Increased drought tolerance and wider adaptability of qDTY 12.1 conferred by its interaction with qDTY 2.3 and qDTY 3.2 Shalabh Dixit • B. P. Mallikarjuna Swamy • Prashant Vikram • Jerome Bernier • M. T. Sta Cruz • Modesto Amante • Dinesh Atri • Arvind Kumar Received: 12 August 2011 / Accepted: 5 June 2012 / Published online: 23 June 2012 Ó Springer Science+Business Media B.V. 2012 Abstract The genetic basis of high grain yield under reproductive-stage drought was studied using an F3- derived population generated from the cross of upland rice (Oryza sativa L.) cultivars Vandana and Way Rarem. Contributed by the susceptible parent Way Rarem, locus qDTY 12.1 was hypothesized to have interaction with loci from the Vandana genome to enhance the grain yield of tolerant line Vandana under drought. A test of the digenic interaction of qDTY 12.1 showed that two loci, qDTY 2.3 on chromosome 2 and qDTY 3.2 on chromosome 3, significantly increased the yield and harvest index of qDTY 12.1 -positive lines under severe upland and lowland drought conditions. qDTY 2.3 and qDTY 3.2 , in interaction with qDTY 12.1 , reduced days to flowering and plant height of qDTY 12.1 -positive lines under stress and non-stress conditions in upland. BC2F3-derived backcross inbred lines (BILs) were used to validate these results and identify new quantitative trait loci. Lines with qDTY 2.3 and qDTY 12.1 showed increased yield over Way Rarem under severe and moderate stress conditions, in upland. IR84996-50-4-B-4, a selection from one of the BILs, yielded more than the popular drought- tolerant cultivars Apo, UPLRi7, and IR74371-54-1-1 under severe stress conditions. Introgressed segments from Vandana also improved yield under non-stress conditions. The results indicate that digenic interac- tions can explain the genetic control of complex quantitative traits such as grain yield under drought, and a few interacting loci with large effects on grain yield or yield-related traits may enhance drought response across a wide range of genetic backgrounds and environments when introgressed together. Keywords Rice  Drought  Yield  QTL  Non-allelic interactions Introduction Understanding the genetic architecture of complex traits is a major challenge in the post-genomic era (Yang et al. 2007). In contrast to Mendelian traits, phenotypic variations of complex traits result from the segregation of alleles at multiple loci (Mackay 2001). These interactions include epistasis, quantitative trait locus (QTL)-by-sex interactions and QTL-by-environment Electronic supplementary material The online version of this article (doi:10.1007/s11032-012-9760-5) contains supplementary material, which is available to authorized users. S. Dixit  B. P. Mallikarjuna Swamy  P. Vikram  J. Bernier  M. T. Sta Cruz  M. Amante  A. Kumar (&) International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines e-mail: a.kumar@cgiar.org S. Dixit  D. Atri Dr. Hari Singh Gour Central University, Sagar, India J. Bernier Monsanto, 37437 State Highway 16, Woodland, CA, USA 123 Mol Breeding (2012) 30:1767–1779 DOI 10.1007/s11032-012-9760-5