Ferreira Dos Santos Thaís Cristina, Silva Evandro Neves, Frezarim Gabriela Bonfá, Salatta Bruna Maria, Baldi Fernando, Simielli Fonseca Larissa Fernanda, De Albuquerque Lucia Galvão, Magalhães Muniz Maria Malane, Dos Santos Silva Danielly Beraldo
University José do Rosário Vellano (UNIFENAS), Alfenas, Minas Gerais, Brazil; Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil.
University José do Rosário Vellano (UNIFENAS), Alfenas, Minas Gerais, Brazil; Universidade Federal de Alfenas (UNIFAL), Alfenas, Minas Gerais, Brazil.
Gene. 2025 Feb 10;937:149138. doi: 10.1016/j.gene.2024.149138. Epub 2024 Dec 3.
The combination of transcriptional profiling and genotype data analyses enables the identification of genetic variants that may affect gene expression (eQTL - expression quantitative trait loci). This study aimed to identify cis-eQTL in Nellore cattle muscle tissue and determine their biological processes related to the immune system and involved eGenes. Genotypic data (SNP-Chip) and gene expression data (RNA-Seq) from a commercial population of 80 Nellore animals were evaluated. For the cis-eQTL identification, association tests were conducted for all variants near the gene (cis variants), followed by permutation tests to correct for multiple comparisons. Our analyses revealed 828 top cis-eQTL related to 1,062 genes of which most of these variants were in intronic and intergenic regions. The eQTLs rs109525554, rs109589165, rs110192253, rs133127698, rs137742430, rs41803313, rs43366333, and rs43711242 were associated with susceptibility and resistance to infections in cattle. Additionally, interferon family eGenes, such as IFNT3, IFN-TAU, IFNK, FYN, and IFNW1, and endothelial leukocyte migration, such as PRKCG and CXCL10 were found. These eGene families were linked to biological processes of innate and adaptive immune responses and associated with somatic cell scores in cattle, respectively. Our results may have implications for selecting desirable resistance traits in animals bred for production and highlight the importance of studying genetic variants involved in quantitative traits to improve our understanding of genetic mechanisms underlying gene expression regulation of adaptive traits in cattle.
转录谱分析和基因型数据分析相结合，能够识别可能影响基因表达的遗传变异（表达数量性状位点-eQTL）。本研究旨在鉴定内洛尔牛肌肉组织中的顺式eQTL，并确定其与免疫系统相关的生物学过程以及涉及的e基因。对来自80头内洛尔商业牛群的基因型数据（SNP芯片）和基因表达数据（RNA测序）进行了评估。为了鉴定顺式eQTL，对基因附近的所有变异（顺式变异）进行了关联测试，随后进行置换测试以校正多重比较。我们的分析揭示了828个与1062个基因相关的顶级顺式eQTL，其中大多数变异位于内含子和基因间区域。eQTL rs109525554、rs109589165、rs110192253、rs133127698、rs137742430、rs41803313、rs43366333和rs43711242与牛对感染的易感性和抗性相关。此外，还发现了干扰素家族的e基因，如IFNT3、IFN-TAU、IFNK、FYN和IFNW1，以及内皮白细胞迁移相关的基因，如PRKCG和CXCL10。这些e基因家族分别与先天性和适应性免疫反应的生物学过程相关，并与牛的体细胞评分相关。我们的结果可能对选择用于生产的动物的理想抗性性状具有启示意义，并突出了研究参与数量性状的遗传变异对于增进我们对牛适应性性状基因表达调控潜在遗传机制理解的重要性。
