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

Abstract

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.