In silico characterization of QTL regions associated with drought tolerance traits in rice (Oryza sativa L.)

An attempt was made to carry out in silico characterization of 14 putative QTL regions identified on chromosomes 1, 2, 4, 5, 6 and 8 associated with drought tolerance. A total of 354 BAC/PAC clones were detected in the underlying regions of putative QTLs mapped. These BAC/PAC clone nucleotide sequences were used for mining SSRs and primer designing. The tri-nucleotide motif was the most abundant class which was followed by tetra, di, penta and hexa nucleotide repeats. A total of 1849 class I SSR markers were designed from QTL regions. The underlying regions of putative QTL displayed different functional categories of drought tolerance genes, transcription factors (45.65%), protein kinases (33.94%), stress proteins (10.11%), phytohormones (9.75%) and aquaporins (0.72%). The massively parallel signature sequence (MPSS) analysis of candidate genes showed higher expression for transcription factor having WRKY and zinc finger super family (LOC_Os02g08440) in stem, immature panicle, developing seeds, mature leaves, mature roots, merismatic tissues, cold, drought and salt stressed young roots transcript tissue library. The functional validation identified putative genes based on MPSS signatures will facilitate to unravel the complexity of drought tolerance at molecular level and further will accelerate the genetic improvement of drought tolerance in rice.