A QTL for high grain yield under lowland drought in the background of popular rice variety Sabitri from Nepal

Abstract

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 BC1-derived mapping population developed from the cross IR77298-5-6-18/2*Sabitri, a large-effect QTL, qDTY3.2, 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 qDTY3.2 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.