Characterization of quantitative trait loci for number of primary branches in near‐isogenic lines from a cross between the Oryza sativa cultivar ‘Hwayeongbyeo’ and the wild relative Oryza rufipogon

In our previous study, a quantitative trait locus (QTL) qpb2 for primary branches (PB) was mapped on chromosome 2 using introgression lines from an interspecific cross between 'Hwayeongbyeo' and an Asian common wild rice (Oryza rufipogon Griff.), W1944. To confirm this QTL, CR6076 (BC3F6) was selected and backcrossed to 'Hwayeongbyeo' to produce near-isogenic line (NIL) populations in the BC4F3, BC4F4 and BC4F5 generations. QTL analysis in three generations revealed five QTLs including plant height and PB that were mapped in the same interval. The O. rufipogon alleles decreased of PB. By substitution mapping, qpb2 was narrowed down to a 575-kb region. Colocalization of five QTLs suggests that this locus was associated with panicle structure with pleiotropic effects. The finding that QTLs for panicle traits have been mapped mainly from wild species in a similar location as qpb2 suggest that qpb2 might have played an important role in the regulation of PB during the domestication of rice panicle. The NIL populations and molecular markers are useful materials for cloning of the qpb2.