title: Allele diversity for abiotic stress responsive candidate genes in chickpea reference set using gene based SNP markers.
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.
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics Hyderabad, India ; University School of Biotechnology, Guru Gobind Singh Indraprastha University Delhi, India.
authors.forename: Manish
authors.initials: M
authors.lastname: Roorkiwal
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics Hyderabad, India ; Agronomy Department, University of Florida Gainesville, FL, USA.
authors.forename: Spurthi N
authors.initials: SN
authors.lastname: Nayak
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics Hyderabad, India.
authors.forename: Mahendar
authors.initials: M
authors.lastname: Thudi
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics Hyderabad, India.
authors.forename: Hari D
authors.initials: HD
authors.lastname: Upadhyaya
authors.affiliation: Etude de Polymorphisme des Génomes Végétaux, INRA Evry, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Brunel
authors.affiliation: UMR AGAP, CIRAD, Montpellier Cedex France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Mournet
authors.affiliation: UMR AGAP, Montpellier SupAgro Montpellier, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: This
authors.affiliation: University School of Biotechnology, Guru Gobind Singh Indraprastha University Delhi, India.
authors.forename: Prakash C
authors.initials: PC
authors.lastname: Sharma
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics Hyderabad, India.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
keywords: abiotic stress; candidate genes; chickpea; genetic diversity; single nucleotide polymorphism