Combining QTL mapping and transcriptomics to identify candidate genes for cold tolerance during the budding and seedling stages in rice.

Background: Rice, being a thermophilic crop, exhibits high sensitivity to low-temperature stress throughout its growth and development. Consequently, enhancing cold tolerance (CT) has been a paramount objective in rice breeding programs. The budding and seedling stages are particularly susceptible to low-temperature damage, making it crucial to improve CT during these stages to ensure the stable establishment and development of the rice population.

Results: In this study, we exposed the parental lines Nipponbare (NIP) and Searice 86 (SR86), along with their derived 170 doubled-haploid (DH) population lines, to cold treatments during both the budding and seedling stages. Quantitative trait locus (QTL) mapping was performed using statistical indices such as the survival rate at the budding stage (SRBS), severity of damage at the budding stage (SDBS), survival rate at the seedling stage (SRSS), and wilting degree at the seedling stage (WDSS). This analysis identified four QTLs at the budding stage and eight QTLs at the seedling stage. Furthermore, by integrating differentially expressed genes (DEGs) from transcriptomic data with genes located within the QTL regions, we identified 10 candidate genes for the budding stage and 11 candidate genes for the seedling stage. Based on DNA sequence variations between the parental lines, changes in gene expression under cold treatment, and haplotype analyses, the key candidate genes were ultimately determined to be Os02g0250600 for the budding stage and Os06g0696600 for the seedling stage. Additionally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of transcriptomic data from both stages revealed significant differences in the regulatory pathways involved in CT between the budding and seedling stages.

Conclusion: The results indicate that Os02g0250600 is the pivotal gene responsible for CT at the budding stage, with haplotype 4 exhibiting the highest level of CT. Meanwhile, Os06g0696600 plays a crucial role in CT at the seedling stage, where haplotypes 2 and 4 have been identified as advantageous. A comprehensive analysis integrating QTL and transcriptome data from both stages revealed distinct differences in CT mechanisms, highlighting stage-specific variations. This study provides valuable theoretical insights and practical references for the cloning of CT genes and the development of cold-tolerant rice varieties during the budding and seedling stages.