Genome-wide interaction study reveals epistatic interactions for beef lipid-related traits in Nellore cattle

Author(s)

Amorim, S. T. ^[1] ; Stafuzza, N. B. ^[2] ; Kluska, S. ^[1] ; Peripolli, E. ^[1] ; Pereira, A. S. C. ^[3] ; Muller da Silveira, L. F. ^[3] ; de Albuquerque, L. G. ^[1] ; Baldi, F. ^[1]

Affiliation

^[1] Univ Estadual Paulista, Fac Ciencias Agr & Vet, Dept Zootecnia, Via Acesso Prof Paulo Donato Castellane S-No, BR-14884900 Jaboticabal - Brazil

^[2] Inst Zootecnia, Ctr Pesquisa Bovinos Corte, Rodovia Carlos Tonanni, Km94, BR-14884900 Sertaozinho - Brazil

^[3] Univ Sao Paulo, Fac Zootecnia & Engn Alimentos, Ucleo Apoio Pesquisa Melhoramento Anim Biotecnol, Rua Duque Caxias Norte 225, BR-13635900 Pirassununga - Brazil

• Document type: Journal article
• Source: ANIMAL GENETICS; v. 53, n. 1 AUG 2021.
• Web of Science Citations: 0

Abstract

Gene-gene interactions cause hidden genetic variation in natural populations and could be responsible for the lack of replication that is typically observed in complex traits studies. This study aimed to identify gene-gene interactions using the empirical Hilbert-Schmidt Independence Criterion method to test for epistasis in beef fatty acid profile traits of Nellore cattle. The dataset contained records from 963 bulls, genotyped using a 777 962k SNP chip. Meat samples of Longissimus muscle, were taken to measure fatty acid composition, which was quantified by gas chromatography. We chose to work with the sums of saturated (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), omega-3 (OM3), omega-6 (OM6), SFA:PUFA and OM3:OM6 fatty acid ratios. The SNPs in the interactions where P<10-8 were mapped individually and used to search for candidate genes. Totals of 602, 3, 13, 23, 13, 215 and 169 candidate genes for SFAs, MUFAs, PUFAs, OM3s, OM6s and SFA:PUFA and OM3:OM6 ratios were identified respectively. The candidate genes found were associated with cholesterol, lipid regulation, low-density lipoprotein receptors, feed efficiency and inflammatory response. Enrichment analysis revealed 57 significant GO and 18 KEGG terms (P < 0.05), most of them related to meat quality and complementary terms. Our results showed substantial genetic interactions associated with lipid profile, meat quality, carcass and feed efficiency traits for the first time in Nellore cattle. The knowledge of these SNP-SNP interactions could improve understanding of the genetic and physiological mechanisms that contribute to lipid-related traits and improve human health by the selection of healthier meat products. (AU)

• FAPESP's process: 09/16118-5 - Genomic tools to genetic improvement of direct economic important traits in Nelore cattle
• Grantee: Lucia Galvão de Albuquerque
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 11/21241-0 - Study of the genetic variability of meat fatty acid profile in Nelore cattle finished in feedlot
• Grantee: Fernando Sebastián Baldi Rey
• Support Opportunities: Research Grants - Young Investigators Grants
• FAPESP's process: 18/19463-4 - Epistatic interactions associated with fatty acid profile of beef from Nelore cattle
• Grantee: Sabrina Thaise Amorim
• Support Opportunities: Scholarships in Brazil - Master