Integrated Transcriptome and GWAS Analysis to Identify Candidate Genes for Ustilago maydis Resistance in Maize

Bingyu Yin, Linjie Xu, Jianping Li, Yunxiao Zheng, Weibin Song, Peng Hou, Liying Zhu, Xiaoyan Jia, Yongfeng Zhao, Wei Song () and Jinjie Guo ()
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Bingyu Yin: State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Sub-Center of National Maize Improvement Center of China, College of Agronomy, Hebei Agricultural University, Baoding 071000, China
Linjie Xu: State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Sub-Center of National Maize Improvement Center of China, College of Agronomy, Hebei Agricultural University, Baoding 071000, China
Jianping Li: State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Sub-Center of National Maize Improvement Center of China, College of Agronomy, Hebei Agricultural University, Baoding 071000, China
Yunxiao Zheng: State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Sub-Center of National Maize Improvement Center of China, College of Agronomy, Hebei Agricultural University, Baoding 071000, China
Weibin Song: State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
Peng Hou: Key Laboratory of Crop Physiology and Ecology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
Liying Zhu: State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Sub-Center of National Maize Improvement Center of China, College of Agronomy, Hebei Agricultural University, Baoding 071000, China
Xiaoyan Jia: State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Sub-Center of National Maize Improvement Center of China, College of Agronomy, Hebei Agricultural University, Baoding 071000, China
Yongfeng Zhao: State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Sub-Center of National Maize Improvement Center of China, College of Agronomy, Hebei Agricultural University, Baoding 071000, China
Wei Song: Key Laboratory of Crop Genetics and Breeding of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
Jinjie Guo: State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Sub-Center of National Maize Improvement Center of China, College of Agronomy, Hebei Agricultural University, Baoding 071000, China

Agriculture, 2024, vol. 14, issue 6, 1-24

Abstract: Maize Ustilago maydis is a disease that severely affects maize yield and quality. In this paper, we employed transcriptome sequencing and GWAS analysis to identify candidate genes and reveal disease-resistant germplasm resources, thereby laying the foundation for further analysis of the molecular mechanism of maize Ustilago maydis resistance and genetic improvement. The results of transcriptome sequencing revealed that a considerable number of receptor kinase genes, signal-transduction-related protein genes, redox-response-related genes, WRKYs, and P450s genes were significantly upregulated. There was a wide range of mutations of Ustilago maydis in maize inbred lines. Thirty-two high-resistance maize inbred lines were selected, and 16 SNPs were significantly associated with the disease index. By integrating the results of GWAS and RNA-seq, five genes related to disease resistance were identified, encoding the chitinase 1 protein, fatty acid elongase (FAE), IAA9, GATA TF8, and EREB94, respectively. It provides a certain reference for the cloning of maize anti-tumor smut genes and the breeding of new varieties.

Keywords: maize; Ustilago maydis; transcriptome sequencing; genome-wide association analysis; candidate genes (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2024
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