Integrating GWAS and Gene Expression Analysis Identifies Candidate Genes for Root Morphology Traits in Maize at the Seedling Stage
Integrating GWAS and Gene Expression Analysis Identifies Candidate Genes for Root Morphology Traits in Maize at the Seedling Stage
复制标题
整合 GWAS 和基因表达分析，鉴定玉米幼苗期根部形态性状的候选基因
作者：
Wang Houmiao;Wei Jie;Li Pengcheng;Wang Yunyun;Ge Zhenzhen;Qian Jiayi;Fan Yingying;Ni Jinran;Xu Yang;Yang Zefeng;Xu Chenwu
根系在植物吸收水分和养分方面起着重要作用。了解根系发育的遗传基础，将有助于培育根系高效的玉米新品种，提高资源利用效率。本研究以297份玉米自交系为材料，分析了13个根系和3个地上部性状的自然变异，并进行了全基因组关联分析。所有测量的性状表现出2.02- 21.36倍的变异。共检测到13个性状的34个数量性状基因座（QTL），每个QTL可解释表型变异的5.7%~ 15.9%。SNP_2_104416607与侧根长（LRL）、根表面积（RA）、0 ~ 0.5mm直径的根长（RL 005）和总根长（TRL）相关; SNP_2_184016997与RV和RA相关，SNP_4_168917747与LRL、RA和TRL相关。利用RNA-seq技术对3个长根系和3个短根系的根系QTL候选基因的表达水平进行了分析。共5个基因表现出差异表达之间的长和短根线被确定为有前途的候选基因的目标性状。这些QTL和潜在的候选基因是了解玉米根系发育和根系性状遗传改良的重要基础数据。
Root system plays an essential role in water and nutrient acquisition in plants. Understanding the genetic basis of root development will be beneficial for breeding new cultivars with efficient root system to enhance resource use efficiency in maize. Here, the natural variation of 13 root and 3 shoot traits was evaluated in 297 maize inbred lines and genome-wide association mapping was conducted to identify SNPs associated with target traits. All measured traits exhibited 2.02- to 21.36-fold variations. A total of 34 quantitative trait loci (QTLs) were detected for 13 traits, and each individual QTL explained 5.7% to 15.9% of the phenotypic variance. Three pleiotropic QTLs involving five root traits were identified; SNP_2_104416607 was associated with lateral root length (LRL), root surface area (RA), root length between 0 and 0.5mm in diameter (RL005), and total root length (TRL); SNP_2_184016997 was associated with RV and RA, and SNP_4_168917747 was associated with LRL, RA and TRL. The expression levels of candidate genes in root QTLs were evaluated by RNA-seq among three long-root lines and three short-root lines. A total of five genes that showed differential expression between the long- and short-root lines were identified as promising candidate genes for the target traits. These QTLs and the potential candidate genes are important source data to understand root development and genetic improvement of root traits in maize.