Chinese Journal OF Rice Science >
Cloning of Cold6 Conferring Cold Tolerance in Rice
Received date: 2024-07-13
Revised date: 2024-08-20
Online published: 2025-11-19
【Objective】 Exploring cold-tolerant germplasm and identifying cold-tolerant genes are essential strategies to mitigate cold stress in rice. 【Method】 We treated the japonica rice variety Sasanishiki with ethyl methanesulfonate (EMS) to select mutants exhibiting enhanced cold tolerance at the seed germination stage. Candidate genes underwent cloning and functional analysis using fine mapping, CRISPR/Cas9 gene editing, expression profiling, and haplotype analysis. 【Result】 We identified the mutant M34, which displayed markedly improved cold tolerance at the seed germination stage. Genetic analysis suggested that a single recessive gene governs this trait. Fine mapping pinpointed Cold6 as the target gene. CRISPR/Cas9-mediated knockout of Cold6 confirmed its role in regulating cold tolerance during germination. Cold6 expression was observed in all rice organs, peaking in the panicles, and it encodes a protein containing several functional domains, including SNF2. Evolutionary analysis indicated differentiation of Cold6 between indica and japonica varieties, with haplotype analysis revealing 10 distinct Cold6 haplotypes. The predominant haplotypes are I-III; haplotype I is prevalent in japonica rice, whereas II and III are common in indica rice. 【Conclusion】 This study identified Cold6 as a novel regulator of cold tolerance in rice at the seed germination stage, encoding an SNF2 protein. Investigating the molecular mechanism of Cold6 enhances our understanding of the SNF2 gene family's role in rice, offering a theoretical foundation and germplasm resources for breeding cold-tolerant, high-yield northern japonica rice.
Key words： rice; cold tolerance; map-based cloning; gene editing; haplotype analysis
TAO Shibo, XU Na, XU Zhengjin, LIU Chang, XU Quan . Cloning of Cold6 Conferring Cold Tolerance in Rice[J]. Chinese Journal OF Rice Science, 2025 , 39(6) : 751 -759 . DOI: 10.16819/j.1001-7216.2025.240709
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