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Journal of Integrative Agriculture
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GWAS analysis reveals candidate genes associated with dense tolerance (ear leaf structure) in maize (Zea mays L.)
Chunxiang Li1*, Yongfeng Song1*, Yong Zhu1, Mengna Cao1, Xiao Han1, Jinsheng Fan2, Zhichao Lv1, Yan Xu1, Yu Zhou1, Xing Zeng1, Lin Zhang1, Ling Dong1, Dequan Sun2, Zhenhua Wang1#, Hong Di1#

1 College of Agricultural, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education.Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold Land of Heilongjiang Province, Harbin 150030, China

2 Institute of Forage and grassland Sciences Heilongjiang Academy of Agricultural Science, Harbin 150086, Heilongjiang Province, China 

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摘要  种植密度是影响玉米产量的主要限制因素,培育耐密植品种已成为玉米生产中亟待解决的问题。玉米穗叶的叶片结构是制约玉米种植密度和产量构成的主要因素。本研究利用201个玉米自交系自然群体进行全基因组关联分析,在染色体258910上鉴定出9个与穗叶型结构显著相关的SNPqRT-PCR进一步验证了5个候选基因与这些SNP的关联,其中Zm00001d008651基因在紧凑型和扁平型玉米自交系中表现出显著的表达差异, GO和KEGG富集分析表明该基因参与糖酵解过程。该基因的基本特性分析表明,其编码一种由593个氨基酸组成的稳定的碱性蛋白,具有一定的疏水性。启动子区域包含与应激和激素(ABA)相关的元件。该基因突变体穗位叶的叶角和穗下第一片叶的叶角分别比野生型增加4.96°0.97°。本研究揭示了玉米穗叶结构对密度耐受性的调控机制,为培育新品种提供了坚实的基础。

Abstract  Planting density is a major limiting factor for maize yield, and breeding for density tolerance breeding has become an urgent issue.  The leaf structure of the maize ear leaf is the main factor that restricts planting density and yield composition.  In this study, a natural population of 201 maize inbred lines was used for genome-wide association analysis, which identified nine SNPs on chromosomes 2, 5, 8, 9, and 10 that were significantly associated with ear leaf type structure.  Further verification through qRT-PCR confirmed the association of five candidate genes with these SNPs, with the Zm00001d008651 gene showing significant differential expression in compact and flat maize inbred lines.  Enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) suggested that this gene is involved in the glycolysis process.  The analysis of the basic properties of this gene revealed that it encodes a stable, basic protein consisting of 593 amino acids with some hydrophobic ability.  The promoter region contains stress and hormone (ABA) related elements.  The mutant of this gene increased the uppermost ear leaf angle (eLA) and the first leaf below the uppermost ear (bLA) by 4.96° and 0.97° compared with normal inbred lines.  Overall, this research sheds light on the regulatory mechanism of ear and leaf structure that influence density tolerance and provides solid foundational work for the development of new varieties.
Keywords:  maize       planting density              ear leaf structure              GWAS              candidate genes  
Online: 02 February 2024  
About author:  Chunxiang Li, E-mail: lcx990127@163.com; Yongfeng Song, E-mail: song18182746326@163.com; #Correspondence Zhenhua Wang, Tel: +86-451-55190021, E-mail: zhenhuawang_2006@163.com; Hong Di, Tel: +86-451-55190202, E-mail: dihongdh@163.com * indicates the authors who contributed equally to this study

Cite this article: 

Chunxiang Li, Yongfeng Song, Yong Zhu, Mengna Cao, Xiao Han, Jinsheng Fan, Zhichao Lv, Yan Xu, Yu Zhou, Xing Zeng, Lin Zhang, Ling Dong, Dequan Sun, Zhenhua Wang, Hong Di. 2024. GWAS analysis reveals candidate genes associated with dense tolerance (ear leaf structure) in maize (Zea mays L.). Journal of Integrative Agriculture, Doi:10.1016/j.jia.2024.01.023

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