Integrating a genome-wide association and transcriptome analysis to provide molecular insights into growth rates in sheep

作者：Liming Zhao, Fadi Li, Xiaoxue Zhang, Lvfeng Yuan, Huibin Tian, Dan Xu, Deyin Zhang, Yukun Zhang, Yuan Zhao, Kai Huang, Xiaolong Li, Jiangbo Cheng, Zongwu Ma, Quanzhong Xu, Xiaobin Yang, Kunchao Han, Xiuxiu Weng, Weimin Wang · 发表于：Journal of Integrative Agriculture · 年份：2024 · DOI：10.1016/j.jia.2024.08.011 · 被引用次数：8 · 研究领域：Genetic and phenotypic traits in livestock、Cancer-related molecular mechanisms research、Genetic Mapping and Diversity in Plants and Animals

Investigating genetic markers and key genes associated with sheep growth rate using integrated multi-omics approaches could provide valuable insights for the sheep industry. Based on the average daily gain (ADG), fast-growing ( N case =70) and slow-growing ( N control =70) Hu sheep were selected for a genome-wide association study (GWAS). Ten Hu sheep (fast-growing, n = 5; slow-growing, n = 5) and ten Dorper sheep (fast-growing, n = 5; slow-growing, n =5) were selected for comparative transcriptome analysis. We identified hub genes and tissue-specific genes (TSGs) using weighted gene co-expression network analysis (WGCNA) and RNA sequencing (RNA-Seq) data from ten tissues, respectively. Ten genes were found within 50 kb distances of the significant single nucleotide polymorphisms (SNPs). Based on a comparative transcriptomic analysis, a total of 501 and 441 differentially expressed genes (DEGs) were identified in the HF vs. HS and DF vs. DS comparisons, respectively. We found some important signaling pathways closely associated with fat metabolism and energy metabolism, such as “regulation of lipolysis in adipocytes”, “Oxidative phosphorylation”, and “Thermogenesis”. Several DEGs play a crucial role in fat deposition (such as ADRB3 , PDE3B , FABP4 , SERPINE1 , PLIN1 , and FOXO6 ) and muscle development ( MYL3 ). Using the WGCNA analysis, 15 genes were considered as hub genes associated with ADG. Integration of GWAS and RNA-Seq data indicates that BRINP3 and PENK may further i...