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

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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
    These authors contributed equally to this work.)

  • 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
    These authors contributed equally to this work.)

  • 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
    State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, 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)

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.

Suggested Citation

  • Bingyu Yin & Linjie Xu & Jianping Li & Yunxiao Zheng & Weibin Song & Peng Hou & Liying Zhu & Xiaoyan Jia & Yongfeng Zhao & Wei Song & Jinjie Guo, 2024. "Integrated Transcriptome and GWAS Analysis to Identify Candidate Genes for Ustilago maydis Resistance in Maize," Agriculture, MDPI, vol. 14(6), pages 1-24, June.
    • Handle: RePEc:gam:jagris:v:14:y:2024:i:6:p:958-:d:1417675
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    References listed on IDEAS

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    1. Jörg Kämper & Regine Kahmann & Michael Bölker & Li-Jun Ma & Thomas Brefort & Barry J. Saville & Flora Banuett & James W. Kronstad & Scott E. Gold & Olaf Müller & Michael H. Perlin & Han A. B. Wösten &, 2006. "Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis," Nature, Nature, vol. 444(7115), pages 97-101, November.
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