中国水稻科学2026，Vol.40Issue(1)：61-71,11.DOI:10.16819/j.1001-7216.2026.250211
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
Bioinformatics Analysis,Development and Application of Molecular Markers for Seed Dormancy Gene Sdr4 in Rice
摘要
Abstract
[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.关键词
穗发芽/Sdr4/水稻/生物信息学/分子标记辅助选择Key words
pre-harvest sprouting/Sdr 4/rice/bioinformatics analysis/molecular marker-assisted selection引用本文复制引用
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):61-71,11.基金项目
浙江省农业(水稻)新品种选育重大科技专项(2021C02063-4) （水稻）
中央级公益性科研院所基本科研业务费专项(CPSIBRF-CNRRI-202306) （CPSIBRF-CNRRI-202306）
国家重点研发计划资助项目(2022YFD1201505). （2022YFD1201505）
