Genetic dissection of cold tolerance at the budding stage of rice in an indica-japonica recombination inbred line population

• Published in: Plant physiology and biochemistry 2023-11, Vol.204, p.108086-108086, Article 108086
• Main Authors: Yang, Jing, Miao, Jiahao, Li, Nan, Zhou, Zixian, Dai, Kunyan, Ji, Faru, Yang, Min, Tan, Chen, Liu, Jing, Wang, Hongyang, Tang, Wei
• Format: Article
• Language: English
• Subjects: Candidate genes; Cold tolerance; QTL analysis; Rice; Transcriptomics
• ISSN: 0981-9428; 1873-2690
• DOI: 10.1016/j.plaphy.2023.108086

Rice is highly cold-sensitive, and thus, the promotion of cold resistance in buds is essential. In this study, we conducted a mapping analysis to identify quantitative trait loci (QTLs) associated with cold tolerance in buds. The analysis was performed using a recombinant inbred line (RIL) population consisting of 192 lines derived from the cold-tolerant strain 02428 and the cold-sensitive strain YZX. Seven additive loci on chromosomes 1, 4, 5, and 6 were identified, of which loci 3 and 7 were found in two crop seasons, indicating stability. Three epistatic interactions, one present over two seasons, were found. Loci 3 and 7 pyramided with two main-effect QTLs observed to control the rate of low-temperature germination in our previous study. Two materials with good cold resistance at the germination and bud stages were obtained, namely, G93 and G146. Transcriptome sequencing analysis of the two parent buds after cold treatment found that genes expressed differentially between the two parents were related to photosynthesis, energy metabolism, and reactive oxygen scavenging. Five candidate genes, namely, Os01g0385400, Os01g0388000, Os06g0287700, Os06g0289200, and Os06g0291100, were selected in the two stable intervals based on gene expression profiles and annotations. These genetic loci exhibit strong potential as targets for breeding cold tolerance in buds and require additional investigation. In conclusion, this work provides valuable genetic resources that can be utilized to improve the cold tolerance of rice. •Cold tolerance at the budding stage is a quantitative genetic trait.•Seven additive loci and three pairs of epistatic interactions were identified.•The energy metabolism pattern causes the difference in cold tolerance in the bud stage between indica rice and japonica rice.•Five candidate genes were identified in two major effect loci.