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 r²and |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.

Weight records of Brazilian Nelore cattle, from birth to 630 d of age, recorded every 3 mo, were analyzed using random regression models. Independent variables were Legendre polynomials of age at recording. The model of analysis included contemporary groups as fixed effects and age of dam as a linear and quadratic covariable. Mean trends were modeled through a cubic regression on orthogonal polynomials of age. Up to four sets of random regression coefficients were fitted for animals' direct and maternal, additive genetic, and permanent environmental effects. Changes in measurement error variances with age were modeled through a variance function. Orders of polynomial fit from three to six were considered, resulting in up to 77 parameters to be estimated. Models fitting random regressions modeled the pattern of variances in the data adequately, with estimates similar to those from corresponding univariate analysis. Direct heritability estimates decreased after birth and tended to be lowest at ages at which maternal effect estimates tended to be highest. Maternal heritability estimates increased after birth to a peak around 110 to 120 d of age and decreased thereafter. Additive genetic direct correlation estimates between weights at standard ages (birth, weaning, yearling, and final weight) were moderate to high and maternal genetic and environmental correlations were consistently high.

The objective of this study was to identify genomic regions that are associated with meat quality traits in the Nellore breed. Nellore steers were finished in feedlots and slaughtered at a commercial slaughterhouse. This analysis included 1,822 phenotypic records of tenderness and 1,873 marbling records. After quality control, 1,630 animals genotyped for tenderness, 1,633 animals genotyped for marbling, and 369,722 SNPs remained. The results are reported as the proportion of variance explained by windows of 150 adjacent SNPs. Only windows with largest effects were considered. The genomic regions were located on chromosomes 5, 15, 16 and 25 for marbling and on chromosomes 5, 7, 10, 14 and 21 for tenderness. These windows explained 3,89% and 3,80% of the additive genetic variance for marbling and tenderness, respectively. The genes associated with the traits are related to growth, muscle development and lipid metabolism. The study of these genes in Nellore cattle is the first step in the identification of causal mutations that will contribute to the genetic evaluation of the breed.

The objective of this study was to perform a genome-wide association study (GWAS) to detect chromosome regions associated with indicator traits of sexual precocity in Nellore cattle. Data from Nellore animals belonging to farms which participate in the DeltaGen^® and Paint^® animal breeding programs, were used. The traits used in this study were the occurrence of early pregnancy (EP) and scrotal circumference (SC). Data from 72,675 females and 83,911 males with phenotypes were used; of these, 1,770 females and 1,680 males were genotyped. The SNP effects were estimated with a single-step procedure (WssGBLUP) and the observed phenotypes were used as dependent variables. All animals with available genotypes and phenotypes, in addition to those with only phenotypic information, were used. A single-trait animal model was applied to predict breeding values and the solutions of SNP effects were obtained from these breeding values. The results of GWAS are reported as the proportion of variance explained by windows with 150 adjacent SNPs. The 10 windows that explained the highest proportion of variance were identified. The results of this study indicate the polygenic nature of EP and SC, demonstrating that the indicator traits of sexual precocity studied here are probably controlled by many genes, including some of moderate effect. The 10 windows with large effects obtained for EP are located on chromosomes 5, 6, 7, 14, 18, 21 and 27, and together explained 7.91% of the total genetic variance. For SC, these windows are located on chromosomes 4, 8, 11, 13, 14, 19, 22 and 23, explaining 6.78% of total variance. GWAS permitted to identify chromosome regions associated with EP and SC. The identification of these regions contributes to a better understanding and evaluation of these traits, and permits to indicate candidate genes for future investigation of causal mutations.

The aim of the present study was to evaluate the genetic correlations among real-time ultrasound carcass, BW, and scrotal circumference (SC) traits in Nelore cattle. Carcass traits, measured by real-time ultrasound of the live animal, were recorded from 2002 to 2004 on 10 farms across 6 Brazilian states on 2,590 males and females ranging in age from 450 to 599 d. Ultrasound records of LM area (LMA) and backfat thickness (BF) were obtained from cross-sectional images between the 12th and 13th ribs, and rump fat thickness (RF) was measured between the hook and pin bones over the junction between gluteus medius and biceps femoris muscles. Also, BW (n = 22,778) and SC (n = 5,695) were recorded on animals born between 1998 and 2003. The BW traits were 120, 210, 365, 450, and 550-d standardized BW (W120, W210, W365, W450, and W550), plus BW (WS) and hip height (HH) on the ultrasound scanning date. The SC traits were 365-, 450-, and 550-d standardized SC (SC365, SC450, and SC550). For the BW and SC traits, the database used was from the Nelore Breeding Program—Nelore Brazil. The genetic parameters were estimated with multivariate animal models and REML. Estimated genetic correlations between LMA and other traits were 0.06 (BF), −0.04 (RF), 0.05 (HH), 0.58 (WS), 0.53 (W120), 0.62 (W210), 0.67 (W365), 0.64 (W450 and W550), 0.28 (SC365), 0.24 (SC450), and 0.00 (SC550). Estimated genetic correlations between BF and with other traits were 0.74 (RF), −0.32 (HH), 0.19 (WS), −0.03 (W120), −0.10 (W210), 0.04 (W365), 0.01 (W450), 0.06 (W550), 0.17 (SC365 and SC450), and −0.19 (SC550). Estimated genetic correlations between RF and other traits were −0.41 (HH), −0.09 (WS), −0.13 (W120), −0.09 (W210), −0.01 (W365), 0.02 (W450), 0.03 (W550), 0.05 (SC365), 0.11 (SC450), and −0.18 (SC550). These estimates indicate that selection for carcass traits measured by real-time ultrasound should not cause antagonism in the genetic improvement of SC and BW traits. Also, selection to increase HH might decrease subcutaneous fat as correlated response. Therefore, to obtain animals suited to specific tropical production systems, carcass, BW, and SC traits should be considered in selection programs. Copyright © 2010. American Society of Animal Science .

Dados de 19.458 animais da raça Nelore, nascidos entre 1975 e 2002 e pertencentes a oito fazendas participantes do Programa de Melhoramento Genético da Raça Nelore (PMGRN), foram utilizados para estimar componentes de covariância, herdabilidade e correlações genéticas dos pesos ao nascimento, à desmama, ao sobreano e aos 2, 3 e 5 anos de idade. Utilizou-se o método da máxima verossimilhança restrita, em análises uni, bi e multicaracterísticas, com modelos que incluíram o efeito genético aditivo direto, como aleatório, além dos efeitos fixos de grupo de contemporâneos e os efeitos linear e quadrático da idade do animal à pesagem (com exceção do modelo para peso ao nascer) e da idade da mãe ao parto. O efeito aleatório de ambiente permanente materno também foi incluído nos modelos de análise do peso ao nascer, peso à desmama e peso ao sobreano e o efeito aleatório genético materno somente no modelo do peso à desmama. As herdabilidades estimadas em análise multicaracterística para os pesos ao nascer, à desmama, ao sobreano, aos 2, 3 e aos 5 anos de idade foram 0,25; 0,33; 0,34; 0,32; 0,33 e 0,35, respectivamente. As correlações genéticas estimadas entre os pesos foram positivas e de moderadas a altas magnitudes e tenderam a diminuir com o aumento da distância entre as pesagens, o que indica que a seleção para peso em qualquer idade deverá promover mudança genética nos pesos nas demais idades, inclusive no peso adulto de fêmeas da raça Nelore. As estimativas de herdabilidade obtidas na análise multicaracterística foram superiores, sobretudo para os pesos aos 3 e aos 5 anos de idade, o que sugere melhor partição das variâncias genética e de ambiente em comparação às análises uni e bicaracterísticas, porém a alta demanda de recursos computacionais em análises de muitas características pode ainda dificultar o uso dessas análises em grandes bancos de dados.