Allele diversity for abiotic stress responsive candidate genes in chickpea reference set using gene based SNP markers
2014
Roorkiwal, Manish | Nayak, Spurthi N. | Thudi, Mahendar | Upadhyaya, Hari D. | Brunel, Dominique | Mournet, Pierre | This, Dominique | Sharma, Prakash C. | Varshney, Rajeev K. | International Crops Research Institute for the Semi-Arid Tropics [Inde] (ICRISAT) ; Consultative Group on International Agricultural Research [CGIAR] (CGIAR) | University School of Biotechnology ; Guru Gobind Singh Indraprastha University | Agronomy Department ; University of Florida [Gainesville] (UF) | Etude du Polymorphisme des Génomes Végétaux (EPGV) ; Institut National de la Recherche Agronomique (INRA) | Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) | Int Crops Res Inst Semi Arid Trop, Hyderabad 502324, Andhra Pradesh, India ; International Crops Research Institute for the Semi-Arid Tropics [Inde] (ICRISAT) ; Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR)
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.
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