Genome scan for postmortem carcass traits in Nellore cattle1

Abstract

Carcass traits measured after slaughter are economically relevant traits in beef cattle. In general, the slaughter house payment system is based on HCW. Ribeye area (REA) is associated with the amount of the meat in the carcass, and a minimum of backfat thickness (BFT) is necessary to protect the carcass during cooling. The aim of this study was to identify potential genomic regions harboring candidate genes affecting those traits in Nellore cattle. The data set used in the present study consisted of 1,756 Nellore males with phenotype records. A subset of 1,604 animals had both genotypic and phenotypic information. Genotypes were generated based on a panel with 777,962 SNPs from the Illumina Bovine HD chip. The SNP effects were calculated based on the genomic breeding values obtained by using the single-step GBLUP approach and a genomic matrix re-weighting procedure. The proportion of the variance explained by moving windows of 100 consecutive SNPs was used to assess potential genomic regions harboring genes with major effects on each trait. The top 10 non-overlapping SNP-windows explained 8.72%, 11.38%, and 9.31% of the genetic variance for REA, BFT, and HCW, respectively. These windows are located on chromosomes 5, 7, 8, 10, 12, 20, and 29 for REA; chromosomes 6, 8, 10, 13, 16, 17, 18, and 24 for BFT; and chromosomes 4, 6, 7, 8, 14, 16, 17, and 21 for HCW. For REA, there were identified genes ( and ) involved in the cell cycle biological process which affects many aspects of animal growth and development. The and genes, both from AA transporter family, was also associated with REA. The AA transporters are essential for cell growth and proliferation, acting as carriers of tissue nutrient supplies. Various genes identified for BFT (, , , , , and ) have been associated with lipid metabolism in different mammal species. One of the most promising genes identified for HCW was the . There is evidence, in the literature, that this gene is located in putative QTL affecting carcass weight in beef cattle. Our results showed several genomic regions containing plausible candidate genes that may be associated with carcass traits in Nellore cattle. Besides contributing to a better understanding of the genetic control of carcass traits, the identified genes can also be helpful for further functional genomic studies.

Comparative muscle transcriptome associated with carcass traits of Nellore cattle

“…Endocytosis acts on the regulation of several processes, like cell adhesion and migration, extracellular signal transduction, cell growth and differentiation [45]. Junior et al [24] also found genes involved in cell cycle regulation and transportation of cellular substances associated with REA in Nellore cattle.…”

“…Studies with knockout mice for the NEDD4 gene showed that loss of NEDD4 reduced IGF-1 and insulin signaling, delayed embryonic development, and reduced growth and body weight [46]. Junior et al [24] in a GWAS study associated with REA, BFT and hot carcass weight found this gene enriched for the GO terms “cellular protein metabolic process” and “protein metabolic process” related to protein turnover and, consequently animal growth and development. In the present study, NEDD4 and NEDD4L were down-regulated in LowREA group, emphasizing their importance in regulating muscle growth.…”

“…Gomes et al [23] have already reported that genes related to protein turnover were associated with growth and carcass traits in Nellore cattle. Latterly, Junior et al [24] also found GO terms related to protein turnover in an association study with REA, BFT and hot carcass weight in Nellore. These findings show us the important role of ubiquitination and ubiquitin proteins for muscle growth, and consequently to improve REA in the animals.…”

“…Gomes et al [23] reported that SNPs in genes related to protein turnover, like genes regulating the ubiquitin-proteasome system, may be associated with growth and carcass traits in bovine. Junior et al [24] found SNP-windows located on chromosomes 5, 6, 7, 8, 10, 12, 13, 16, 17, 20, 24 and 29 that together explained 8.72% and 11.38% of the genetic variance for REA and BFT in a population of Nellore cattle.…”

Transcriptome and DNA Methylation Analyses of the Molecular Mechanisms Underlying with Longissimus dorsi Muscles at Different Stages of Development in the Polled Yak

“…Fzd7 acts as a receptor for Wnt7a, and the signaling pathway comprising the two directly activates myogenic lineage progression at different stages [68]. In addition, Júnior et al used the BovineHD chip to correlate the carcass traits of Nellore cattle, finding that the REA (Ribeye area) trait was significantly associated with the bta8 (Bos taurus chromosome) 107978188bp-108270826bp region in cattle, which includes the CDKN2A gene [69]. In the comparison of 6-month-old with fetal (M-vs.-E) group the longissimus dorsi muscle methylation differential gene analysis, the steroid biosynthesis pathway was significantly enriched.…”