hiva Seyedimoradi | Reza Talebi | Amirmohammad Naji | Ezzat Karami | Homayoun Kanouni

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URL :   http://research.shahed.ac.ir/WSR/WebPages/Report/PaperView.aspx?PaperID=148189
Date :  2020/07/25
Publish in :    Brazilian Journal of Botany
DOI :  https://doi.org/https://doi.org/10.1007/s40415-020-00634-3
Link :  http://dx.doi.org/https://doi.org/10.1007/s40415-020-00634-3
Keywords :Chickpea · Linkage disequilibrium · Genotyping-by-sequencing · Phylogeny

Abstract :

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Chickpea (Cicer arietinum L.) is the third most important legume crop as a stable protein source in human feed. Breeding efforts in chickpea need to find the genotypes with diverse genome background for crossing to produce progenies that are used in the evaluation of favorable traits. In this study, we employed DArTseq-generated SilicoDArT markers for assessment of genetic diversity, population structure and linkage disequilibrium in a panel of 90 chickpea advanced breeding lines. Totally, 9824 SilicoDArT markers generated through DArTseq genotyping and, after filtering, 2053 markers with an average of 265.5 markers per chromosome were used for genetic diversity analysis. Polymorphism information content (PIC) value of SilicoDArT markers ranged from 0.05 to 0.50, with an average of 0.25. Extensive and low level of LD decay in long distances with average r2 = 0.15 was observed. Chickpea genotypes showed high genetic diversity with average kinship value and genetic distance of − 0.54 and 0.36, respectively. Results of cluster analysis, population structure and discriminant analysis of principal component (DAPC) were consistent together in grouping chickpea genotypes into four distinct clusters. These findings demonstrated the efficiency of SilicoDArT markers for large-scale diversity analysis in chickpea, and results can be used for future genomic studies in chickpea such as genome-wide association study and genomic selection for important traits such as seed yield and resistance to abiotic and biotic stresses.