Association of single nucleotide polymorphisms with carcass traits in Nellore cattle

Abstract

The association between two single nucleotide polymorphisms (SNPs), T945M and UCP1SNP1, with hot carcass weight (HCW, kg, N = 618), longissimus dorsi muscle area (REA, cm(2), N = 633), and backfat thickness (BF, mm, N = 625), measured in Nellore cattle in Brazil, was evaluated. Likelihood ratio tests were used to evaluate reduced (fixed effects of general mean, contemporary group, yearling weight, age at slaughter, and random effect of infinitesimal genetic value) and full model (reduced model effects plus quantitative trait locus effects). Additive and dominance effects were tested for each SNP. Genotypic and gene frequencies were also obtained for the SNPs and a descriptive phenotype analysis was made. Mean values for HCW, REA and BF were equal to 288.13 +/- 0.55 kg, 73.14 +/- 0.27 cm(2), and 4.28 +/- 0.07 mm, respectively; the coefficients of variation were 4.74, 9.24, and 42.43%, respectively. Gene frequencies for T945M and UCP1SNP1 were f(C) = 0.89, f(T) = 0.11, f(C) = 0.81, and f(G) = 0.19. The SNP T945M had a genotypic frequency of only three animals for TT genotype. Additive effects were observed for T945M on REA and BF, while UCP1SNP1 affected HCW and BF. Based on the significant additive effects of the SNPs and the gene frequencies that we found, we can expect genetic gains with marker assisted selection.

Association of single nucleotide polymorphisms in the bovine leptin and leptin receptor genes with growth and ultrasound carcass traits in Nellore cattle

“…In a previous study in Nellore cattle, this marker was significantly associated with REA and BFAT of carcass after slaughter (Ferraz et al, 2009). In the present study, no association of T945M with BFAT or RFAT was found when the traits were evaluated using ultrasound measurements.…”

“…All leptin markers were polymorphic in Nellore cattle; therefore, the minor allele frequencies of E2JW, A59V, and UASMS 2 were very low (<0.01). Consequently, very low allelic and genotype frequencies are always a problem in estimating additive effects because the mean value of the rare genotype might have been under-or overestimated (Ferraz et al, 2009). The markers E2JW, A59V, and UASMS2 had very low allelic frequencies, and they were not analyzed because they were almost fixed.…”

“…Since the discovery of the leptin gene by Zhang et al (1994) and of the leptin receptor gene by Tartaglia (1997), many studies have been published on polymorphisms in both genes in several species. Associations of single nucleotide polymorphisms (SNPs) in the leptin and leptin receptor genes with economically relevant traits have been reported in cattle by several authors (Buchanan et al, 2002;Liefers et al, 2004;Nkrumah et al, 2004Nkrumah et al, , 2005Ferraz et al, 2009;Souza et al, 2010).…”

Protein synthesis and degradation gene SNPs related to feed intake, feed efficiency, growth, and ultrasound carcass traits in Nellore cattle

“…The large estimation errors may also explain this change. On the other hand, we could notice that the magnitude of allelic substitution effects was, in some cases, greater than that reported elsewhere (e.g., Sherman et al, 2008;Ferraz et al, 2009), suggesting the need for other adjustments in the model.…”

Tissue expression and predicted protein structures of the bovine ANGPTL3 and association of novel SNPs with growth and meat quality traits

“…Bovine ANGPTL3 is located on chromosome 3 (from approximately 83.49 to 83.58 Mb). Alignment of bovine chromosome 3 on the radiation hybrid (RH) map of the USDA-MARC cattle Database indicated that QTLs associated with growth traits in this region (DIK4116), such as BW at birth (McClure et al, 2010), calving traits (HH51 marker), such as calf size (Mai et al, 2010;Sahana et al, 2011), meat quality traits, such as CW and fat thickness at the 12 th rib (Ferraz et al, 2009;McClure et al, 2010) (details are shown in Table 5). Our association analysis showed that the SNP1, SNP2 and SNP3 mutations were significantly associated with BW (birth and 24 months), hipbone width (6, 12, 18 and 24 months), WBSF and RA, respectively.…”