Utilization of natural alleles and haplotypes of Ctb1 for rice cold adaptability

• Published in: Gene Vol. 941; p. 149225
• Main Authors: Li, Lingling, Cheng, Gongye, Li, Wenyu, Zhang, Di, Yu, Jianghui, Zhou, Huang, Ding, Xiaoping, Wang, Zhijun, Zhu, Wanjing, Li, Jiajia, He, Jiwai, Duan, Meijuan, Liu, Citao
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 15.03.2025
• Subjects: Adaptation, Physiological - genetics; Alleles; altitude; booting stage; Breeding; cold; cold stress; Cold Temperature; cold tolerance; Cold-Shock Response - genetics; Ctb1 gene; Gene Expression Regulation, Plant; genes; Haplotypes; InDel; INDEL Mutation; NIL-Ctb1HapI; Oryza - genetics; Oryza - physiology; Oryza sativa; Plant Breeding; Plant Proteins - genetics; Plant Proteins - metabolism; pollen; Polymorphism, Single Nucleotide; Promoter Regions, Genetic; rice; Rice cold tolerance; seedlings; PIF3; FIMO; QTL; K; AtFRS9; ChIP; EMSAs; N; P; SNK; Y1H; HZ; NIL-Ctb1HapI; CDS; CBFs; SNP; phyB; cDNA; LUC; fLUC; rLUC; Breeding; FAA; Rice cold tolerance; NIL; Ctb1 gene; InDel; I2-KI; NIL-Ctb1(HapI)
• ISSN: 0378-1119; 1879-0038; 1879-0038
• DOI: 10.1016/j.gene.2025.149225

•The InDel at −1,302  bp in the Ctb1 promoter enhances gene expression and cold tolerance.•The InDel improves rice cold adaptability at seedling and booting stages.•Incorporation of the InDel into NILs (NIL-Ctb1HapI) increases rice cold tolerance and yield.•The −1,302 fragment of InDel may be used as a marker for breeding cold-tolerant rice. Cold stress during the booting stage of rice (Oryza sativa) significantly reduces yields, particularly in temperate and high-altitude regions. This study investigates the Ctb1 gene, critical for booting-stage cold tolerance, to improve breeding of resilient rice varieties. Re-sequencing the Ctb1 promoter in 202 accessions identified six Insertions and/or deletions (InDels) and four Single nucleotide polymorphisms (SNPs), with an InDel at −1,302 bp significantly boosting Ctb1 expression and cold tolerance. Accessions carrying this InDel (Haplotype I) exhibited the highest tolerance. Near-isogenic lines (NIL-Ctb1HapI) introduced Haplotype I into the cold-sensitive Huazhan (HZ) variety, resulting in a 5.9-fold increase in Ctb1 expression, higher seedling survival, improved pollen fertility, a 64.2 % increase in seed setting rate, and a 12 g per plant yield boost under cold stress. These findings confirm the critical role of the −1,302 InDel in cold tolerance and establish NIL-Ctb1HapI as a valuable breeding tool for cold-resilient rice.