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Pathway analysis for carcass traits in Nellore cattle: a preliminary study

Gerardo Alves Fernandes Júnior ; Daniel Gustavo Mansan Gordo ; Rafael Espigolan ; Tiago Bresolin  ; Ana Fabrícia Braga Magalhães  ; Fernando Baldi ; Luis Arthur Loyola Chardulo ; Lúcia Galvão de Albuquerque
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Pathway association analysis can provide important insights into the genetic architecture of complex traits. The aim of this research was to identify and study the pathways statistically associated with the expression of the following post mortem traits in Nellore cattle: hot carcass weight (HCW), ribeye area (REA), and backfat thickness (BFT). The dataset used in this study was composed of 1,749 Nellore steers with phenotype records for REA, and BFT and 1,566 for HCW. A subset of 1,569 animals had both phenotypic and genotypic information (462,518 SNP - Single Nucleotide Polymorphism) for REA, 1,568 (462,688 SNPs) for BFT, and 1,409 (450,971 SNPs) for HCW. Genotypes were generated based on the Illumina(R) Bovine HD chip. For each trait, the SNP effects were calculated based on the genomic breeding values obtained by using the single-step GBLUP approach and genomic matrix re-weighting procedure. The SNPs were assigned to genes if they were located within or 10 kb upstream or downstream of an annotated gene. Each gene that contained at least one of the top 10% SNPs with major effect on each trait was defined as candidate gene. In this study, a total of 22,511, 22,509, and 22,480 annotated genes in the UMD3.1 bovine genome assembly was used in the pathway analysis of REA, BFT, and HCW traits, respectively, being 2143, 2062, and 2151 of these genes defined as candidate for each trait. The derived gene lists were processed in DAVID software in order to identify pathways that are statistically associated to each carcass trait analyzed. Only terms with a Fisher Exact P-Value <= 0.01 were considered significant. In total, there were identified 99, 83, and 86 terms for REA, BFT, and HCW, respectively. Among of these terms, growth regulation, protein tyrosine kinase activity, regulation of cell killing, peptide binding were associated to REA; lipoprotein, ATPase, and acetylation were related to BFT; muscle cell differentiation and development, and myosin complex were associated to HCW. In general, these results suggest that the expression of carcass traits in Nellore cattle are associated to various terms involved with protein turnover, lipid metabolism and regulation of cell growth and differentiation. Acknowledgments: Fapesp Grants # 2009/16118-5 and 2015/06140-4.