2012. Genome wide association mapping of drought resistance traits in rice

2012.  Genome wide association mapping of drought resistance traits in rice

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ABTRACT

Rice, (Oryza sativa L.) is one of the most important crops providing staple food for a large segment of the world population. Drought stress is a major limitation to rice yields and its stability in rainfed areas. Developing drought resistant cultivars will help to increase production of rice in rainfed area. However, conventional breeding for drought resistance is slow in attaining progress due to poor understanding of genetic control of drought resistance and difficulty in phenotyping breeding progenies for drought tolerance. Molecular markers help in identification of quantitative trait loci (QTLs) associated with drought resistance traits and their use in breeding high yielding rice varieties suitable for drought-prone areas through marker-assisted breeding, thus reducing the need for extensive field testing over space and time. Conventional QTL mapping requires genotyping large mapping progenies derived from biparental crossing, demanding time and labour. Genome-wide association mapping is a powerful approach to identify associations between traits of interest and genetic markers using diverse genotypes. Thus, in the present study, a total of 48 rice accessions from different geographic locations and ecotypes were evaluated for plant production and root traits under irrigated and rainfed conditions in target populations of environment. Rice accessions showed significant differences for plant phenology, production and root traits. The rice accessions were screened using a total of 510 SSR markers selected from across the rice genome. Among them, 323 SSR markers were found to be polymorphic among the accessions. Structure analysis grouped the 48 accessions into six populations, broadly corresponding to the major geographic regions. Genome-wide association analysis using TASSEL identified a total of 444 marker-trait associations at P<0.05, P<0.001 and PO.OOOl for the various traits. Among them, 155 markers were associated with yield traits and 82 markers for root traits in these rice accessions. The markers viz., RM170 chromosome 6 (ch. 6), RM5720 (ch. 7), RM318 (ch. 2), RM3843 (ch. 4), RM29 (ch. 2), RM540 (ch. 6), RM585 (ch. 6) and RM36 (ch. 3) are linked to both yield and root traits under drought stress in this study. These markers were earlier identified to be linked to drought resistance and yield traits in rice through conventional QTL mapping efforts. The consistent markers for yield and root traits can be used in marker-assisted breeding for rainfed rice improvement. Thus, genome wide association mapping is ideal to detect markers linked to plant production and drought resistance traits in rice using diverse genotypes  .