Genome-wide Association Analysis and Candidate Gene Prediction of Important Agronomic Traits of Forage Oat

doi:10.11733/j.issn.1007-0435.2025.11.005

Acta Agrestia Sinica ›› 2025, Vol. 33 ›› Issue (11): 3526-3539.DOI: 10.11733/j.issn.1007-0435.2025.11.005

Genome-wide Association Analysis and Candidate Gene Prediction of Important Agronomic Traits of Forage Oat

LIU Xiao-xia^1,2,3, AN Wen^1,2,3, LI Lin^1,2,3, ZHANG Xin-yu^1,2,3, LANG Si-rui^4,5, MA Qiao-li⁶, MA Dong-mei^1,2,3

1. Cultivation Base of State Key Laboratory of Northwest Land Degradation and Ecosystem Restoration, Ningxia University, Yinchuan, Ningxia 750021, China;
2. Key Laboratory of Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ministry of Education, Yinchuan, Ningxia 750021, China;
3. College of Ecology and Environment, Ningxia University, Yinchuan, Ningxia 750021, China;
4. School of Life Sciences, Ningxia University, Yinchuan, Ningxia 750021, China;
5. Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, Ningxia 750021, China;
6. College of Forestry and Grassland, Ningxia University, Yinchuan, Ningxia 750021, China

Received:2024-11-05 Revised:2025-02-15 Published:2025-11-13

饲用燕麦重要农艺性状的全基因组关联分析和候选基因预测

刘晓霞^1,2,3, 安雯^1,2,3, 李琳^1,2,3, 张新宇^1,2,3, 郎思睿^4,5, 马巧利⁶, 麻冬梅^1,2,3

1. 宁夏大学西北土地退化与生态系统恢复国家重点实验室培养基地, 宁夏银川 750021;
2. 西北退化生态系统恢复与重建教育部重点实验室, 宁夏银川 750021;
3. 宁夏大学生态环境学院, 宁夏银川 750021;
4. 宁夏大学生命科学学院, 宁夏银川 750021;
5. 宁夏大学西部特色生物资源保护与利用教育部重点实验室, 宁夏银川 750021;
6. 宁夏大学林业与草业学院, 宁夏银川 750021

通讯作者: 麻冬梅,E-mail:576494584@qq.com
作者简介:刘晓霞（1989-），女，汉族，山西大同人，博士，助理研究员，主要从事牧草抗逆分子育种研究，E-mail：liuxiaoxia0856@163.com；
基金资助:
宁夏回族自治区重点研发项目（2022BBF02030）；宁夏回族自治区重点研发项目（2022BDE92070）资助

Abstract

Abstract: Forage oat （Avena sativa L.） plays a crucial role in grassland animal husbandry and ecological sustainable development， yet the genetic mechanisms of its agronomic traits remain poorly understood. In this study， genome resequencing of 69 oat accessions was performed， yielding 47 993 754 high-quality SNPs for genome-wide association analysis （GWAS） of nine key agronomic traits. A total of 210 significantly associated SNPs were identified， distributing across all chromosomes， with the highest density on chromosome 3C. Further analysis revealed 120 candidate genes， including receptor kinase genes （ORK45， LRK45） and the E3 ubiquitin ligase gene At1g63170 associated with plant height， both known to regulate height in other species. Traits such as flag leaf length， spikelet number per plant， and seed number per spikelet were linked to a zinc finger CCCH domain-containing protein gene， which played a role in plant growth and stress responses. Chlorophyll content was associated with ABC transporter genes， the HY5 transcription factor， and an ethylene-responsive transcription factor gene， and all involved in light response. Haplotype analysis of 10 SNPs corresponding to 16 key candidate genes showed 2-4 haplotypes per locus， with most exhibiting significant phenotypic variation. This study provides valuable genetic resources and a theoretical basis for future molecular breeding in forage oat.

Key words: Forage oat, Agronomic traits, Genome-wide association analysis, Candidate gene

摘要： 饲用燕麦（Avena sativa L.）在草地畜牧业和生态可持续发展中具有重要作用，但其优良性状的遗传机制尚不明确。本研究通过对69份燕麦材料进行基因组重测序，筛选出47 993 754个SNP位点，并对9个农艺性状进行全基因组关联分析（GWAS），共鉴定到210个显著关联的SNP位点，分布于各染色体，其中3C染色体分布最多，并挖掘出120个候选基因。分析发现，株高性状关联到受体激酶基因（ORK45、LRK45）和E3泛素连接酶基因At1g63170，其家族基因在其他物种中已被证实调控株高；剑叶长、小穗数及种子数关联到含锌指CCCH结构域的蛋白基因，该基因参与植物生长发育及胁迫响应；叶绿素含量关联到ABC转运蛋白基因、HY5及乙烯应答转录因子基因，均与光反应相关。进一步对16个关键候选基因的10个SNP位点进行单倍型分析，发现多数位点不同单倍型间性状差异显著。本研究为饲用燕麦遗传改良提供了重要的基因资源和理论依据。

关键词: 饲用燕麦, 农艺性状, 全基因组关联分析, 候选基因

CLC Number:

S322.6

LIU Xiao-xia, AN Wen, LI Lin, ZHANG Xin-yu, LANG Si-rui, MA Qiao-li, MA Dong-mei. Genome-wide Association Analysis and Candidate Gene Prediction of Important Agronomic Traits of Forage Oat[J]. Acta Agrestia Sinica, 2025, 33(11): 3526-3539.

刘晓霞, 安雯, 李琳, 张新宇, 郎思睿, 马巧利, 麻冬梅. 饲用燕麦重要农艺性状的全基因组关联分析和候选基因预测[J]. 草地学报, 2025, 33(11): 3526-3539.

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Genome-wide Association Analysis and Candidate Gene Prediction of Important Agronomic Traits of Forage Oat

饲用燕麦重要农艺性状的全基因组关联分析和候选基因预测

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