Allele diversity for abiotic stress responsive candidate genes in chickpea reference set using gene based SNP markers.

Manish Roorkiwal,Spurthi N. Nayak,Prakash C. Sharma,Mahendar Thudi,Hari D. Upadhyaya,Rajeev K. Varshney,Dominique This,Dominique Brunel,Pierre Mournet

doi:10.3389/fpls.2014.00248

Abstract

Chickpea is an important food legume crop for the semi-arid regions, however, its productivity is adversely affected by various biotic and abiotic stresses. Identification of candidate genes associated with abiotic stress response will help breeding efforts aiming to enhance its productivity. With this objective, 10 abiotic stress responsive candidate genes were selected on the basis of prior knowledge of this complex trait. These 10 genes were subjected to allele specific sequencing across a chickpea reference set comprising 300 genotypes including 211 genotypes of chickpea mini core collection. A total of 1.3 Mbp sequence data were generated. Multiple sequence alignment (MSA) revealed 79 SNPs and 41 indels in nine genes while the CAP2 gene was found to be conserved across all the genotypes. Among 10 candidate genes, the maximum number of SNPs (34) was observed in abscisic acid stress and ripening (ASR) gene including 22 transitions, 11 transversions and one tri-allelic SNP. Nucleotide diversity varied from 0.0004 to 0.0029 while polymorphism information content (PIC) values ranged from 0.01 (AKIN gene) to 0.43 (CAP2 promoter). Haplotype analysis revealed that alleles were represented by more than two haplotype blocks, except alleles of the CAP2 and sucrose synthase (SuSy) gene, where only one haplotype was identified. These genes can be used for association analysis and if validated, may be useful for enhancing abiotic stress, including drought tolerance, through molecular breeding.

Highlights

Chickpea (Cicer arietinum L., 2n = 16), a self-pollinated, diploid annual species which ranks second worldwide as a food legume crop, is primarily a crop of developing countries contributing to a larger part of human food and animal feed in these areas
The present study was initiated with the objective of the identification of favorable alleles in abiotic stress responsive genes in the chickpea reference set
Due to lack of genome sequence information of the chickpea genome until recently (Varshney et al, 2013), identification of genes responsible for complex traits like drought tolerance was a daunting task at the time of initiation of this study

Summary

Introduction

Productivity of chickpea is adversely affected by several abiotic stresses of which drought, heat and cold are the major constraints affecting seed yield (Ruelland et al, 2002). Application of available approaches to improve crop productivity under adverse environmental conditions requires a better understanding of the mechanisms involved during crop’s response to abiotic stress. Genomic technologies and comparative genomics approaches that have emerged during the past decade can be exploited to identify some of the genes involved in drought tolerance mechanisms. Candidate genes for stress tolerance may be used in crop improvement programs directly (transgenic approach) or indirectly (through identification of linked SNPs) (Schena et al, 1995; Kudapa et al, 2013). The reference set (Upadhyaya et al, 2008) includes four C. reticulatum genotypes and three C. echinospermum genotypes, but the majority (293 genotypes) is C. arietinum (Upadhyaya et al, 2006)

Methods

Results

Conclusion