Uncovering the genomic regions associated with yield maintenance in rice under drought stress using an integrated meta-analysis approach

Abstract

The complex trait of yield is controlled by quantitative trait loci (QTLs). Considering the global water deficit problem, rice varieties that are suitable for non-flooded cultivation are of great importance in breeding programs. The powerful approach of Meta-QTL (MQTL) analysis can be used for the genetic dissection of complicated quantitative traits. A comprehensive MQTL analysis was done to detect consistent QTL regions associated with drought tolerance and yield-related traits under water deficit conditions in rice. Totally, 1087 QTLs from 134 rice populations published from 2000 to 2021 were utilized in the analysis. Distinct MQTL analysis of the related traits led to the identification of 213 stable MQTLs. The confidence interval (CI) of the detected MQTLs was between 0.12 and 19.66 cM. In comparison with the CI mean of the initial QTLs, the CI mean of the identified MQTLs (4.68 cM) was 2.74 times narrower. Remarkably, 63 MQTLs overlapped with SNP peak positions detected by genome-wide association studies (GWAS) for yield and drought tolerance-associated traits under water deficit conditions in rice. Considering the genes located both in the SNP peak positions and QTL-overview peaks, 19 genes were introduced as novel candidate genes, which are associated with drought response index, plant height, panicle number, biomass, and grain yield. On the other hand, an inclusive MQTL analysis was performed on all the traits to obtain “Breeding MQTLs”. Performing inclusive MQTL analysis on all the traits resulted in the identification of 96 MQTLs with a CI ranging from 0.01 to 9 cM. The CI mean of the obtained MQTLs was 2.33 cM, which was 4.66 times narrower than the CI mean of the initial QTLs. Thirteen MQTLs having more than 10 initial QTLs, CI < 1 cM, and a PVE mean of the initial QTLs > 10 were identified as “Breeding MQTLs”. We hope that the obtained results can help breeders to enhance rice yield under drought stress conditions.