%O 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.
%K Candidate gene-based association analysis, Drought tolerance, Haplotype analysis, Haplotype-based breeding, pigeonpea
%A P Sinha
%A V K Singh
%A R K Saxena
%A A W Khan
%A R Abbai
%A A Chitikineni
%A A Desai
%A J Molla
%A H D Upadhyaya
%A A Kumar
%A R K Varshney
%I Wiley Open Access
%L icrisat11570
%J Plant Biotechnology Journal (TSI)
%P 1-9
%R doi:10.1111/pbi.13422
%D 2020
%X 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.
%T Superior haplotypes for haplotype‐based breeding for drought tolerance in pigeonpea ( Cajanus cajan L.)