Fine mapping of consistent quantitative trait loci for yield under drought stress using rice (Oryza sativa) recombinant inbred lines adapted to rainfed environment

Genetic mapping of physiological traits associated with terminal stage drought tolerance in rice

BACKGROUND

Drought during reproductive stage is among the main abiotic stresses responsible for drastic reduction of grain yield in rainfed rice. The genetic mechanism of reproductive stage drought tolerance is very complex. Many physiological and morphological traits are associated with this stress tolerance. Robust molecular markers are required for detection and incorporation of these correlated physiological traits into different superior genetic backgrounds. Identification of gene(s)/QTLs controlling reproductive stage drought tolerance and its deployment in rainfed rice improvement programs are very important.

RESULTS

QTLs linked to physiological traits under reproductive stage drought tolerance were detected by using 190 F₇ recombinant inbred lines (RIL) mapping population of CR 143-2-2 and Krishnahamsa. Wide variations were observed in the estimates of ten physiological traits studied under the drought stress. The RIL population was genotyped using the bulk- segregant analysis (BSA) approach. A total of 77 SSR polymorphic markers were obtained from the parental polymorphisms survey of 401 tested primers. QTL analysis using inclusive composite interval mapping detected a total of three QTLs for the physiological traits namely relative chlorophyll content (qRCC1.1), chlorophyll a (qCHLa1.1), and proline content (qPRO3.1) in the studied RIL population. The QTL, qPRO3.1 is found to be a novel one showing LOD value of 13.93 and phenotypic variance (PVE) of 78.19%. The QTL was located within the marker interval of RM22-RM517 on chromosome 3. Another novel QTL, qRCC1.1 was mapped on chromosome 1 at a distance of 142.8 cM and found to control relative chlorophyll content during terminal drought stress. A third novel QTL was detected in the population that controlled chlorophyll a content (qCHLa1.1) under the terminal stress period. The QTL was located on chromosome 1 at a distance of 81.8 cM and showed 64.5% phenotypic variation.

CONCLUSIONS

The three novel QTLs, qRCC1.1, qCHLa1.1 and qPRO3.1 controlling relative chlorophyll content, chlorophyll a and proline content, respectively were identified in the mapping population derived from CR 143-2-2 and Krishnahamsa. These 3 QTLs will be useful for enhancement of terminal drought stress tolerance through marker-assisted breeding approach in rice.

Genome-wide Association Study of a Panel of Vietnamese Rice Landraces Reveals New QTLs for Tolerance to Water Deficit During the Vegetative Phase

BACKGROUND

Drought tolerance is a major challenge in breeding rice for unfavorable environments. In this study, we used a panel of 180 Vietnamese rice landraces genotyped with 21,623 single-nucleotide polymorphism markers to perform a genome-wide association study (GWAS) for different drought response and recovery traits during the vegetative stage. These landraces originate from different geographical locations and are adapted to different agrosystems characterized by contrasted water regimes. Vietnamese landraces are often underrepresented in international panels used for GWAS, but they can contain original genetic determinants related to drought resistance.

RESULTS

The panel of 180 rice varieties was phenotyped under greenhouse conditions for several drought-related traits in an experimental design with 3 replicates. Plants were grown in pots for 4 weeks and drought-stressed by stopping irrigation for an additional 4 weeks. Drought sensitivity scores and leaf relative water content were measured throughout the drought stress. The recovery capacity was measured 2 weeks after plant rewatering. Several QTLs associated with these drought tolerance traits were identified by GWAS using a mixed model with control of structure and kinship. The number of detected QTLs consisted of 14 for leaf relative water content, 9 for slope of relative water content, 12 for drought sensitivity score, 3 for recovery ability and 1 for relative crop growth rate. This set of 39 QTLs actually corresponded to a total of 17 different QTLs because 9 were simultaneously associated with two or more traits, which indicates that these common loci may have pleiotropic effects on drought-related traits. No QTL was found in association with the same traits in both the indica and japonica subpanels. The possible candidate genes underlying the quantitative trait loci are reviewed.

CONCLUSIONS

Some of the identified QTLs contain promising candidate genes with a function related to drought tolerance by osmotic stress adjustment.

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

BACKGROUND

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. 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.

RESULTS

The 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.

CONCLUSION

The 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.

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

BACKGROUND

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. 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.

RESULTS

The 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.

CONCLUSION

The 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.