Genome-Wide Association Study Reveals the Genetic Basis of Stalk Cell Wall Components in Maize

Lignin, cellulose and hemicellulose are the three main components of the plant cell wall and can impact stalk quality by affecting cell wall structure and strength. In this study, we evaluated the lignin (LIG), cellulose (CEL) and hemicellulose (HC) contents in maize using an association mapping panel that included 368 inbred lines in seven environments. A genome-wide association study using approximately 0.56 million SNPs with a minor allele frequency of 0.05 identified 22, 18 and 24 loci significantly associated with LIG, CEL and HC at P < 1.0×10−4, respectively. The allelic variation of each significant association contributed 4 to 7% of the phenotypic variation. Candidate genes identified by GWAS mainly encode enzymes involved in cell wall metabolism, transcription factors, protein kinase and protein related to other biological processes. Among the association signals, six candidate genes had pleiotropic effects on lignin and cellulose content. These results provide valuable information for better understanding the genetic basis of stalk cell wall components in maize.

木质素（Lignin，简称LIG）、纤维素（Cellulose，简称CEL）与半纤维素（Hemicellulose，简称HC）是植物细胞壁的三大核心组分，可通过调控细胞壁结构与强度进而影响玉米茎秆品质。本研究以涵盖7个环境下368个自交系的关联作图群体（association mapping panel）为试验材料，对玉米中的上述三种细胞壁组分含量进行了系统测定。本研究采用次要等位基因频率（minor allele frequency）为0.05的约56万个单核苷酸多态性（Single Nucleotide Polymorphism，简称SNP）标记开展全基因组关联分析（Genome-wide Association Study，简称GWAS），在P < 1.0×10^-4的显著性阈值下，分别鉴定到与木质素、纤维素和半纤维素含量显著关联的遗传位点各22个、18个与24个。每个显著关联位点的等位变异可解释4%至7%的表型变异。通过GWAS鉴定到的候选基因主要编码参与细胞壁代谢的酶类、转录因子（transcription factor）、蛋白激酶（protein kinase）以及参与其他生物学过程的相关蛋白。在上述关联信号中，共有6个候选基因对木质素与纤维素含量存在多效性调控作用。本研究结果为深入解析玉米茎秆细胞壁组分的遗传基础提供了重要参考依据。