Genome wide association study on beef production traits in Marchigiana cattle breed

Abstract

A genomewide association study was carried out on a sample of Marchigiana breed cattle to detect markers significantly associated with carcass and meat traits. Four hundred and nine young bulls from 117 commercial herds were genotyped by Illumina 50K BeadChip assay. Eight growth and carcass traits (average daily gain, carcass weight, dressing percentage, body weight, skin weight, shank circumference, head weight and carcass conformation) and two meat quality traits (pH at slaughter and pH 24 h after slaughter) were measured. Data were analysed with a linear mixed model that included fixed effects of herd, slaughter date, fixed covariables of age at slaughter and SNP genotype, and random effects of herd and animal. A permutation test was performed to correct SNP genotype significance level for multiple testing. A total of 96 SNPs were significantly associated at genomewide level with one or more of the considered traits. Gene search was performed on genomic regions identified on the basis of significant SNP position and level of linkage disequilibrium. Interesting loci affecting lipid metabolism (SOAT1), bone (BMP4) and muscle (MYOF) biology were highlighted. These results may be useful to better understand the genetic architecture of growth and body composition in cattle.

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

“…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. SOAT1 (sterol O-acyltransferase 1) acts as an enzyme encoding a network involved in steroid and lipogenesis/fat decomposition, and has been used as a candidate gene for bovine growth traits [70].…”

Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle

“…Genome-wide association studies (GWAS) are robust statistical tools are that broadly identify candidate genes with significant SNPs involved in production traits [14][15][16], growth traits [17,18], carcass quality traits and fertility traits [19,20]. In beef cattle, various SNPs, genes, and haplotype blocks have been found to associate with growth, however the current GWAS-based studies focus mainly on only one growth parameter [21], such as the weaning size [22], yearling weight or stature upon slaughter [23]. Furthermore, loci controlling growth traits may be variable in different growth stages, and some loci may control traits throughout the lifetime of the animal [24].…”

Identifying Loci Under Positive Selection in Yellow Korean Cattle (Hanwoo)

“…11,20 To further identify signals displaying strong footprints of selection, scan statistics were used to identify chromosomal selective regions harboring a greater than expected number of signals. 24 A total of nine statistically significant selective regions were 34 Cole et al, 35 Hawken et al, 36 Tenghe et al, 37 Duran Aguilar et al, 38 41 Fortes et al, 42 Buzanskas et al 43 de Oliveira Silva et al, 46 Magalhaes et al, 47 Rempel et al, 48 Ali et al, 49 Saatchi et al, 50 Nayeri et al, 51 Snelling et al, 52 Richardson et al, 53 Sorbolini et al, 54 Mota et al, 55 Mapholi et al, 56 Hawken et al, 36 Fortes et al, 57 Cole et al, 35 Martinez et al, 58 Yurchenko et al, 59 and Michenet et al 40 61 Sorbolini et al, 54 Seabury et al, 45 63 Buzanskas et al, 43 and Pryce et al 64 65 Nalaila et al, 66 Aguilar et al, 38 wang et al, 67 detected ( Table 1 and Table S2), which led to a list of 138 candidate genes. These genes may be an outcome of selection that is closely related to traits of interest, presenting availability of genomic information to be applied on examination of the phenotypic differences between Yellow Hanwoo and Jeju Black.…”