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Background  Restoration of fertility ( Rf ) is an important trait for pigeonpea hybrid breeding. Few coarse quantitative trait locus (QTL) studies conducted in the past identified QTLs with large confidence intervals on the genetic map and could not provide any information on possible genes responsible for  Rf  in pigeonpea. Therefore, a larger population comprising of 369 F 2 s derived from ICPA 2039 × ICPL 87119 was genotyped with high density Axiom  Cajanus  SNP Array with 56 K single nucleotide polymorphism (SNPs) for high resolution mapping of  Rf .    Results  A genetic map with 4867 markers was developed and a total of four QTLs for  Rf  were identified. While one major effect QTL ( qRf 8.1) was co-localized with the QTL identified in two previous studies and its size was refined from 1.2 Mb to 0.41 Mb. Further analysis of  qRf 8.1 QTL with genome sequence provided 20 genes including two genes namely flowering locus protein T and 2-oxoglutarate/Fe (II)-dependent dioxygenases (2-ODDs) superfamily protein with known function in the restoration of fertility.    Conclusion  The  qRf 8.1 QTL and the potential candidate genes present in this QTL will be valuable for genomics-assisted breeding and identification of causal genes/nucleotides for the restoration of fertility in the hybrid breeding program of pigeonpea.

bmc genomics

High resolution mapping of restoration of fertility (Rf) by combining large population and high density genetic map in pigeonpea [Cajanus cajan (L.) Millsp]