Genome-wide association mapping revealed a major QTL for Septoria tritici blotch resistance in wheat

doi:10.1016/j.jia.2025.12.013

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Xiaoqian Wang¹, Chenchen Zhao², Qinglan Wei¹, Chengdao Li^3,⁴, Zhong-Hua Chen⁵, Rajeev Varshney³, Sergey Shabala⁶, Meiqin Lu⁷, Yunlong Pang¹^#, Meixue Zhou²^#

¹National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China

²Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS 7250, Australia

³Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA 6150 Australia

⁴Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA 6150 Australia

⁵School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia

⁶School of Biological Science, University of Western Australia, Crawley 6009, Australia

⁷Australian Grain Technologies, Narrabri, NSW 2390, Australia

Highlights

l GWAS of 318 diverse wheat accessions identified 14 QTLs for Septoria tritici blotch resistance.

l Three stable QTLs (qSTB-3B.1, qSTB-4A.2, and qSTB-6B) were consistently detected across environments.

l The qSTB-4A.2 allele reduced disease scores from 5.4 to 3.9, and it acted additively with qSTB-6B for enhanced resistance.

Abstract
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摘要

摘要:由真菌病原体小麦壳针孢（Zymoseptoria tritici）引起的小麦壳针孢叶枯病（STB）对全球小麦生产构成严重威胁，显著影响产量和籽粒品质。为解析STB抗性遗传位点，本研究利用13,098个高质量SNP对318份多样化小麦种质（包括澳大利亚商业品种、澳大利亚谷物基因库资源、中国商业品种和中国地方品种）进行全基因组关联分析。通过连续两年的田间抗性评价，结合群体结构和主成分分析，发现中国地方品种与其他群体存在明显遗传分化，且中国地方品种中抗病种质比例最高。共鉴定到14个与STB抗性相关的数量性状位点（QTL），其中qSTB-3B.1、qSTB-4A.2和qSTB-6B在全部环境中稳定表达，qSTB-4A.2被确定为主效抗病位点。选择qSTB-4A.2等位基因可使平均病情评分从5.4降低至3.9。进一步研究发现，同时携带qSTB-4A.2和qSTB-6B抗性等位基因的种质，其病情评分显著低于仅携带qSTB-4A.2的种质，表明存在加性效应。在稳定QTL区间内通过候选基因分析鉴定出27个潜在抗病基因，包括已知抗病相关基因同源物（如Lr34/Yr18/Pm38和OsWAK1）。本研究深化了对STB抗性遗传机制的理解，为培育持久抗病小麦品种提供了可靠的分子标记和候选基因资源。

Abstract

Septoria tritici blotch (STB), caused by the fungal pathogen Zymoseptoria tritici, poses a major threat to global wheat production, adversely affecting both yield and grain quality. To identify the genetic loci controlling STB resistance, a genome-wide association study (GWAS) was conducted using 13,098 high-quality SNPs across a diverse panel of 318 wheat accessions including Australian commercial varieties, Australian Grains Genebank, Chinese commercial varieties, and Chinese landraces. Disease resistance was evaluated over two consecutive years under field conditions. Population structure and principal component analyses revealed distinct genetic differentiation between Chinese landraces and other groups. Notably, Chinese landraces exhibited the highest proportion of resistant accessions. We identified a total of 14 quantitative trait loci (QTLs) associated with STB resistance. Notably, three QTLs (qSTB-3B.1, qSTB-4A.2, and qSTB-6B) were consistently detected across all environments, with qSTB-4A.2 as a major resistance locus. Selection for the qSTB-4A.2 allele reduced the average disease score from 5.4 to 3.9. Furthermore, an additive effect was observed, where accessions carrying resistance alleles at both qSTB-4A.2 and qSTB-6B exhibited significantly lower disease scores than those with only the qSTB-4A.2 allele. Candidate gene analysis within these stable QTLs identified 27 promising genes including homologs of known disease resistance-related genes such as Lr34/Yr18/Pm38, and OsWAK1. These findings enhance our understanding of STB resistance genetics and provide robust markers and candidate genes for marker-assisted selection in breeding durable and disease-resistant wheat cultivars.

Keywords: wheat septoria tritici blotch GWAS QTLs candidate genes

Online: 08 December 2025

Fund:

This work was supported by the Shandong Provincial Natural Science Foundation, China (ZR2024YQ069 and ZR2024QC053), the Grains Research and Development Corporation (GRDC), the Taishan Scholars Program, and the Open Project Program (WIKF202401) of State Key Laboratory of Wheat Improvement.

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Xiaoqian Wang, Chenchen Zhao, Qinglan Wei, Chengdao Li, Zhong-Hua Chen, Rajeev Varshney, Sergey Shabala, Meiqin Lu, Yunlong Pang, Meixue Zhou. 2025. Genome-wide association mapping revealed a major QTL for Septoria tritici blotch resistance in wheat. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2025.12.013

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