EcoTILLING-Based Association Mapping Efficiently Delineates Functionally Relevant Natural Allelic Variants of Candidate Genes Governing Agronomic Traits in Chickpea

Bajaj, D and Srivastava, R and Nath, M and Tripathi, S and Bharadwaj, C and Upadhyaya, H D and Tyagi, A K and Parida, S K (2016) EcoTILLING-Based Association Mapping Efficiently Delineates Functionally Relevant Natural Allelic Variants of Candidate Genes Governing Agronomic Traits in Chickpea. Frontiers in Plant Science, 07 (450). 01-09. ISSN 1664-462X

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Abstract

The large-scale mining and high-throughput genotyping of novel gene-based allelic variants in natural mapping population are essential for association mapping to identify functionally relevant molecular tags governing useful agronomic traits in chickpea. The present study employs an alternative time-saving, non-laborious and economical pool-based EcoTILLING approach coupled with agarose gel detection assay to discover 1133 novel SNP allelic variants from diverse coding and regulatory sequence components of 1133 transcription factor (TF) genes by genotyping in 192 diverse desi and kabuli chickpea accessions constituting a seed weight association panel. Integrating these SNP genotyping data with seed weight field phenotypic information of 192 structured association panel identified eight SNP alleles in the eight TF genes regulating seed weight of chickpea. The associated individual and combination of all SNPs explained 10–15 and 31% phenotypic variation for seed weight, respectively. The EcoTILLING-based large-scale allele mining and genotyping strategy implemented for association mapping is found much effective for a diploid genome crop species like chickpea with narrow genetic base and low genetic polymorphism. This optimized approach thus can be deployed for various genomics-assisted breeding applications with optimal expense of resources in domesticated chickpea. The seed weight-associated natural allelic variants and candidate TF genes delineated have potential to accelerate marker-assisted genetic improvement of chickpea.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Allele, Association mapping, Chickpea, EcoTILLING, Seed weight, SNP, Transcription factor
Subjects: Mandate crops > Chickpea
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 26 Sep 2016 05:45
Last Modified: 26 Sep 2016 05:46
URI: http://oar.icrisat.org/id/eprint/9692
Official URL: http://dx.doi.org/10.3389/fpls.2016.00450
Projects: UNSPECIFIED
Funders: Department of Biotechnology (DBT), Government of India
Acknowledgement: The authors gratefully acknowledge the financial support by the Department of Biotechnology (DBT), Government of India, through their research grant (102/IFD/SAN/2161/2013-14) for this research work. This article was submitted to Crop Science and Horticulture, a section of the journal Frontiers in Plant Science.
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