Roorkiwal, M and Nayak, S N and Thudi, M and Upadhyaya, H D and Brunel, D and Mournet, P and This, D and Sharma, P C and Varshney, R K (2014) Allele diversity for abiotic stress responsive candidate genes in chickpea reference set using gene based SNP markers. Frontiers in Plant Science, 5 (248). pp. 1-11. ISSN 1664-462X
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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.
| Item Type: | Article |
|---|---|
| Divisions: | RP-Grain Legumes |
| CRP: | CGIAR Research Program on Grain Legumes |
| Uncontrolled Keywords: | chickpea,abiotic stress,single nucleotide polymorphism,genetic diversity,candidate genes |
| Subjects: | Mandate crops > Chickpea Others > Genetics and Genomics |
| Depositing User: | Mr Siva Shankar |
| Date Deposited: | 06 Jun 2014 03:35 |
| Last Modified: | 06 Jun 2014 03:35 |
| URI: | http://oar.icrisat.org/id/eprint/8097 |
| Official URL: | http://dx.doi.org/10.3389/fpls.2014.00248 |
| Projects: | UNSPECIFIED |
| Funders: | CGIAR Generation Challenge Programme(GCP), Mexico, Government of India - Department of Biotechnology |
| Acknowledgement: | Authors are thank- ful to Dr.Julie Hoffer for hercomments/suggestions to improve the MS. This work has been under taken as part of the CGIAR Research Program on Grain Legumes.ICRISAT is a member of CGIAR Consortium. Thanks are also due to several colleagues at ICRISAT, GGSIPU and partners in collaborating centers. |
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