Linkage analysis, GWAS, transcriptome analysis to identify candidate genes for rice seedlings in response to high temperature stress

Abstract Background: With the increase of global temperature, rice yield decline caused by the rising temperature is becoming more and more prominent. Mining heat-resistant genes and applying them to rice breeding is a feasible and effective way to solve the problem. Result: Three main biomass traits, including shoot length, dry weight, and fresh weight, changed after abnormally high temperature treatment in the seedling stage of a recombinant inbred line and natural groups. Based on a comparison of the results of linkage analysis and genome-wide association analysis, the presence of two sections with lengths of 57 kb and 69 kb in qDW7 and qFW6 , respectively, was associated with the rice response to abnormally high temperatures in the seedling stage. Meanwhile, based on integrated transcriptome analysis, some genes are considered as candidate genes for subsequent research and analysis. Combining with reports of known genes and analysis of homologous genes, it was found that there are 8 genes in candidate genes that need to be focused in subsequent research. Conclusions: The results indicated several relevant loci, which would help researchers to further discover excellent heat-resistant genes that can be applied to rice heat-resistant breeding.