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Drought stress is a serious constraint, especially in rainfed rice production, and breeding for drought tolerance by selection based on yield under stress, though effective, is slow Mapping quantitative trait loci (QTLs) for yield and its components under drought stress predominant in rainfed target populations of environment (TPE) will help overcome this limitation. In the present study, a subset of 143 F8 and F9 recombinant inbred (RI) lines derived from IR62266-42-6-2 (IR62266), a high-yielding indica ecotype and Norungan, a landrace from TPE, was used to map QTLs for yield and its components under drought predominant in TPE. A large effect yield QTL observed under drought stress in TPE was consistent across two years with a phenotypic variation of 31.3% and 37.9% and additive effect of 629.2 and 424.9 kg/ha Further, this region was fine-mapped to 94.0 kb with positive effect on grain yield under stress.

Keywords

Comparative genomics, drought stress, fine mapping, quantitative trait locus, rice.

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References

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Comparative Genome-Wide Association Studies for Plant Production Traits under Drought in Diverse Rice (Oryza sativa L.) Lines Using SNP and SSR Markers

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Authors

C. Muthukumar ¹, T. Subathra ¹, J. Aiswarya ¹, V. Gayathri ¹, R. Chandra Babu ¹

Affiliations
1 Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, IN

Source

Current Science, Vol 109, No 1 (2015), Pagination: 139-147

Abstract

Rice is the major staple food crop for more than half of the world's population, but its productivity is often reduced by drought, especially when grown under rainfed conditions. Identification of molecular markers associated with plant production traits under drought, especially in the target populations of the environment (TPE) presents an opportunity to improve rainfed rice production using genomics tools. Marker-trait associations were studied using 1168 simple sequence repeat (SSR) markers and 911,153 single nucleotide polymorphisms (SNPs) with 17 diverse rice lines from different geographical regions and hydrological habitats. STRUCTURE analysis discriminated the rice accessions into three subpopulations. Significant genotypic linkage disequilibrium (LD) was found in the rice accessions using SSR markers. A total of 130 and 118 water-trait associations were obtained with SSR and SNP markers respectively, under stress. Comparison of SSR and SNP marker-trait associations revealed 23 consistent associations. Five marker-trait associations with genic SNPs were observed out of 23 associations. These genomic regions may be potential candidates for application in marker-assisted breeding of rice cultivars suitable for water-limited environments.

Keywords

Drought Tolerance, Linkage Disequilibrium, Marker–Trait Association, Rice.

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