# Identification of candidate genes for heat tolerance in rice by genome-wide association study and transcriptome sequencing

## TL;DR

This study identifies genes in rice that help it tolerate heat during the critical heading stage, using genetic and transcriptomic data.

## Contribution

The study combines GWAS and transcriptome sequencing to identify five key candidate genes for heat tolerance in rice.

## Key findings

- 206 genes related to heat tolerance were identified through GWAS.
- 57 genes were co-detected by GWAS and transcriptome sequencing.
- Five candidate genes showed consistent expression trends verified by qRT-PCR.

## Abstract

Heat stress during the heading stage has a particularly negative impact on rice. In this study, we employed 159 core rice germplasms as materials, set up high-temperature and normal-temperature treatments during the heading stage, and measured the phenotypic traits such as the seed-setting rate, the number of grains per panicle, and the thousand-grain weight. Combining the results and data from whole-genome sequencing, we employed genome-wide association study (GWAS) to identify the heat tolerance-related genes or QTLs in rice. Additionally, we selected two heat-tolerant and two heat-intolerant varieties for transcriptome sequencing after high-temperature treatment during the heading stage, and further screened and analyzed the candidate genes based on GWAS and transcriptome sequencing. As a result, a total of 206 genes related to heat tolerance during rice heading were detected by GWAS, and 57 genes were co-detected by GWAS and transcriptome sequencing. Further gene function annotation and haplotype analysis identified five important candidate genes related to heat tolerance, including LOC_Os03g18010, LOC_Os07g43700, LOC_Os10g22980, LOC_Os10g41660, and LOC_Os11g39020. qRT-PCR verified that the trends of relative expression of these five genes were highly consistent with the RNA-seq data. The findings may lay an important foundation for mining and cloning heat-tolerant genes in rice for biotechnological improvement.

The online version contains supplementary material available at 10.1186/s12870-026-08324-0.