Dos Santos Thaís Cristina Ferreira, Silva Evandro Neves, Frezarim Gabriela Bonfá, Salatta Bruna Maria, Baldi Fernando, Fonseca Larissa Fernanda Simielli, Albuquerque Lucia Galvão De, Muniz Maria Malane Magalhães, Silva Danielly Beraldo Dos Santos
Universidade Professor Edson Antônio Velano (UNIFENAS), Rodovia 179, Km 0, Alfenas, MG, 37132440, Brasil.
Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brasil.
Mamm Genome. 2025 Mar;36(1):106-117. doi: 10.1007/s00335-024-10100-0. Epub 2025 Jan 18.
This study aimed to identify splicing quantitative trait loci (cis-sQTL) in Nelore cattle muscle tissue and explore the involvement of spliced genes (sGenes) in immune system-related biological processes. Genotypic data from 80 intact male Nelore cattle were obtained using SNP-Chip technology, while RNA-Seq analysis was performed to measure gene expression levels, enabling the integration of genomic and transcriptomic datasets. The normalized expression levels of spliced transcripts were associated with single nucleotide polymorphisms (SNPs) through an analysis of variance using an additive linear model with the MatrixEQTL package. A permutation analysis then assessed the significance of the best SNPs for each spliced transcript. Functional enrichment analysis was performed on the sGenes to investigate their roles in the immune system. In total, 3,187 variants were linked to 3,202 spliced transcripts, with 83 sGenes involved in immune system processes. Of these, 31 sGenes were enriched for five transcription factors. Most cis-sQTL effects were found in intronic regions, with 27 sQTL variants associated with disease susceptibility and resistance in cattle. Key sGenes identified, such as GSDMA, NLRP6, CASP6, GZMA, CASP4, CASP1, TREM2, NLRP1, and NAIP, were related to inflammasome formation and pyroptosis. Additionally, genes like PIDD1, OPTN, NFKBIB, STAT1, TNIP3, and TREM2 were involved in regulating the NF-kB pathway. These findings lay the groundwork for breeding disease-resistant cattle and enhance our understanding of genetic mechanisms in immune responses.
本研究旨在鉴定内洛尔牛肌肉组织中的剪接数量性状基因座（顺式-sQTL），并探索剪接基因（sGenes）在免疫系统相关生物学过程中的作用。使用SNP芯片技术获得了80头完整雄性内洛尔牛的基因型数据，同时进行RNA测序分析以测量基因表达水平，从而实现基因组和转录组数据集的整合。通过使用MatrixEQTL软件包的加性线性模型进行方差分析，将剪接转录本的标准化表达水平与单核苷酸多态性（SNP）相关联。然后通过置换分析评估每个剪接转录本最佳SNP的显著性。对sGenes进行功能富集分析，以研究它们在免疫系统中的作用。总共3187个变异与3202个剪接转录本相关联，其中83个sGenes参与免疫系统过程。其中，31个sGenes富集了五种转录因子。大多数顺式-sQTL效应存在于内含子区域，有27个sQTL变异与牛的疾病易感性和抗性相关。鉴定出的关键sGenes，如GSDMA、NLRP6、CASP6、GZMA、CASP4、CASP1、TREM2、NLRP1和NAIP，与炎性小体形成和细胞焦亡有关。此外，PIDD1、OPTN、NFKBIB、STAT1、TNIP3和TREM2等基因参与调节NF-κB通路。这些发现为培育抗病牛奠定了基础，并增进了我们对免疫反应遗传机制的理解。
