Superior haplotypes for haplotype‐based breeding for drought tolerance in pigeonpea ( Cajanus cajan L.)

Sinha, P and Singh, V K and Saxena, R K and Khan, A W and Abbai, R and Chitikineni, A and Desai, A and Molla, J and Upadhyaya, H D and Kumar, A and Varshney, R K (2020) Superior haplotypes for haplotype‐based breeding for drought tolerance in pigeonpea ( Cajanus cajan L.). Plant Biotechnology Journal (TSI). pp. 1-9. ISSN 1467-7644

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Haplotype-based breeding, a recent promising breeding approach to develop tailor-made crop varieties, deals with identification of superior haplotypes and their deployment in breeding programmes. In this context, whole genome re-sequencing data of 292 genotypes from pigeonpea reference set were mined to identify the superior haplotypes for 10 droughtresponsive candidate genes. A total of 83, 132 and 60 haplotypes were identified in breeding lines, landraces and wild species, respectively. Candidate gene-based association analysis of these 10 genes on a subset of 137 accessions of the pigeonpea reference set revealed 23 strong marker-trait associations (MTAs) in five genes influencing seven drought-responsive component traits. Haplo-pheno analysis for the strongly associated genes resulted in the identification of most promising haplotypes for three genes regulating five component drought traits. The haplotype C. cajan_23080-H2 for plant weight (PW), fresh weight (FW) and turgid weight (TW), the haplotype C. cajan_30211-H6 for PW, FW, TW and dry weight (DW), the haplotype C. cajan_26230-H11 for FW and DW and the haplotype C. cajan_26230-H5 for relative water content (RWC) were identified as superior haplotypes under drought stress condition. Furthermore, 17 accessions containing superior haplotypes for three drought-responsive genes were identified. The identified superior haplotypes and the accessions carrying these superior haplotypes will be very useful for deploying haplotype-based breeding to develop nextgeneration tailor-made better drought-responsive pigeonpea cultivars.

Item Type: Article
Divisions: Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC)
Uncontrolled Keywords: Candidate gene-based association analysis, Drought tolerance, Haplotype analysis, Haplotype-based breeding, pigeonpea
Subjects: Others > Drought Tolerance
Others > Plant Breeding
Mandate crops > Pigeonpea
Others > Genetics and Genomics
Depositing User: Mr Arun S
Date Deposited: 26 Aug 2020 07:14
Last Modified: 26 Aug 2020 07:15
Official URL:
Acknowledgement: Authors would like to thank the Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India, Department of Agriculture Cooperation & Farmers Welfare, Ministry of Agriculture, Government of India and Bill & Melinda Gates Foundation (in part) for financial support. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals. ICRISAT is a member of CGIAR Consortium.
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