全基因组关联分析识别与湖羊饲料效率性状相关的新位点

doi:10.1016/j.jia.2023.10.011

Journal of Integrative Agriculture ›› 2025, Vol. 24 ›› Issue (4): 1259-1269.DOI: 10.1016/j.jia.2023.10.011

全基因组关联分析识别与湖羊饲料效率性状相关的新位点

收稿日期:2023-04-28 接受日期:2023-09-22 出版日期:2025-04-20 发布日期:2025-03-14

Genome-wide association study identifies novel loci associated with feed efficiency traits in Hu lambs

Deyin Zhang¹, Xiaolong Li¹, Fadi Li¹, Xiaoxue Zhang², Yuan Zhao¹, Yukun Zhang¹, Zongwu Ma², Huibin Tian¹, Xiuxiu Weng¹, Weimin Wang^1#

¹State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs/Engineering Research Center of Grassland Industry, Ministry of Education/College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
²College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China

Received:2023-04-28 Accepted:2023-09-22 Online:2025-04-20 Published:2025-03-14
About author:Deyin Zhang, E-mail: zdy1213@163.com; #Correspondence Weimin Wang, E-mail: wangweimin@lzu.edu.cn
Supported by:
This research was supported by the National Key R&D Program of China (2021YFD1300901), the National Key R&D Young Scientists Project of China (2022YFD1302000), the Education Department of Gansu Province: Outstanding Postgraduate “Innovation Star”, China (2022CXZX-086), and the Major Science and Technology Project of Gansu Province, China (22ZD6NC069).

摘要/Abstract

摘要：

在集约化养羊生产中，饲料效率是影响盈利能力的重要经济性状，通常用剩余采食量和饲料转化率两个指标来评价饲料利用效率。然而，目前关于绵羊饲料效率相关性状的潜在遗传机制尚不完全清楚。因此，为了从全基因组水平上鉴别出影响绵羊饲料效率的关键基因和遗传变异，本研究随机选取系谱信息清晰、出生日龄相近、健康状况良好的1280湖羊公羔，利用单栏饲养系统测定了饲料效率相关性状并对其进行描述性统计和相关分析，研究结果显示，饲料效率相关性状具有很大的变异，且剩余采食量与平均日采食量和饲料转化率呈显著正相关。同时，利用全基因组重测序数据对平均日采食量、饲料转化率和剩余采食量性状进行了全基因组关联分析，在全基因组水平筛选到12、6和4个SNPs位点，分别与平均日采食量、饲料转化率和剩余采食量性状显著相关，通过位点注释，发现8个候选基因（LOC101121953, LOC101110202, CTNNA3, IZUMO3, PPM1E, YIPF7, ZSCAN12 和LOC105603808）与绵羊的饲料效率相关。最后，为进一步验证与剩余采食量性状显著相关的两个候选SNPs位点（chr20: g. 32767656 A > G 和 chr20: g. 32963610 T > C）对生长和饲料效率性状的影响，利用Sequenom MassARRAY SNP分型技术对候选位点在扩大试验群体中进行分型和关联分析，结果表明，两个SNPs与生长性状无显著相关性（P > 0.05），但与RFI性状呈显著相关（P < 0.05）。上述研究结果为绵羊饲料效率性状的遗传改良提供了参考数据，并从全基因组水平上筛选出影响湖羊饲料效率的关键SNPs位点，为绵羊饲料效率性状的分子标记辅助选择提供可靠、有效的分子标记。

Abstract:

Feed efficiency (FE) is a crucial economic trait that significantly impacts profitability in intensive sheep production, and can be evaluated by the residual feed intake (RFI) and feed conversion ratio (FCR). However, the underlying genetic mechanisms that underlie FE-related traits in sheep are not fully understood. Herein, we measured the FE-related traits of 1,280 Hu sheep and conducted the phenotype statistics and correlation analysis, the result showcase that there was a large variation for FE-related traits, and RFI was significant positive correlation with average daily feed intake (ADFI) and FCR. Moreover, a genome-wide association study (GWAS) was conducted using whole-genome resequencing data to investigate the genetic associations of ADFI, FCR and RFI. For ADFI and FCR traits, 2 and one single nucleotide polymorphisms (SNPs) exceeded the genome-wide significance threshold, whereas ten and 5 SNPs exceeded the suggestive significance threshold. For RFI traits, only 4 SNPs exceeded the suggestive significance threshold. Finally, a total of 8 genes (LOC101121953, LOC101110202, CTNNA3, IZUMO3, PPM1E, YIPF7, ZSCAN12 and LOC105603808) were identified as potential candidate genes for FE-related traits. Simultaneously, we further analyzed the effects of 2 candidate SNPs associated with RFI on growth and FE traits in enlarged experimental population, the results demonstrated that these 2 SNPs was not significantly associated with growth traits (P>0.05), but significantly related to RFI traits (P<0.05). These findings will provide valuable reference data and key genetic variants that can be used to effectively select feed-efficient individual in sheep breeding programs.

Key words: Sheep , feed efficiency , GWAS , re-sequencing , RFI , FCR

Deyin Zhang, Xiaolong Li, Fadi Li, Xiaoxue Zhang, Yuan Zhao, Yukun Zhang, Zongwu Ma, Huibin Tian, Xiuxiu Weng, Weimin Wang. 全基因组关联分析识别与湖羊饲料效率性状相关的新位点[J]. Journal of Integrative Agriculture, 2025, 24(4): 1259-1269.

Deyin Zhang, Xiaolong Li, Fadi Li, Xiaoxue Zhang, Yuan Zhao, Yukun Zhang, Zongwu Ma, Huibin Tian, Xiuxiu Weng, Weimin Wang. Genome-wide association study identifies novel loci associated with feed efficiency traits in Hu lambs[J]. Journal of Integrative Agriculture, 2025, 24(4): 1259-1269.

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全基因组关联分析识别与湖羊饲料效率性状相关的新位点

Genome-wide association study identifies novel loci associated with feed efficiency traits in Hu lambs

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