PRUNE2 gene has a potential effect on residual feed intake in Nellore cattle

• Published in: Journal of animal science 2016-10, Vol.94, p.152-153
• Main Authors: Lima, A O D, Oliveira, P S N, Tizioto, P C, Somavilla, A L, Diniz, W J S, Silva, J V D, Andrade, S C S, Boschiero, C, Cesar, A S M, Souza, M M, Rocha, M I P, Afonso, J, Buss, C E, Mudadu, M A, Mourao, G B, Coutinho, L L, Regitano, L C A
• Format: Article
• Language: English
• Subjects: Animal breeding; Animal husbandry; Beef cattle; Biological activity; Bovidae; Cattle; Economics; Effects; Emissions; Emissions control; Feed efficiency; Feeds; Filtration; Fruit flies; Gene expression; Genes; Genetic diversity; Genetic effects; Genomes; Genotypes; Haplotypes; Homology; Land use; Liver; Livestock; Livestock production; Metal ions; Methane; Oxidation; Oxidation-reduction potential; Profitability; Quality control; Reduction (metal working); Regression analysis; Ribonucleic acid; RNA; Single-nucleotide polymorphism; Target recognition
• ISSN: 0021-8812; 1525-3163

Residual feed intake (RFI) can increase the profitability of producers, reduce methane emission and land allocation to livestock production. However, this trait has late and costly measurements. Identifying gene expression changes combined with polymorphisms that affect residual feed intake variation is important for identify target regulatory polymorphisms that can be used in animal breeding programs. Diverse studies performed by our research group in a Nellore population, such as genome-wide association (GWA), association weight matrix (AWM) and RNA-seq analysis of liver tissue have been pointed Prune homolog 2 (Drosophila) (PRUNE2) as a potential candidate gene influencing feed efficiency. For this reason, we select this gene for a more detailed analysis considering haplotypes consisting of SNPs presented in the Illumina Bovine HD Bead Chip. For this, we used a population consisted of 591 steers with genotypes and RFI estimates available. After quality control filtering, performed by PLINK and Bioconductor/R, we used a total of 449.203 SNPs in our haplotype analysis. Genotype phasing and missing genotype imputation were performed using BEAGLE and the LDexplorer software was used for haplotype block recognition. After adjust the RFI estimates for fixed effects of contemporary group, which included type of pen, birth place, feedlot location and age of the animal effect as covariate, the genetic effects of haplotypes in PRUNE2 gene was estimated by PLINK using a linear regression method. We identified 1 haplotype constituted of 4 SNPs: rs136298898 (C/T); rs133593644 (C/T); rs137799737 (A/C); rs132675549 (C/T), for which two out of 4 haplotype combinations had significant effect (P ≤ 0.05) on RFI. Haplotype variation (1111) (p-value = 0.0345) with 35.29% frequency was associated to lower RFI (β = -0.0776). On the other hand, haplotype variation (1112) (p-value = 0.0351) presenting 11.13% frequency was associated with high RFI (β = 0.0846). The PRUNE2gene has a potential role in biological processes, such as oxidation-reduction, metal ion and polyphosphate catabolic. Our findings indicated that this gene influence genetic variation of RFI, it is a strong candidate gene to be incorporated in Nellore breeding programs, nevertheless more studies considering this gene should be realized to understand better its biological role on feed efficiency in beef cattle.