Multi-trait genome-wide association studies reveal forage yield-related candidate genes and favorable haplotypes in hulled oats (Avena sativa)

doi:10.1016/j.jia.2025.06.025

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Multi-trait genome-wide association studies reveal forage yield-related candidate genes and favorable haplotypes in hulled oats (Avena sativa)

Jin Li¹, Xu Zhao¹, Jingbo Yu¹, Qingping Zhou¹, Shiyong Chen^{1, 2#}

¹Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu 610041, China

²College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China

Highlights

1. Fourteen stable QTLs and 35 candidate genes related to six forage yield traits were identified using RTM- and Blink-GWAS.

2. Favorable haplotypes with consistent phenotypic effects provide targets for oat yield improvement.

Abstract
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摘要

【目的】燕麦（Avena sativa）是一种重要的世界性栽培的粮饲兼用作物。在全球气候变化和人口增长的背景下，优异燕麦品种的培育对维护全球食物安全具有重要的作用。作为重要的饲用作物，目前关于其饲草产量相关性状的遗传基础研究还较少，严重阻碍了其分子育种的研究。本研究旨在借助全基因组关联分析（GWAS）解析皮燕麦中与饲草产量相关性状的遗传基础，为饲用燕麦的分子育种提供理论依据。【方法】本研究以来自全球的266份皮燕麦种质材料为研究对象，在5个不同生态环境下对其株高、茎长、穗长、旗叶长、旗叶宽和茎粗6个饲草产量相关性状进行表型测定。利用高通量重测序技术获得34,896个高质量SNP位点，并分别采用RTM-GWAS和Blink-GWAS方法开展GWAS分析。【结果】研究结果表明，6个饲草产量相关性状在不同环境下均表现出较大的变异和相对较高的遗传力，性状之间呈显著正相关（r = 0.23~0.93）。GWAS分析共鉴定出54个SNP连锁不平衡区块（SNPLDBs）和52个与农艺性状显著相关的SNP位点，共定位到105个QTLs，其中14个QTLs在多个环境和模型中均重复出现，具有高度的稳定性。进一步对代表性QTLs进行连锁不平衡分析，构建了对应的单倍型区块，发现相关的性状均存在具有显著表型差异的优异单倍型，且表现出良好的环境稳定性。同时，结合QTLs区间基因注释结果、转录组数据及同源比对信息，最终筛选鉴定出35个候选基因，涉及信号转导、转录调控、物质运输、激素响应与细胞发育等多个生物学过程。其中多个QTLs与已研究报道的燕麦株高、茎长等QTLs高度相关。【结论】综上，本研究通过GWAS揭示了皮燕麦中6个饲草产量相关性状的遗传基础，鉴定了相关的QTL、优异单倍型与候选基因，研究结果为燕麦分子设计育种和优异等位变异的挖掘利用提供了重要的参考。【创新性】本研究联合两种GWAS模型进行饲用燕麦多性状综合分析，显著提升了QTL定位的准确性与稳定性；同时结合转录组信息和连锁区块进行单倍型优选，鉴定出了可用于饲用燕麦分子育种的目标位点和关键候选基因。

Abstract

Hulled oat is an important cereal crop for both animal feed and human consumption, as climate change accelerates and the world's population grows, improving oat breeding is crucial to ensure a stable food supply. Genome-wide association studies (GWAS) are instrumental in pinpointing single nucleotide polymorphisms (SNPs) associated with phenotypic variations within germplasm collections. This study assessed six crucial agronomic traits (plant height, stem length, spike length, flag leaf length, flag leaf width, and stem diameter) across five environments in 266 globally sourced hulled oat varieties, employing 34,896 SNPs for a comprehensive genetic analysis via restricted two-stage multi-locus multi-allele (RTM)- and Bayesian-information and linkage-disequilibrium iteratively nested keyway (Blink)-GWAS methodologies. Our analysis identified 54 SNP linkage disequilibrium blocks (SNPLDBs), and 52 SNPs associated with the six agronomic traits. A total of 105 quantitative trait loci (QTLs) were identified within a ±2 Mb physical region surrounding these loci. Of these, 14 stable QTLs were consistently detected across multiple environments and by both GWAS methods. Haplotype analysis within these QTL regions identified three to five haplotype alleles, each significantly influencing the phenotypic variation of traits across different environments. Combining gene annotation, literature review, and transcriptome data, we identified 35 candidate genes involved in signal transduction, transcriptional regulation, metabolism, and cell development. These findings provide valuable genetic resources for enhancing agronomic traits and yield in oat breeding programs under diverse environmental conditions.

Keywords: Forage oats Agronomic trait GWAS QTL Haplotypes Candidate genes

Online: 24 June 2025

Fund:

This work was supported by the Key Research & Development Program of Sichuan province (2021YFYZ0013, 2023NZZJ0002), and the Double First-Class program of Southwest Minzu University (CX2023017).

About author: #Correspondence: Shiyong Chen; E-mail: chensy@swun.edu.cn

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Jin Li, Xu Zhao, Jingbo Yu, Qingping Zhou, Shiyong Chen. 2025. Multi-trait genome-wide association studies reveal forage yield-related candidate genes and favorable haplotypes in hulled oats (Avena sativa). Journal of Integrative Agriculture, Doi:10.1016/j.jia.2025.06.025

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