Whole Genome Diversity, Population Structure, and Linkage Disequilibrium Analysis of Chickpea (Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers

Somayeh Farahani; Mojdeh Maleki; Rahim Mehrabi; Homayoun Kanouni; Armin Scheben; Jacqueline Batley; Reza Talebi

doi:10.3390/genes10090676

Whole Genome Diversity, Population Structure, and Linkage Disequilibrium Analysis of Chickpea (Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers

Genes (Basel). 2019 Sep 4;10(9):676. doi: 10.3390/genes10090676.

Authors

Somayeh Farahani¹, Mojdeh Maleki¹, Rahim Mehrabi², Homayoun Kanouni³, Armin Scheben⁴, Jacqueline Batley⁴, Reza Talebi⁵

Affiliations

¹ Department of Plant Protection, Varamin-Pishva Branch, Islamic Azad University, Varamin, P.O.Box: 33817-74895, Iran.
² Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan P.O. Box: 8415683111, Iran.
³ Kordestan Agricultural and Natural Resources and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Sanandaj, P.O.Box:714, Iran.
⁴ School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia.
⁵ Department of Agronomy & Plant Breeding, College of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, P.O. Box:618, Iran. srtalebi@yahoo.com.

Abstract

Characterization of genetic diversity, population structure, and linkage disequilibrium is a prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes, including advanced "Kabuli" breeding lines and Iranian landrace "Desi" chickpea genotypes, were genotyped using DArTseq-Based single nucleotide polymorphism (SNP) markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that was covered by SNPs varied from 16,236.36 kbp (LG8) to 67,923.99 kbp (LG5), while LG4 showed a higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6, and LG8 showed higher mean PIC value than average. Unweighted neighbor joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and discriminant analysis of principal component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r² ≥ 0.8, while 2961 pairs of markers showed complete LD (r² = 1), and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggest the presence of a high genetic diversity among the studied chickpea genotypes. This study also demonstrates the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits, such as seed yield, abiotic, and biotic stresses, and therefore can be efficiently used in breeding programs to improve chickpea.

Keywords: DArTseq-SNP markers; chickpea; genetic diversity; linkage disequilibrium.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cicer / genetics*
Genotype
Linkage Disequilibrium*
Polymorphism, Single Nucleotide*