Drought is the major cause of the yield reduction in rainfed rice
areas. High GXE interaction in multi-location trials is a major challenge
for breeders in developing breeding lines with a stable performance over
diverse environments. In a BC"1-derived mapping population developed from
the cross IR77298-5-6-18/2*Sabitri, a large-effect QTL, qDTY"3"."2, was
identified on the short arm of chromosome 3 near RM231. This QTL explained
23.4% of the phenotypic variance for grain yield under severe lowland
drought and had a consistent effect across varying water stress severities
in the Philippines and Nepal in DS2011, WS2011 and WS2012. Although this
QTL co-localizes with the HD9 locus related to flowering time, an effect of
this QTL was seen on the grain yield of QTL-positive lines under severe and
moderate drought stress conditions regardless of the flowering time in this
population. The gene content analysis of this locus showed the presence of
a wide range of genes related to stress tolerance along with those related
to flowering time. The study used bulk segregant analysis (BSA) coupled
with screening at more than one location to simultaneously identify and
test the effect of qDTY"3"."2 in the target environment. These results
indicate that managed dry-season screening coupled with phenotyping of
mapping populations at the target site and genotyping approaches such as
BSA allow the identification and validation of the effect of QTLs on grain
yield under drought that will lead to the rapid development of
drought-tolerant versions of popular varieties through marker-assisted
breeding of the identified QTLs.
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