Identification of candidate genes associated with growth habit in pigeonpea (Cajanus cajan (L) Millsp.)

With an objective to investigate growth habit in pigeonpea, a set of 96 to 142 lines including 58 determinate (DT) and 84 indeterminate (IDT) lines with a range of photoperiod sensitivity were used for genotyping with DArT arrays (with 15,360 features) and a 768 SNP GoldenGate assay, and for sequencing of seven candidate genes (AP1, FCA, FLD, FKF1, GI, TFL1, TFL2) implicated in the control of determinacy and photoperiod sensitivity in Arabidopsis. Association analysis using the TASSEL programme showed significant (p= <0.01) association of determinacy trait with 19 SNP and 6 DArT markers explaining 8.1-8.6% and 7.3-14.5% of phenotypic variation respectively. Detailed sequence analysis of all the seven candidate genes in the 142 lines led to the identification of 3 SNPs significantly associated with determinacy: one each in the pigeonpea homologs of genes AP, GI and TFL1. The SNP identified in TFL1 showed the strongest association with determinacy, flowering time and plant height. For making SNP genotyping cost-effective and easy-to-use, the three SNPs were converted in to CAPS, dCAPS or allele specific-priming markers. By using these molecular markers in a ICPA 2039 × ICPL 2447 bi-parental F₂ mapping population where the growth habit phenotype segregates, two candidate genes, GI and TFL1 were mapped to LG7 and LG4 of pigeonpea, respectively. Characterization of nucleotide variation and expression profiling of these genes is in progress.