Drought is a major abiotic stress limiting rice production and yield stability in rainfed ecosystems. Identifying quantitative trait loci (QTL) for rice yield and yield components under water limited environments will help to develop drought resilient cultivars using marker assisted breeding (MAB) strategy. A total of 232 recombinant inbred lines of IR62266/Norungan were used to map QTLs for plant phenology and production traits under rainfed condition in target population of environments. A total of 79 QTLs for plant phenology and production traits with phenotypic variation ranging from 4.4 to 72.8% were detected under non-stress and drought stress conditions across two locations. Consistent QTLs for phenology and production traits were detected across experiments and water regimes. The QTL region, RM204-RM197-RM217 on chromosome 6 was linked to days to 50% flowering and grain yield per plant under both rainfed and irrigated conditions. The same genomic region, RM585-RM204-RM197 was also linked to harvest index under rainfed condition with positive alleles from Norungan, a local landrace. QTLs for plant production and drought resistance traits co-located near RM585-RM204-RM197-RM217 region on chromosome 6 in several rice genotypes. Thus with further fine mapping, this region may be useful as a candidate QTL for MAB, map-based cloning of genes and functional genomics studies for rainfed rice improvement.
Drought is the most predominant constraint to rainfed rice production. Identifying molecular markers associated with drought resistance traits and deploying them in marker-assisted breeding will hasten the development of drought-resilient cultivars. A total of 49 diverse rice accessions, including traditional landraces, were evaluated for plant production and root traits under natural drought stress in rainfed target populations of environment (TPE) in six successive field trials from 2010 to 2015. Significant variation for phenology, plant production and root traits under drought was noticed among the accessions. Genotyping of the rice accessions using 599 polymorphic simple sequence repeat (SSR) markers showed considerable variation among them. STRUCTURE analysis grouped the 49 accessions into three subpopulations. Similarly, three clusters were observed in Neighbor joining tree created using Nei's genetic distance. The subpopulation POP1 consisted mostly of landraces, while subpopulation POP3 consisted of advanced breeding lines and POP2 accessions from all groups. Genome-wide association mapping detected 61 markers consistently associated in two or more trials with phenology, plant production and root traits under drought in TPE. The markers PSM52 (Chr 3), RM6909 (Chr 4), RM242 (Chr9) and RM444 (Chr 9) were consistently associated with grain yield and root traits under drought. The markers PSM127 (Chr 3) and PSM133 (Chr 4) were consistently associated with yield, plant height and spikelet fertility. These markers with pleiotropic and consistent associations with yield and secondary traits under drought in TPE may be robust candidates for marker-assisted breeding for drought resistance in rice.
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