Integrated analyses of genomic and transcriptomic data reveal candidate variants associated with carcass traits in Huaxi cattle 1

IF 4.6 1区农林科学 Q1 AGRICULTURE, MULTIDISCIPLINARY

Journal of Integrative Agriculture Pub Date : 2024-01-20 DOI:10.1016/j.jia.2024.01.028

Yapeng Zhang, Wentao Cai, Qi Zhang, Qian Li, Yahui Wang, Ruiqi Peng, Haiqi Yin, Xin Hu, Zezhao Wang, Bo Zhu, Xue Gao, Yan Chen, Huijiang Gao, Lingyang Xu, Junya Li, Lupei Zhang

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引用次数: 0

Abstract

Cattle carcass traits are economically important in the beef industry. In the present study, we identified 184 significant genes and 822 alternative genes for 7 carcass traits using genome-wide association studies (GWASs) in 1566 Huaxi beef cattle. We then identified 5,860 unique cis-genes and 734 trans-genes in 227 longissimus dorsi muscle (LDM) samples to better understand the genetic regulation of gene expression. Our integration study of the GWAS and cis-eQTL analysis detected 13 variants regulating 12 identical genes, in which one variant was also detected in fine-mapping analysis. Moreover, using a transcriptome-wide association study (TWAS), we identified 4 genes (TTC30B, HMGA1, PRKD3 and FXN) that were significantly related to carcass chest depth (CCD), carcass length (CL), carcass weight (CW) and dressing percentage (DP). This study identified variants and genes that may be useful for understanding the molecular mechanism of carcass traits in beef cattle.

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基因组和转录组数据的综合分析揭示了与华西牛胴体性状相关的候选变异 1

牛的胴体性状在牛肉产业中具有重要的经济意义。在本研究中，我们利用全基因组关联研究（GWAS）在 1566 头华西肉牛中鉴定出了 7 个胴体性状的 184 个重要基因和 822 个备选基因。然后，我们在 227 份背阔肌 (LDM) 样本中鉴定了 5860 个独特的顺式基因和 734 个反式基因，以更好地了解基因表达的遗传调控。我们对 GWAS 和顺式-eQTL 分析进行了整合研究，发现了 13 个调节 12 个相同基因的变体，其中一个变体在精细图谱分析中也被检测到。此外，利用全转录组关联研究（TWAS），我们发现了 4 个基因（TTC30B、HMGA1、PRKD3 和 FXN）与胴体胸深（CCD）、胴体长度（CL）、胴体重量（CW）和去衣率（DP）显著相关。这项研究发现的变异和基因可能有助于了解肉牛胴体性状的分子机制。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Integrative Agriculture AGRICULTURE, MULTIDISCIPLINARY-

CiteScore

7.90

自引率

4.20%

发文量

4817

审稿时长

3-6 weeks

期刊介绍： Journal of Integrative Agriculture publishes manuscripts in the categories of Commentary, Review, Research Article, Letter and Short Communication, focusing on the core subjects: Crop Genetics & Breeding, Germplasm Resources, Physiology, Biochemistry, Cultivation, Tillage, Plant Protection, Animal Science, Veterinary Science, Soil and Fertilization, Irrigation, Plant Nutrition, Agro-Environment & Ecology, Bio-material and Bio-energy, Food Science, Agricultural Economics and Management, Agricultural Information Science.