Abstract
BackgroundThe identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping.ResultsThe drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%. There was a wider phenotypic and molecular diversity within the panel, indicating the suitability of the population for quantitative trait loci (QTL) mapping. Structure analyses clearly grouped the accessions into three subgroups with admixtures. Linkage disequilibrium (LD) analysis revealed that LD decreased with an increase in distance between marker pairs and the LD decay varied from 5–20 cM. The Mixed Linear model-based structured association mapping identified 80 marker trait associations (MTA) for grain yield (GY), plant height (PH) and days to flowering (DTF). Seven MTA were identified for GY under drought stress, four of these MTA were consistently identified in at least two of the three analyses. Most of these MTA identified were on chromosomes 2, 5, 10, 11 and 12, and their phenotypic variance (PV) varied from 5% to 19%. The in silico analysis of drought QTL regions revealed the association of several drought-responsive genes conferring drought tolerance. The major-effect QTLs are useful in marker-assisted QTL pyramiding to improve drought tolerance.ConclusionThe results have clearly shown that structured association mapping is one of the feasible options to identify major-effect QTLs for drought tolerance-related traits in rice.
Highlights
The identification and introgression of major-effect quantitative trait loci (QTL) for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties
Drought Screening Drought was imposed in the dry season (DS) by draining out all the water one month after transplanting
The results showed that there was moderate to severe drought stress during the reproductive stage of the crop in both seasons
Summary
The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. Drought is one of the most severe climate-related risks for rice production in rainfed areas of Asia and Africa (Pandey, 2007). Several major-effect grain yield QTLs under drought have been identified and successfully used in marker-assisted breeding (MAB) (Swamy et al 2011). The drought QTLs identified from different studies and meta-analysis of qDTYs have clearly shown that only a few major-effect qDTYs have been consistently and repeatedly identified, indicating limited exploration of genetic resources to identify novel major-effect qDTYs (Swamy et al 2011; Kumar et al 2014)
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