Identification and validation of stripe rust resistance on 7BL in wheat cultivar Aikang 58 through linkage and association analysis

doi:10.1016/j.jia.2025.04.030

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Xiaoting Wang¹^*, Xinying Zhou¹^*, Jinyu Han¹^*, Wenjie Yue¹, Weihang Sun¹, Tiantian Gao¹, Dan Liu¹, Chenchen Li¹, Xuehong Ma¹, Pingtao Jiang¹, Songhan Ji¹, Haohao Yan², Weijun Zheng¹, Chunlian Li¹, Qingdong Zeng², Shengjie Liu², Xinmei Zhang³, Zhensheng Kang², Dejun Han^1*, Zhiyong Liu⁴^#, Jianhui Wu¹^#

¹State Key Laboratory of Crop Stress Resistance and High-Efficiency Production/College of Agronomy, Northwest A&F University, Yangling 712100, China

²State Key Laboratory of Crop Stress Resistance and High-Efficiency Production/College of Plant Protection, Northwest A&F University, Yangling 712100, China

³State Key Laboratory of Crop Stress Resistance and High-Efficiency Production/College of Life Sciences, Northwest A&F University, Yangling 712100, China

⁴Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

Highlights:

A genomic region spanning over 30 Mb on chromosome arm 7BL carring multiple loci for durable resistance to stripe rust was identified in wheat cultivar Aikang 58.

GWAS and sweep selection analyses revealed the specific genomic regions on chromosome arm 7BL with artificial selection signals in different breeding groups.

High-throughput molecular markers have been developed to accelerate the deployment of YrAK58.1, YrAK58.2, YrAK58.3 in breeding programs.

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摘要

由条锈菌（Puccinia striiformis f. sp. tritici , Pst）引起的条锈病是影响我国小麦安全生产的重要病害。小麦品种矮抗58（AK58）自2005年推广以来一直对条锈病表现出较高水平的抗性，但是其抗条锈病遗传基础尚不清楚。用AK58分别与Avocet S和科农9204杂交产生含有128个家系的AAK F_2:8重组自交系(RIL)和含有1042个家系的KAK F_2:3群体解析AK58的抗条锈病遗传基础。此外，对688份小麦种质（Panel 1）组成的自然群体进行全基因组关联分析（GWAS）和选择性清除分析（sweep selection）以验证目标区段的抗病单倍型和对388份中国小麦品种与高代育种系（Panel 2）组成的自然群体进行分子标记检测评估AK58中抗病位点的使用情况。其中两个遗传群体的表型和基因型来源分别是杨凌(YL)和贵阳(GY)两地五个生长季(2017-2022)的表型数据和GBW16K SNP芯片基因型数据以及KASP标记的基因分型。通过QTL定位，在染色体1BL、2BS、2BL、5BL和7BL（3个QTL）上共检测到7个抗条锈病QTL位点。其中，位于2BL的QYrak.nwafu-2BL经分析鉴定为抗病基因Yr5b，对条锈菌生理小种V32L表现全生育期抗性；位于7BL染色体715.77 - 733.25 Mb（基于中国春 RefSeq v.2.1）区域内的三个QTL位点分别被命名为YrAK58.1、YrAK58.2和YrAK58.3。其中，YrAK58.1为抗病基因Yr6，YrAK58.2对多个Pst小种具有全生育期抗性并且在田间也表现出有效抗性，而YrAK58.3在所有田间环境中都表现出稳定的成株期抗性。其余QTL的抗性受环境影响，且作用效果较小。通过GWAS和选择性清除分析显示，在不同育种群体中，7BL染色体上的3个QTL所在区域存在人工选择信号。利用与Yr6、YrAK58.2和YrAK58.3紧密连锁的分子标记能够检测三个位点的单倍型组合，并且在Panel 2中仅有3.6%的小麦材料同时检测到这三个基因，表明三个位点的抗性基因组合在未来抗性育种改良中具有很大应用前景。

Abstract

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a serious disease affecting wheat production in China. Wheat cultivar Aikang 58 (AK58) has exhibited effective resistance to stripe rust since its release in 2005. But the genetic basis of its stripe rust resistance remains unknown. Two genetic populations from the crosses of Avocet S/AK58 (128 recombinant inbred lines) and Kenong 9204/AK58 (1,042 F_2:3 families) were used to dissect the genetic basis of stripe rust resistance in AK58, respectively. In addition, Panel 1 consisting of 688 wheat accessions were used for genome-wide association study (GWAS) and sweep selection analysis to validate the presence of the resistance haplotype of the target region and Panel 2 consisting of 388 Chinese cultivars and breeding lines was genotyped using molecular markers to evaluate the prevalence and distribution of the resistant loci in AK58. The genetic populations were evaluated for stripe rust responses at Yangling and Guiyang over five cropping seasons (2017-2022) and genotyped using GBW16 K SNP array and KASP markers. Using quantitative trait loci (QTLs) analysis, seven QTL were detected on chromosome arms 1BL, 2BS, 2BL, 5BL and 7BL (three QTLs). Among them, QYrak.nwafu-2BL identified as Yr5b conferred all-stage resistance to Pst race V32L; three QTL within the 7BL chromosome arm region 715.77-733.25 Mb based on Chinese Spring RefSeq v.2.1, were designated YrAK58.1, YrAK58.2 and YrAK58.3, respectively. YrAK58.1 confirmed as Yr6, and YrAK58.2 conferred all-stage resistance to multiple Pst races and were also effective in field environments. YrAK58.3 contributed stable resistance in all field environments. The remaining QTL were environment-dependent with minor effect. GWAS and sweep selection analyses revealed specific genomic regions with artificial selection signals for the three QTL on chromosome arm 7BL in different breeding groups. A haplotype combination of high-throughput molecular markers tightly flanking Yr6, YrAK58.2 and YrAK58.3 detected all three genes in 3.6% of entries in Panel 2. The same marker set can be used to further exploit the resistance gene combination in breeding programs.

Keywords: Aikang 58 stripe rust resistance QTL mapping Yr6 YrAK58.2 YrAK58.3

Online: 25 April 2025

Fund:

This study was financially supported by the National Key R&D Program of China (2023YFD1200400), the National Natural Science Foundation of China (32272088, 32372562 and 32472103), the Natural Science Basic Research Plan in Shaanxi Province of China (2019JCW-18 and 2020JCW-16).

About author: #Correspondence Dejun Han, E-mail: handj@nwafu.edu.cn; Zhiyong Liu, E-mail: zyliu@genetics.ac.cn; Jianhui Wu, E-mail: wujh@nwafu.edu.cn *These authors contributed equally.

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Xiaoting Wang, Xinying Zhou, Jinyu Han, Wenjie Yue, Weihang Sun, Tiantian Gao, Dan Liu, Chenchen Li, Xuehong Ma, Pingtao Jiang, Songhan Ji, Haohao Yan, Weijun Zheng, Chunlian Li, Qingdong Zeng, Shengjie Liu, Xinmei Zhang, Zhensheng Kang, Dejun Han, Zhiyong Liu, Jianhui Wu. 2025. Identification and validation of stripe rust resistance on 7BL in wheat cultivar Aikang 58 through linkage and association analysis. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2025.04.030

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