联合全基因组关联分析和转录组数据揭示玉米抗南方锈病的遗传基础

doi:10.1016/j.jia.2023.10.039

Journal of Integrative Agriculture ›› 2025, Vol. 24 ›› Issue (2): 453-466.DOI: 10.1016/j.jia.2023.10.039

联合全基因组关联分析和转录组数据揭示玉米抗南方锈病的遗传基础

收稿日期:2023-06-20 接受日期:2023-09-28 出版日期:2025-02-20 发布日期:2025-01-21

A genome-wide association study and transcriptome analysis reveal the genetic basis for the Southern corn rust resistance in maize

Yang Wang^{1, 2*}, Chunhua Mu^3*, Xiangdong Li⁴, Canxing Duan², Jianjun Wang⁵, Xin Lu², Wangshu Li², Zhennan Xu², Shufeng Sun^{1, 2}, Ao Zhang¹, Zhiqiang Zhou², Shenghui Wen⁵, Zhuanfang Hao², Jienan Han², Jianzhou Qu¹, Wanli Du^1#, Fenghai Li^#, Jianfeng Weng^2#

¹College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
²Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
³Institute of Maize Research, Shandong Academy of Agricultural Sciences, Jinan 250100, China
⁴College of Plant Protection, Shandong Agricultural University, Tai’an 250100, China
⁵Institute of Maize, Shanxi Agricultural University, Xinzhou 034000, China

Received:2023-06-20 Accepted:2023-09-28 Online:2025-02-20 Published:2025-01-21
About author:#Correspondence Wanli Du, E-mail: dwl2014@syau.edu.cn; Fenghai Li, E-mail: lifenghai@126.com; Jianfeng Weng, E-mail: wengjianfeng@caas.cn * These authors contributed equally to this study.
Supported by:
The work was supported by the National Key R&D Program of China (2022YFD1201802), the Shandong Key R&D Program, China (2022CXGC010607), the Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences (CAAS-ZDRW202109), the Sub-project of the Major Project of Science and Technology in Shanxi Province, China (202201140601025-1-02), and the Agricultural Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences (CAAS-ASTIP-2017-ICS). We thank Prof. Yule Li (Tsinghua University) and Tao Zhou (China Agricultural University) for providing the VIGS vectors.

摘要/Abstract

摘要：

玉米南方锈病（Southern Corn Rust, SCR）是由多堆柄锈菌（Puccinia polysora Underw）引起的气传性真菌病害，在世界范围玉米产区普遍发生，严重影响玉米的产量和品质，而发掘优异抗性位点和候选基因，开展抗病遗传解析，将为解析抗玉米南方锈病抗病育种提供理论参考。本研究以487份温带玉米自交系为材料，利用15,232,270个高质量SNPs结合2021年南宁、2021年三亚和2022年济南三个环境下的玉米南方锈病抗性表型进行全基因组关联分析（Genome wide association study, GWAS），共检测到91个QTLs，其中13个QTLs同时在三个环境被检测到，共涉及94个候选基因（B73_RefGen_v4）。进一步结合转录组测序（RNA sequencing, RNA-seq）分析候选基因，共鉴定到4个候选基因影响玉米南方锈病抗性，其中ZmHCT9编码羟基肉桂酰转移酶，在感病自交系8112中显著上调表达，进一步基于候选基因功能注释，单倍型分析，P. polysora接种后表达量及病毒诱导的基因沉默，发现ZmHCT9负调控玉米南方锈病抗性。

Abstract:

Southern corn rust (SCR) is an airborne fungal disease caused by Puccinia polysora Underw. (P. polysora) that adversely impacts maize quality and yields worldwide. Screening for new elite SCR-resistant maize loci or genes has the potential to enhance overall resistance to this pathogen. Using phenotypic SCR resistance-related data collected over two years and three geographical environments, a genome-wide association study was carried out in this work, which eventually identified 91 loci that were substantially correlated with SCR susceptibility. These included 13 loci that were significant in at least three environments and overlapped with 74 candidate genes (B73_RefGen_v4). Comparative transcriptomic analyses were then performed to identify the genes related to SCR infection, with 2,586 and 797 differentially expressed genes (DEGs) ultimately being identified in the resistant Qi319 and susceptible 8112 inbred lines following P. polysora infection, respectively, including 306 genes common to both lines. Subsequent integrative multi-omics investigations identified four potential candidate SCR response-related genes. One of these genes is ZmHCT9, which encodes the protein hydroxycinnamoyl transferase 9. This gene was up-regulated in susceptible inbred lines and linked to greater P. polysora resistance as confirmed through cucumber mosaic virus (CMV)-based virus induced-gene silencing (VIGS) system-mediated gene silencing. These data provide important insights into the genetic basis of the maize SCR response. They will be useful for for future research on potential genes related to SCR resistance in maize.

Key words: maize , southern corn rust , genome-wide association study , transcriptome

Yang Wang, Chunhua Mu, Xiangdong Li, Canxing Duan, Jianjun Wang, Xin Lu, Wangshu Li, Zhennan Xu, Shufeng Sun, Ao Zhang, Zhiqiang Zhou, Shenghui Wen, Zhuanfang Hao, Jienan Han, Jianzhou Qu, Wanli Du, Fenghai Li, Jianfeng Weng. 联合全基因组关联分析和转录组数据揭示玉米抗南方锈病的遗传基础[J]. Journal of Integrative Agriculture, 2025, 24(2): 453-466.

Yang Wang, Chunhua Mu, Xiangdong Li, Canxing Duan, Jianjun Wang, Xin Lu, Wangshu Li, Zhennan Xu, Shufeng Sun, Ao Zhang, Zhiqiang Zhou, Shenghui Wen, Zhuanfang Hao, Jienan Han, Jianzhou Qu, Wanli Du, Fenghai Li, Jianfeng Weng. A genome-wide association study and transcriptome analysis reveal the genetic basis for the Southern corn rust resistance in maize[J]. Journal of Integrative Agriculture, 2025, 24(2): 453-466.

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联合全基因组关联分析和转录组数据揭示玉米抗南方锈病的遗传基础

A genome-wide association study and transcriptome analysis reveal the genetic basis for the Southern corn rust resistance in maize

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