Genome-wide association study and pathway analysis for fat deposition traits in nellore cattle raised in pasture-based systems

Rafaela Martins; Pamela C Machado; Luis Fernando B Pinto; Marcio R Silva; Flavio S Schenkel; Luiz F Brito; Victor B Pedrosa

doi:10.1111/jbg.12525

Genome-wide association study and pathway analysis for fat deposition traits in nellore cattle raised in pasture-based systems

J Anim Breed Genet. 2021 May;138(3):360-378. doi: 10.1111/jbg.12525. Epub 2020 Nov 24.

Authors

Rafaela Martins¹, Pamela C Machado¹, Luis Fernando B Pinto², Marcio R Silva³, Flavio S Schenkel⁴, Luiz F Brito⁵, Victor B Pedrosa¹

Affiliations

¹ Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, Brazil.
² Department of Animal Sciences, Federal University of Bahia, Ondina, Brazil.
³ Melhore Animal and Katayama Agropecuaria Lda, Guararapes, Brazil.
⁴ Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada.
⁵ Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.

PMID: 33232564
DOI: 10.1111/jbg.12525

Abstract

Genome-wide association study (GWAS) is a powerful tool to identify candidate genes and genomic regions underlying key biological mechanisms associated with economically important traits. In this context, the aim of this study was to identify genomic regions and metabolic pathways associated with backfat thickness (BFT) and rump fat thickness (RFT) in Nellore cattle, raised in pasture-based systems. Ultrasound-based measurements of BFT and RFT (adjusted to 18 months of age) were collected in 11,750 animals, with 39,903 animals in the pedigree file. Additionally, 1,440 animals were genotyped using the GGP-indicus 35K SNP chip, containing 33,623 SNPs after the quality control. The single-step GWAS analyses were performed using the BLUPF90 family programs. Candidate genes were identified through the Ensembl database incorporated in the BioMart tool, while PANTHER and REVIGO were used to identify the key metabolic pathways and gene networks. A total of 18 genomic regions located on 10 different chromosomes and harbouring 23 candidate genes were identified for BFT. For RFT, 22 genomic regions were found on 14 chromosomes, with a total of 29 candidate genes identified. The results of the pathway analyses showed important genes for BFT, including TBL1XR1, AHCYL2, SLC4A7, AADAT, VPS53, IDH2 and ETS1, which are involved in lipid metabolism, synthesis of cellular amino acids, transport of solutes, transport between Golgi Complex membranes, cell differentiation and cellular development. The main genes identified for RFT were GSK3β, LRP1B, EXT1, GRB2, SORCS1 and SLMAP, which are involved in metabolic pathways such as glycogen synthesis, lipid transport and homeostasis, polysaccharide and carbohydrate metabolism. Polymorphisms located in these candidate genes can be incorporated in commercial genotyping platforms to improve the accuracy of imputation and genomic evaluations for carcass fatness. In addition to uncovering biological mechanisms associated with carcass quality, the key gene pathways identified can also be incorporated in biology-driven genomic prediction methods.

Keywords: carcass; SNP effects; beef cattle; genomic regions; meat quality; tropical cattle.

MeSH terms

Animals
Cattle
Genome*
Genome-Wide Association Study* / veterinary
Genotype
Phenotype
Polymorphism, Single Nucleotide