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.
Utilizing ML-GWAS to Elucidate the Genetic Basis of Kernel Moisture Content Traits in Maize
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 Chrl_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.
NETL
NSTL
万方数据
