利用ML-GWAS解析玉米籽粒含水量相关性状的遗传基础
作者:
作者单位:

1.河北农业大学农学院/国家玉米改良中心河北分中心/河北省作物种质资源重点实验室,保定 071001;2.石家庄市农林科学研究院,石家庄 050800

作者简介:

研究方向为玉米遗传育种,E-mail: lin248163264@foxmail.com

通讯作者:

祝丽英,研究方向为玉米遗传育种,E-mail: zhuliying73@163.com

中图分类号:

基金项目:

河北省重点研发计划项目(21326325D)


Utilizing ML-GWAS to Elucidate the Genetic Basis of Kernel Moisture Content Traits in Maize
Author:
Affiliation:

1.College of Agronomy,Hebei Agricultural University/Hebei Sub-center of National Maize Improvement Center/ Hebei Key Laboratory of Crop Germplasm Resources,Baoding 071001;2.Shijiazhuang Academy of Agriculture and Forestry Sciences,Shijiazhuang 050800

Fund Project:

Foundation project: The Key Research and Development Project of Hebei Province (21326325D)

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    摘要:

    玉米成熟期籽粒含水量(KMC,kernel moisture content)是影响玉米机械化粒收的关键因素,利用多位点全基因组关联分析(ML-GWAS,multi-locus genome-wide association study)挖掘与籽粒含水量相关性状显著关联的遗传位点,解析其遗传基础,可为适机收玉米品种的选育和遗传改良提供参考。本研究以205份玉米自交系为材料,在4个环境下测定成熟期籽粒、苞叶与穗轴的含水量,使用mrMLM、FASTmrMLM、FASTmrEMMA、pLARmEB、pKWmEB和ISIS EM-BLASSO 6种多位点关联分析方法结合分布于全基因组的76492个单核苷酸多态性位点(SNP,single nucleotide polymorphism)进行关联分析,挖掘其候选基因并进行基因注释。表型分析显示,205份材料的籽粒含水量相关性状的变异系数在10.47%~33.90%,广义遗传率在67.39%~81.24%。6种ML-GWAS方法共检测到26个、15个和23个SNP位点分别与籽粒含水量、苞叶含水量和穗轴含水量显著关联;其中3种及以上方法共同检测到14个显著关联SNP位点,表型贡献率(PVE,phenotypic variation explained)在1.13%~17.21%。6种方法中pLARmEB检测到的显著位点最多,FASTmrEMMA检测到的最少。基于3种及以上方法共同检测到且平均PVE≥5%的显著SNP位点为Chr1_9232728、Chr4_176596174、Chr8_57716249和Chr5_191021635,在这4个SNP位点上下游220 kb共挖掘到17个候选基因,主要富集到细胞解剖实体、新陈代谢过程和细胞进程与催化活性,推测这些基因通过调节细胞代谢与催化活性最终影响玉米籽粒、苞叶和穗轴的含水量。

    Abstract:

    Kernel moisture content (KMC) at maturity is a crucial factor affecting the mechanical harvesting of maize. By utilizing multi-locus genome-wide association study (ML-GWAS),this study aims to explore significant genetic loci associated with KMC and provide insights into the genetic basis,which can contribute to the breeding and genetic improvement of maize varieties for appropriate harvesting. In this research,205 maize inbred lines were used to measure the moisture content of kernels,husks,and cobs at maturity in four different environments. Six ML-GWAS methods,including mrMLM,FASTmrMLM,FASTmrEMMA,pLARmEB,pKWmEB,and ISIS EM-BLASSO,were applied in combination with 76492 single nucleotide polymorphisms (SNPs) distributed throughout the genome for association analysis. Candidate genes were identified and gene annotation was performed. Phenotypic analysis showed that the coefficient of variation for KMC-related traits ranged from 10.47% to 33.90%,with a broad-sense heritability ranging from 67.39% to 81.24%. A total of 26,15,and 23 SNP loci were significantly associated with kernel moisture content,husk moisture content,and cob moisture content,respectively. Among them,14 significant SNP loci were identified by three or more methods,with a phenotypic contribution ranging from 1.13% to 17.21%. pLARmEB detected the most significant loci,while FASTmrEMMA detected the fewest. Based on the detection by three or more methods with an average PVE (Proportion of variance explained)≥5%,significant SNP loci Chr1_9232728,Chr4_176596174,Chr8_57716249,and Chr5_191021635 were identified. Around these loci,within a 220kb upstream and downstream range,a total of 17 candidate genes were excavated. These genes were predominantly enriched in cellular anatomical entities,metabolic processes,and cellular processes with catalytic activity. It is hypothesized that these genes may influence the moisture content of maize kernels,husks,and cobs by modulating cellular metabolism and catalytic activity.

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胡芳林,赵永锋,朱彦辉,等.利用ML-GWAS解析玉米籽粒含水量相关性状的遗传基础[J].植物遗传资源学报,2024,25(7):1070-1082.

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  • 收稿日期:2023-12-18
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  • 在线发布日期: 2024-07-04
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