基于转录组分析挖掘平凉红牛背最长肌肉质性状候选基因

doi:10.11843/j.issn.0366-6964.2023.11.015

畜牧兽医学报 ›› 2023, Vol. 54 ›› Issue (11): 4589-4604.doi: 10.11843/j.issn.0366-6964.2023.11.015

基于转录组分析挖掘平凉红牛背最长肌肉质性状候选基因

王文翔¹, 杜丽丽¹, 胡俊伟², 张琰翔², 马铭昊², 段蕊², 钱聪², 王欣玥², 李三禄³, 张长庆³, 张路培^1,2, 高雪¹, 徐凌洋¹, 李俊雅¹, 高会江^1*

1. 中国农业科学院北京畜牧兽医研究所, 北京 100193;
2. 平凉红牛研究院, 平凉 744000;
3. 平凉市牛产业开发办公室, 平凉 744000

收稿日期:2023-04-25 出版日期:2023-11-23 发布日期:2023-11-26
通讯作者: 高会江,主要从事肉牛育种研究,E-mail:gaohuijiang@caas.cn
作者简介:王文翔(1998-),男,江西南昌人,硕士,主要从事肉牛育种研究,E-mail:bostaurus@163.com
基金资助:
内蒙古自治区科学技术计划(2020GG0210);国家肉牛牦牛产业技术体系(CARS-37);中央级公益性科研院所基本科研业务费专项资金项目(2022-YWF-ZX-04)甘肃省科技重大专项计划(21ZD11NL007);中国农业科学院科技创新工程(ASTIP-IASO3);西部肉牛种质创新基地建设项目(平科任[2021]29号)

Mining Candidate Genes Related to Meat Quality Traits of Longissimus Lumborum in Pingliang Red Steer Based on Transcriptome

WANG Wenxiang¹, DU Lili¹, HU Junwei², ZHANG Yanxiang², MA Minghao², DUAN Rui², QIAN Cong², WANG Xinyue², LI Sanlu³, ZHANG Changqing³, ZHANG Lupei^1,2, GAO Xue¹, XU Lingyang¹, LI Junya¹, GAO Huijiang^1*

1. Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
2. Institute of Pingliang Red Cattle, Pingliang 744000, China;
3. Pingliang Cattle Industry Development Office, Pingliang 744000, China

Received:2023-04-25 Online:2023-11-23 Published:2023-11-26

摘要/Abstract

摘要： 旨在挖掘与平凉红牛背最长肌营养成分含量相关的候选基因,以提高肉品质。本研究选用相同饲养条件下30月龄及750 kg的40头阉牛,测定蛋白质、脂肪和水分3种常规营养成分的含量,分别挑选表型数据具有极端差异的高、低组,每组3个重复。通过主成分分析和比较转录组分析筛选具有显著因子载荷基因(significant factor loading genes, SFLGs)和差异表达基因(differentially expressed genes, DEGs),并进行富集分析。利用所有样本的转录组数据和表型数据进行加权基因共表达网络分析(weighted gene co-expression network analysis, WGCNA),筛选与表型相关的目标基因模块(r>0.35且P<0.05)与Hub基因(hub genes, HGs)。针对蛋白质、脂肪和水分含量3个性状分别鉴定到91、81和80个SFLGs(第一主成分PC1和第二主成分PC2)和18、85和338个DEGs,其中PC1和PC2共有的SFLGs分别有8、4和3个,具有显著因子载荷的DEGs分别有1、3和2个,富集分析结果与相应的表型相关。通过WGCNA分别筛选出2个目标基因模块及10、14和26个HGs,均鉴定到MYADML2和ZBTB14等关键候选基因,其可能在影响三者比例方面发挥重要作用。本研究通过鉴定影响3种常规营养成分含量的候选基因,挖掘到与肉质性状相关的关键基因。研究结果将为平凉红牛的育种工作提供理论基础,同时也为其他肉牛的品质育种提供参考。

关键词: 平凉红牛, 背最长肌, 营养成分含量, 转录组

Abstract: The aim of this study was to mine the candidate genes related to nutrient contents of longissimus lumborum in Pingliang red cattle, so as to improve the meat quality. Forty steers with 30-months-old slaughter age and 750 kg weight under the same feeding conditions were selected, and the contents of 3 conventional nutrients were measured, i.e., protein, fat, and moisture. The high and low groups with extreme differences in phenotypic data were selected, respectively, with 3 replicates each group. Principal component analysis and comparative transcriptome analysis were used to screen significant factor loading genes (SFLGs) and differentially expressed genes (DEGs), and these genes were subjected to enrichment analysis. Weighted gene co-expression network analysis (WGCNA) was performed using all sample transcriptome data and phenotype data to screen target gene modules (r>0.35 and P<0.05) and hub genes (HGs) related to phenotypes. The 91, 81, and 80 SFLGs (the first principal component PC1 and the second principal component PC2) and 18, 85, and 338 DEGs were identified for protein, fat, and moisture content traits, respectively. Among them, 8, 4, and 3 SFLGs were shared in PC1 and PC2, and 1, 3, and 2 DEGs showed significant factor loading, respectively. The enrichment analysis results were related to the corresponding phenotype. WGCNA screened 2 target gene modules respectively as well as 10, 14, and 26 HGs for protein, fat, and moisture contents, and all identified key candidate genes such as MYADML2 and ZBTB14, which might play important roles in influencing the proportional relationship among 3 nutrients. In this study, key genes related to meat quality traits were found by identifying candidates affecting 3 conventional nutrients contents. The research result will provide a theoretical basis for the breeding work of Pingliang red cattle and also provide reference for the quality breeding of other beef cattle.

Key words: Pingliang red steer, longissimus lumborum, nutrient contents, transcriptome

中图分类号:

S823.2

王文翔, 杜丽丽, 胡俊伟, 张琰翔, 马铭昊, 段蕊, 钱聪, 王欣玥, 李三禄, 张长庆, 张路培, 高雪, 徐凌洋, 李俊雅, 高会江. 基于转录组分析挖掘平凉红牛背最长肌肉质性状候选基因[J]. 畜牧兽医学报, 2023, 54(11): 4589-4604.

WANG Wenxiang, DU Lili, HU Junwei, ZHANG Yanxiang, MA Minghao, DUAN Rui, QIAN Cong, WANG Xinyue, LI Sanlu, ZHANG Changqing, ZHANG Lupei, GAO Xue, XU Lingyang, LI Junya, GAO Huijiang. Mining Candidate Genes Related to Meat Quality Traits of Longissimus Lumborum in Pingliang Red Steer Based on Transcriptome[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4589-4604.

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基于转录组分析挖掘平凉红牛背最长肌肉质性状候选基因

Mining Candidate Genes Related to Meat Quality Traits of Longissimus Lumborum in Pingliang Red Steer Based on Transcriptome

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