Genome-Wide Association Study for Carcass Traits in an Experimental Nelore Cattle Population

Abstract

The purpose of this study was to identify genomic regions associated with carcass traits in an experimental Nelore cattle population. The studied data set contained 2,306 ultrasound records for longissimus muscle area (LMA), 1,832 for backfat thickness (BF), and 1,830 for rump fat thickness (RF). A high-density SNP panel (BovineHD BeadChip assay 700k, Illumina Inc., San Diego, CA) was used for genotyping. After genomic data quality control, 437,197 SNPs from 761 animals were available, of which 721 had phenotypes for LMA, 669 for BF, and 718 for RF. The SNP solutions were estimated using a single-step genomic BLUP approach (ssGWAS), which calculated the variance for windows of 50 consecutive SNPs and the regions that accounted for more than 0.5% of the additive genetic variance were used to search for candidate genes. The results indicated that 12, 18, and 15 different windows were associated to LMA, BF, and RF, respectively. Confirming the polygenic nature of the studied traits, 43, 65, and 53 genes were found in those associated windows, respectively for LMA, BF, and RF. Among the candidate genes, some of them, which already had their functions associated with the expression of energy metabolism, were found associated with fat deposition in this study. In addition, ALKBH3 and HSD17B12 genes, which are related in fibroblast death and metabolism of steroids, were found associated with LMA. The results presented here should help to better understand the genetic and physiologic mechanism regulating the muscle tissue deposition and subcutaneous fat cover expression of Zebu animals. The identification of candidate genes should contribute for Zebu breeding programs in order to consider carcass traits as selection criteria in their genetic evaluation.

Conservation Genomic Analysis of the Croatian Indigenous Black Slavonian and Turopolje Pig Breeds

“…FIGURE 4 | Neighbor-joining tree based on the Reynold's genetic distances for selected 32 pig and wild boar populations. (Silva et al, 2017); number of ribs in pigs, MESP1 on SSC7 (Zhu et al, 2015); meat-to-fat ratio in pigs, DEAF1 on SSC2 (Falker-Gieske et al, 2019); pregnancy rate in pigs, PPID on SSC8 (Gu et al, 2014); steroid receptor activity, CYP-40 on SSC8 (Ratajczak et al, 2015); brain development in horses, DLGAP1 on SSC6 (Schubert et al, 2014); salivary secretion in pigs, KCNMA1 on SSC14 (Li et al, 2013); reproduction in pigs, CWH43 on SSC8 (He et al, 2017); bone weight in cattle, FAM184B on SSC8 (Xia et al, 2017) and cardiovascular disease (Pérez-Montarelo et al, 2014); spermiogenesis in mouse, AMPH on SSC9; boar taint, NWD2 on SSC8 (Drag et al, 2018); melanocyte function in dogs, ARHGAP12 on SSC10 (Kluth and Distl, 2013); female pregnancy in pigs, RAPGEF2 on SSC8 (Pérez-Enciso et al, 2009); growth traits in cattle, KSR2 on SSC14 (Puig-Oliveras et al, 2014); vascular smooth muscle contraction in sheep, SPSB4 on SSC13 (Yang et al, 2016); and back-fat fatty acid composition, APBB1IP on SSC10 (Zappaterra et al, 2018). In addition, we identified several SNPs in the two Croatian breeds that were located in non-coding intergenic regions and that were present in various pig breeds as well as to other domestic animal species, including cattle, sheep and horse.…”

A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach

“…Suwannasing, et al [47] using the Porcine SNP60k BeadChip, considered 5-adjacent SNP windows that explained more than 1% of total genetic variance as the threshold to declare significance. de Oliveira Silva, et al [48] using the BovineHD SNP panel, considered 50-adjacent SNP windows (with average of 280 kb) that explained more than 0.50% of additive genetic variance as the threshold to declare significance. The results identified three windows (on BTA3, BTA6, and BTA7) associated with calving interval in primi-and multiparous cows (Figures 1 and 2).…”

Genome‐wide scan for runs of homozygosity in the composite Montana Tropical® beef cattle

“…The XKR4 (XK, Kell blood group complex subunitrelated family, member 4) gene has been associated with several economically important traits in the beef cattle such as intramuscular fat (Ramayo-Caldas et al, 2014) and subcutaneous rump fat thickness (Bolormaa et al, 2011;Porto Neto, Bunch, Harrison, & Barendse, 2012). This gene has also been described to have functions associated with serum prolactin concentrations in the Angus-Simmental-Charolais crossbred (Bastin et al, 2014), feed intake in crossbred steers (Lindholm-Perry et al, 2012), age at puberty in Brahman (Fortes et al, 2012), and backfat thickness (Silva et al, 2017), birth weight (Terakado et al, 2018) and meat tenderness (Magalhães et al, 2016) in the Nellore cattle. The second gene (MT1EI, metallothionein 1E) encodes a protein that exhibits antioxidant activity (Chung, Hogstrand, & Lee, 2006) and displayed a significant negative correlation with dry matter intake in beef steers (Sun, Zhao, Zhou, Chen, & Guan, 2019).…”