种子休眠基因Sdr4的生物信息学分析与分子标记开发和应用
收稿日期: 2025-02-25
修回日期: 2025-03-21
网络出版日期: 2026-01-21
基金资助
浙江省农业(水稻)新品种选育重大科技专项(2021C02063-4);中央级公益性科研院所基本科研业务费专项(CPSIBRF-CNRRI-202306);国家重点研发计划资助项目(2022YFD1201505)
Bioinformatics Analysis, Development and Application of Molecular Markers for Seed Dormancy Gene Sdr4 in Rice
Received date: 2025-02-25
Revised date: 2025-03-21
Online published: 2026-01-21
【目的】水稻收获前穗发芽严重制约产量与品质形成，该性状主要受种子休眠基因调控。解析种子休眠分子机制对改良水稻穗萌抗性具有重要理论价值与育种意义。【方法】综合运用生物信息学分析、分子标记开发及标记辅助选择技术，系统解析种子休眠基因Sdr4(Seed dormancy 4)的生物学功能，探究其分子标记在多基因型种质改良中的应用潜力。【结果】Sdr4启动子区含TATA-box等核心元件及ABA响应元件等多种顺式作用元件，其编码蛋白为低稳定性疏水蛋白(101~150氨基酸区段磷酸化修饰占比25.93%)，三级结构以α-螺旋(15.50%)、β-折叠(15.50%)和无规则卷曲(66.37%)为主。3K单倍型数据库与AlphaFold分析表明Sdr4基因具有6种功能性突变的单倍型，且在强休眠种质Kasalath与弱休眠种质日本晴(Nipponbare)的Sdr4氨基酸序列存在多个位点差异。系统发育分析显示Sdr4在非洲栽培稻(Oryza glaberrima)与沼生菰(Zizania palustris)中具有高度保守性。通过Kasalath与日本晴的Sdr4等位变异，开发了Sdr4-KF/KR与Sdr4-PF/PR两对功能标记，可精准区分种子休眠强度。基于25个水稻品种的分子检测筛选出休眠性显著差异的种质，并利用上述标记成功创制了强休眠型中组18改良系。【结论】Sdr4通过调控种子休眠深度影响水稻穗萌抗性。分子标记筛选表明20个主栽品种均呈种子弱休眠表型，利用Sdr4特异性标记选育的K17与K88新品系具有显著穗萌抗性。本研究为Sdr4功能解析及水稻抗穗萌分子育种提供了理论支撑与技术储备。
黄奇娜, 姜鸿瑞, 杨婕, 于坤宇, 杨长登, 梁燕 . 种子休眠基因Sdr4的生物信息学分析与分子标记开发和应用[J]. 中国水稻科学, 2026 , 40(1) : 61 -71 . DOI: 10.16819/j.1001-7216.2026.250211
【Objective】Pre-harvest sprouting (PHS) severely compromises rice yield and grain quality, which is strongly influenced by seed dormancy genes. This study aims to elucidate the biological function of the seed dormancy gene Sdr4 and develop molecular markers for germplasm improvement, providing theoretical and practical insights for PHS-resistant rice breeding.【Method】A combination of bioinformatics analysis, molecular marker development, and marker-assisted selection was employed to systematically investigate Sdr4 functionality. Allelic variations between the strong-dormancy accession Kasalath and the weak-dormancy accession Nipponbare were analyzed to design genotype-specific markers.【Result】The Sdr4 promoter harbors core regulatory elements (e.g., TATA-box) and ABA-responsive cis-elements. The encoded protein is hydrophobic, exhibits low stability, and is extensively phosphorylated (25.93% within amino acids 101-150). Tertiary structure prediction indicated a composition of 15.50% α-helices, 15.50% β-sheets, and 66.37% random coils. Haplotype analysis of the 3K Rice Genome panel combined with AlphaFold modeling revealed that Sdr4 comprises six functional mutation-associated haplotypes. Furthermore, multiple amino acid sequence differences were identified in the Sdr4 protein between Kasalath and Nipponbare. Phylogenetic analysis demonstrated high conservation with Oryza glaberrima and Zizania palustris. Two functional markers (Sdr4-KF/KR and Sdr4-PF/PR) were developed to discriminate dormancy strength, and their efficacy was validated across 25 rice cultivars. Application of these markers in improving Zhongzhu 18 successfully generated novel lines with enhanced seed dormancy.【Conclusion】Sdr4 plays a critical role in regulating PHS resistance through the modulation of seed dormancy. Molecular screening confirmed weak dormancy phenotypes in 20 commercial varieties. The improved lines K17 and K88, developed via Sdr4-specific markers, exhibited significantly enhanced PHS resistance. This study establishes a framework for Sdr4 functional analysis and accelerates the molecular breeding of PHS-resistant rice germplasm.
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