Zavarez L.B.,Sao Paulo State University |
Utsunomiya Y.T.,Sao Paulo State University |
Carmo A.S.,Sao Paulo State University |
Neves H.H.R.,GenSys Consultores Associados |
And 11 more authors.
Frontiers in Genetics | Year: 2015
The use of relatively low numbers of sires in cattle breeding programs, particularly on those for carcass and weight traits in Nellore beef cattle (Bos indicus) in Brazil, has always raised concerns about inbreeding, which affects conservation of genetic resources and sustainability of this breed. Here, we investigated the distribution of autozygosity levels based on runs of homozygosity (ROH) in a sample of 1,278 Nellore cows, genotyped for over 777,000 SNPs. We found ROH segments larger than 10 Mb in over 70% of the samples, representing signatures most likely related to the recent massive use of few sires. However, the average genome coverage by ROH (> 1 Mb) was lower than previously reported for other cattle breeds (4.58%). In spite of 99.98% of the SNPs being included within a ROH in at least one individual, only 19.37% of the markers were encompassed by common ROH, suggesting that the ongoing selection for weight, carcass and reproductive traits in this population is too recent to have produced selection signatures in the form of ROH. Three short-range highly prevalent ROH autosomal hotspots (occurring in over 50% of the samples) were observed, indicating candidate regions most likely under selection since before the foundation of Brazilian Nellore cattle. The putative signatures of selection on chromosomes 4, 7, and 12 may be involved in resistance to infectious diseases and fertility, and should be subject of future investigation. © 2015 Zavarez, Utsunomiya, Carmo, Neves, Carvalheiro, Ferencakovic, Pérez O'Brien, Curik, Cole, Van Tassell, da Silva, Sonstegard, Sölkner and Garcia.
Utsunomiya Y.T.,Sao Paulo State University |
do Carmo A.S.,Sao Paulo State University |
Carvalheiro R.,GenSys Consultores Associados |
Neves H.H.R.,Sao Paulo State University |
And 13 more authors.
BMC Genetics | Year: 2013
Background: Birth weight (BW) is an economically important trait in beef cattle, and is associated with growth- and stature-related traits and calving difficulty. One region of the cattle genome, located on Bos primigenius taurus chromosome 14 (BTA14), has been previously shown to be associated with stature by multiple independent studies, and contains orthologous genes affecting human height. A genome-wide association study (GWAS) for BW in Brazilian Nellore cattle (Bos primigenius indicus) was performed using estimated breeding values (EBVs) of 654 progeny-tested bulls genotyped for over 777,000 single nucleotide polymorphisms (SNPs).Results: The most significant SNP (rs133012258, PGC = 1.34 × 10-9), located at BTA14:25376827, explained 4.62% of the variance in BW EBVs. The surrounding 1 Mb region presented high identity with human, pig and mouse autosomes 8, 4 and 4, respectively, and contains the orthologous height genes PLAG1, CHCHD7, MOS, RPS20, LYN, RDHE2 (SDR16C5) and PENK. The region also overlapped 28 quantitative trait loci (QTLs) previously reported in literature by linkage mapping studies in cattle, including QTLs for birth weight, mature height, carcass weight, stature, pre-weaning average daily gain, calving ease, and gestation length.Conclusions: This study presents the first GWAS applying a high-density SNP panel to identify putative chromosome regions affecting birth weight in Nellore cattle. These results suggest that the QTLs on BTA14 associated with body size in taurine cattle (Bos primigenius taurus) also affect birth weight and size in zebu cattle (Bos primigenius indicus). © 2013 Utsunomiya et al.; licensee BioMed Central Ltd.
Espigolan R.,Sao Paulo State University |
Baldi F.,Sao Paulo State University |
Baldi F.,University of Sao Paulo |
Boligon A.A.,Sao Paulo State University |
And 17 more authors.
BMC Genomics | Year: 2013
Background: Knowledge of the linkage disequilibrium (LD) between markers is important to establish the number of markers necessary for association studies and genomic selection. The objective of this study was to evaluate the extent of LD in Nellore cattle using a high density SNP panel and 795 genotyped steers.Results: After data editing, 446,986 SNPs were used for the estimation of LD, comprising 2508.4 Mb of the genome. The mean distance between adjacent markers was 4.90 ± 2.89 kb. The minor allele frequency (MAF) was less than 0.20 in a considerable proportion of SNPs. The overall mean LD between marker pairs measured by r2 and |D'| was 0.17 and 0.52, respectively. The LD (r2) decreased with increasing physical distance between markers from 0.34 (1 kb) to 0.11 (100 kb). In contrast to this clear decrease of LD measured by r2, the changes in |D'| indicated a less pronounced decline of LD. Chromosomes BTA1, BTA27, BTA28 and BTA29 showed lower levels of LD at any distance between markers. Except for these four chromosomes, the level of LD (r2) was higher than 0.20 for markers separated by less than 20 kb. At distances < 3 kb, the level of LD was higher than 0.30. The LD (r2) between markers was higher when the MAF threshold was high (0.15), especially when the distance between markers was short.Conclusions: The level of LD estimated for markers separated by less than 30 kb indicates that the High Density Bovine SNP BeadChip will likely be a suitable tool for prediction of genomic breeding values in Nellore cattle. © 2013 Espigolan et al.; licensee BioMed Central Ltd.
Pereira A.G.T.,University of Sao Paulo |
Pereira A.G.T.,International Atomic Energy Agency |
Utsunomiya Y.T.,Sao Paulo State University |
Utsunomiya Y.T.,International Atomic Energy Agency |
And 15 more authors.
PLoS ONE | Year: 2016
Two complementary methods, namely Multi-Trait Meta-Analysis and Versatile Gene-Based Test for Genome-wide Association Studies (VEGAS), were used to identify putative pleiotropic genes affecting carcass traits in Bos indicus (Nellore) cattle. The genotypic data comprised over 777,000 single-nucleotide polymorphism markers scored in 995 bulls, and the phenotypic data included deregressed breeding values (dEBV) for weight measurements at birth, weaning and yearling, as well visual scores taken at weaning and yearling for carcass finishing precocity, conformation and muscling. Both analyses pointed to the pleomorphic adenoma gene 1 (PLAG1) as a major pleiotropic gene. VEGAS analysis revealed 224 additional candidates. From these, 57 participated, together with PLAG1, in a network involved in the modulation of the function and expression of IGF1 (insulin like growth factor 1), IGF2 (insulin like growth factor 2), GH1 (growth hormone 1), IGF1R (insulin like growth factor 1 receptor) and GHR (growth hormone receptor), suggesting that those pleiotropic genes operate as satellite regulators of the growth pathway. © 2016 G. T. Pereira et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Bertoli C.D.,Instituto Federal Catarinense Campus Camboriu IFC CC |
Bertoli C.D.,Federal University of Rio Grande do Sul |
Braccini J.,Federal University of Rio Grande do Sul |
Braccini J.,Brazilian National Council for Scientific and Technological Development |
And 6 more authors.
Livestock Science | Year: 2015
The objectives of this study were to estimate fixed genetic (both additive and non-additive) effects and test different non-additive models. These effects included direct and maternal joint breed additive effects, direct and maternal complementarity (or profit heterosis), direct and maternal heterosis (dominance) and direct and maternal epistatic loss non-additive effects. A large crossbred Angus x Nellore population with approximately 300,000 records for weaning gain (WG) and 150,000 records for post-weaning gain (PG) was used. Phenotypic scores for weaning (WC) and post-weaning (PC) conformation, weaning (WP) and post-weaning (PP) precocity, weaning (WM) and post-weaning (PM) muscling and scrotal circumference (SC) were also used. All models included the fixed contemporary group effect and random animal, maternal genetic and permanent environment effects. Each model was tested against all other models for all nine traits using the likelihood ratio test. The complete model, including all additive and non-additive effects and the model without complementarity, were seen to be the best options to analyze this crossbred population. However, least squares may not be the best methodology due to possible collinearity among estimates that may inflate the variance. In the complete model most effects were statistically significant (. P<0.01) for weaning traits, except for direct and maternal breed additive effects and direct complementarity effect for WM. For post-weaning traits, the direct complementarity effect for phenotypic scores (PC, PP and PM) and the maternal heterosis effect for PG, PC, PM, were not statistically significant. For scrotal circumference the maternal complementarity, direct and maternal heterosis and maternal epistatic loss effects were not statistically significant. All other effects were statistically significant (. P<0.01). For the model without complementarity, the direct breed additive effect for PG and PP was not statistically significant, including the maternal breed additive effect for WC, WD, PP and PM and maternal heterosis, direct and maternal epistatic loss effects for SC. Considering all models, significant direct breed additive effect was mostly positive for weaning traits and was negative for all post-weaning and SC. The significant maternal breed additive and maternal complementarity effects for SC were all negative. The significant direct and maternal epistatic loss effects were negative for all traits and for all models, except for PG in the complete model and for weaning traits in the model including only breed additive and epistatic loss effects. We conclude that the fixed genetic effects are mostly significant, thus it is important to include them in the model when evaluating crossbreed animals and the models including breed additive effects, heterosis and epistatic loss with or without complementarity were the more appropriate. © 2015 Elsevier B.V.