Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.)

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-017-0161-6) contains supplementary material, which is available to authorized users.

Genome-Wide Consistent Molecular Markers Associated with Phenology, Plant Production and Root Traits in Diverse Rice (<i>Oryza sativa</i> L.) Accessions under Drought in Rainfed Target Populations of the Environment

“…A minimum of two to a maximum of 14 alleles were detected among the accessions per marker, with an average of 4.7 alleles. This range is higher compared to 1-11 reported earlier 52 and comparable with that of a recent study involving rice accessions from Malaysia 53 . The PIC varied from 0.0392 to 0.8443, with an average of 0.4034.…”

Genetic Diversity, Population Structure, and Marker-Trait Association for Drought Tolerance in US Rice Germplasm

“…Low spikelet fertility observed under drought stress was responsible for the drastic reduction in grain yield and harvest index. The yield reduction of >50% under drought stress was reported in earlier studies [16][17][18]. A wide variation in yield, spikelet fertility, and harvest index suggested that the US rice germplasm collection includes both drought-tolerant and susceptible genotypes.…”

Identification of QTLs for high grain yield and component traits in New Plant Types of rice

“…The MLM model integrates structure and kinship matrix (Q+K) which supposedly corrects the false-positive error to tune of 62.5%. Hence, MLM model has been popularly used in several cases for marker-traits association [12,19,44,46,72, 81–85].…”

“…It utilizes natural variation [12], hence supposed to have great potential to evaluate and characterize a wide range of alleles. Several researchers have been reported the utility of association analysis in the identification of QTLs for different traits in rice, viz., Grain yield [13], grain yield under water deficit [14], deep root mass and the number of deep roots [15], grain quality traits [16], agronomic traits [17, 18], grain yield under reproductive drought stress [19], panicle architecture and spikelet’s/ panicle [20], plant height and grain yield [21].…”