An Integrated Meta-QTL and Transcriptome Analysis Provides Candidate Genes Associated with Drought Tolerance in Rice Seedlings

Abstract

Drought stress, intensified by climate change, poses a significant threat to global rice security. To identify stable quantitative trait loci (QTL) associated with drought tolerance in rice under different genetic backgrounds and environmental conditions, this study combined 901 drought-tolerant QTLs reported in 52 independent studies published between 2000 and 2023, which were subsequently meta-analyzed and condensed into 77 meta-QTLs (MQTLs). Among them, 23 MQTLs were validated in seven independent genome-wide association studies (GWAS) on drought tolerance in rice, each conducted using different natural populations. The confidence intervals (CIs) of the MQTLs were substantially narrowed, with the reduction factor ranging from 2.44 to 20.40 relative to the original QTLs. To further explore key genes for drought tolerance, we screened for genes located within the MQTL regions and differentially expressed in our RNA-seq data, yielding 3851 drought-responsive differentially expressed genes (DEGs). These DEGs were then subjected to a refinement process that included Mfuzz clustering, cis-regulatory element (CRE) analysis, protein–protein interaction (PPI) network analysis and AlphaFold-based structural modeling of their encoded proteins. This stepwise filtering identified eleven drought-responsive hub proteins, nine with annotated functions and two functionally uncharacterized. Following further prioritization, LOC_Os04g35340 and Os07g0141400 were established as core candidate genes (CGs) for dissecting the genetic and biochemical basis of drought tolerance in rice.