Identification of genomic regions associated with the yield and related traits in pigeonpea (Cajanus cajan L. Millsp.)

Pigeonpea [Cajanus cajan (L) Millsp.] is an important multi-use shrub legume of the tropics, sub-tropics and warmer regions of the world, growing between 30°N and 35°S latitude. The goal of this study was to identify genomic regions associated with yield and related traits in three newly developed F2 mapping populations of pigeonpea; AL 201 × ICPL 20325, ICP 5529 × ICP 7035 and ICP 8863 × ICPL 87119. Genotyping by Sequencing (GBS) platform was used for genetic analysis and linkage analysis was performed using JoinMap version 4. Quantitative Trait Linkage (QTL) analysis of eight yield and yield–related traits were performed using single marker analysis (SMA) employing composite interval (CIM) using stepwise regression linear model. A total of 42 QTLs were detected, with 5 in AL 201 × ICPL 20325, 7 in ICP 5529 × ICP 7035 and 30 in ICP 8863 × ICPL 87119. Individual QTLs ranged from 1-4 per trait and the phenotypic value explained (PVE%) ranged between 10.35 -16.27% in AL 201× ICPL 20325,10.44 -17.9 in ICP 5529 × ICP7035 and 10.71-89.12% in ICP 8863 × ICPL 87119. The detected QTLs were co-localized within the same genomic regions, indicating the presence of pleiotropic effect or close genetic linkage. For further fine mapping and use in marker assisted transfer, validation for the accuracy and consistency of the identified QTLs in several, independent and diverse mapping populations transfer is crucial