摘要
为挖掘与水稻粒长相关的候选基因,以139份西北早粳稻核心种质资源为材料,结合重测序获得的255501个高质量SNPs,利用FarmCPU模型对水稻粒长进行全基因组关联分析,将显著SNPs上下游各延伸50 kb作为候选区间,再将候选区间内CDS区存在差异的基因进行功能注释和单倍型分析。结果表明,139份水稻种质粒长变异系数为9.18%,且近似正态分布,在阈值-log_(10)(p)≥6.41条件下,FarmCPU模型分别在3号、5号、7号、10号染色体上检测到7个显著且有代表性的SNPs,在候选区间内筛选出2个水稻粒长的候选基因。LOC_Os05g10420和LOC_Os05g10560都编码表达蛋白,LOC_Os05g10420通过分型共分为2个单倍型,且含有Hap1的种质粒长极显著低于含有Hap2的种质粒长;LOC_Os05g10560通过分型共分为3个单倍型,含有Hap1的种质粒长极显著低于含有Hap2和Hap3的种质粒长。
In order to explore the candidate genes related to rice grain length,139 core germplasm resources of Northwest early Oryza sativa subsp.japonica were used as materials,combined with 255501 high-quality SNPs obtained by resequencing,and genome-wide association analysis of rice grain length was conducted using FarmCPU model.Significant SNPs extending 50 kb upstream and downstream were used as candidate intervals,and then functional annotation and haplotype analysis were performed for genes with differences in CDS region within the candidate intervals.The results showed that the coefficient of variation of 139 rice germplasm length was 9.18%,and the distribution was approximately normal.Under the condition of threshold-log_(10)(p)≥6.41,seven significant and representative SNPs were detected on chromosomes 3,5,7 and 10,respectively,in the FarmCPU model.Two rice grain length candidate genes were screened within the candidate interval.LOC_Os05g10420 and LOC_Os05g10560 both encoded and expressed proteins.LOC_Os05g10420 was divided into two haplotypes by typing,and the grain length of varieties containing Hap1 was significantly lower than that of varieties containing Hap2.LOCOs05g10560 was divided into three haplotypes,and the length of the germplasm containing Hap1 was significantly lower than that containing Hap2 and Hap3.
作者
刘继虎
于雪然
刘爱婷
徐强
马静
姚鑫杰
张哲
李培富
LIU Jihu;YU Xueran;LIU Aiting;XU Qiang;MA Jing;YAO Xinjie;ZHANG Zhe;LI Peifu(College of Agriculture,Ningxia University/Ningxia Key Laboratory of Modern Molecular Breeding of Dominant Characteristic Crops,Yinchuan 750021,China;Chifeng Institute of Agriculture and Animal Husbandry,Chifeng Inner Mongolia 024000,China)
出处
《种子》
北大核心
2024年第10期98-103,共6页
Seed
基金
宁夏粮食作物种质创制与生长调控科技创新团队(2022BSB03109)
宁夏农业育种专项课题(2018NYYZ0302)。
关键词
粳稻种质
粒长
全基因组关联分析
Oryza sativa subsp.japonica germplasm
grain length
genome-wide association analysis
