Mapping QTLs for Stripe Rust Resistance and Agronomic Traits in Chinese Winter Wheat Lantian 31 Using 15K SNP Array

Xin Li, Wenjing Tan, Junming Feng, Qiong Yan, Ran Tian, Qilin Chen, Qin Li, Shengfu Zhong, Suizhuang Yang, Chongjing Xia () and Xinli Zhou ()
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Xin Li: Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
Wenjing Tan: Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
Junming Feng: Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
Qiong Yan: Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
Ran Tian: Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
Qilin Chen: Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
Qin Li: Department of Biology and Chemistry, Chongqing Industry and Trade Polytechnic, Fuling District, Chongqing 408000, China
Shengfu Zhong: Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
Suizhuang Yang: Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
Chongjing Xia: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Xinli Zhou: Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China

Agriculture, 2025, vol. 15, issue 13, 1-21

Abstract: Wheat stripe rust ( Puccinia striiformis f. sp. tritici , Pst ) resistance and agronomic traits are crucial determinants of wheat yield. Elucidating the quantitative trait loci (QTLs) associated with these essential traits can furnish valuable genetic resources for improving both the yield potential and disease resistance in wheat. Lantian 31 is an excellent Chinese winter wheat cultivar; multi-environment phenotyping across three ecological regions (2022–2024) confirmed stable adult-plant resistance (IT 1–2; DS < 30%) against predominant Chinese Pst races (CYR31–CYR34), alongside superior thousand-kernel weight (TKW) and kernel morphology. Here, we dissected the genetic architecture of these traits using a total of 234 recombinant inbred lines (RILs) derived from a cross between Lantian 31 and the susceptible cultivar Avocet S (AvS). Genotyping with a 15K SNP array, complemented by 660K SNP-derived KASP and SSR markers, identified four stable QTLs for stripe rust resistance ( QYrlt.swust-1B , - 1D , - 2D , - 6B ) and eight QTLs governing plant height (PH), spike length (SL), and kernel traits. Notably, QYrlt.swust-1B (1BL; 29.9% phenotypic variance) likely represents the pleiotropic Yr29 / Lr46 locus, while QYrlt.swust-1D (1DL; 22.9% variance) is the first reported APR locus on chromosome 1DL. A pleiotropic cluster on 1B (670.4–689.9 Mb) concurrently enhanced the TKW and the kernel width and area, demonstrating Lantian 31’s dual utility as a resistance and yield donor. The integrated genotyping pipeline—combining 15K SNP discovery, 660K SNP fine-mapping, and KASP validation—precisely delimited QYrlt.swust-1B to a 1.5 Mb interval, offering a cost-effective model for QTL resolution in common wheat. This work provides breeder-friendly markers and a genetic roadmap for pyramiding durable resistance and yield traits in wheat breeding programs.

Keywords: adult-plant resistance (APR); all-stage resistance (ASR); genetic map; interval composite interval mapping (ICIM); recombinant inbred line (RIL) (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: 2025
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