QTL-seq approach reveals CONSTANS-like as the candidate gene for inducing early flowering in pigeonpea (Cajanus cajan).

Main conclusion: QTL-seq analysis of extreme phenotypic bulks from the F₂ population generated by crossing early-maturing pigeonpea mutant TAT-10 and wild-type parent T21 revealed an SNP in the upstream region of CONSTANS-like. The SNP lead to the loss of DOF factor binding site in promoter region in the TAT-10 background which might induce early flowering in TAT-10 For pigeonpea (Cajanus cajan (L.) Millsp.), early maturity is an important agronomic trait linked with early flowering and short grain filling stages. Early flowering is an effective way to evade environmental stresses enabling the cultivation of multiple crops in a year. For this study, QTL-seq was used to identify genomic regions and candidate genes associated with early flowering in pigeonpea. A segregating F₂ population was developed by crossing the early-maturing pigeonpea mutant TAT-10 with its late-maturing parent T21. The whole genome sequencing data of both the parents (T21 and TAT-10) and extreme bulks (Pool_E and Pool_L) were used for QTL-seq analysis. The QTL-seq analysis identified three significant chromosomal regions (12.3 Mb on CcLG03, 1.1 Mb on CcLG07, and 0.3 Mb on CcLG11) where six candidate flowering-related genes (4 on CcLG03 and 2 on CcLG07) were affected by SNPs in the non-coding regions, mainly in the upstream region. Analysis of Cis-regulatory elements revealed the loss of a DOF binding site due to an SNP in the promoter region of the CONSTANS-like gene in TAT-10. The relative gene expression analysis of the candidate genes during the vegetative stage through to the reproductive stages showed variation between T21 and TAT-10. The higher expression levels of the CONSTANS-like gene in TAT-10 compared to T21 are likely to be associated with the loss of the DOF transcription factor binding site. These identified genomic regions and candidate genes could be utilized for functional analyses and aid in understanding the molecular pathways in early-maturing pigeonpea cultivars.