Map Based Cloning of a Dominant Rust Resistance Gene and Mapping of its Duplicated Paralogues in Cultivated Groundnut (Arachis hypogaea L.)

Abstract Understanding the mechanism and nature of resistance genes in crop plants is essential for its use in new breeding techniques. Previously, a dominant rust resistance gene was fine-mapped within a 1.2 cM interval in chromosome A03 of groundnut. Here, the rust resistance gene, VG9514-Rgene was isolated through map based cloning. Sequencing of the gene from resistant and susceptible plants revealed non-synonymous mutations in the TIR, NBS and LRR region of R-protein. Genetic mapping of these SNPs-based markers confirmed the position of VG9514-Rgene in between FRS 72 and SSR_GO340445 markers in chromosome A03. Homology searching identified four homologous R-genes in groundnut genome. Of them, Arahy.R8KUIR, Arahy.T6DCA5 and Arahy.ZZ0VZ9 are paralogues. These paralogous genes had several small InDels. Mapping of these InDels-based markers revealed tandem duplication of these paralogous R-genes at distal portion of chromosome A03. Ka/Ks calculation revealed that this unique VG9514-Rgene had undergone positive selection. Homology based structure modelling of this R-protein revealed a typical consensus three dimensional folding of TIR-NBS-LRR protein. Non-synonymous mutations in susceptible version of R-protein were mapped in this protein model and found E268Q mutation in hhGRExE motif, Y309F in RNBS-A motif and I579T in MHD motif of NB-ARC domain are probable candidates for loss of function.