Genetic parameters and trends of growth traits in Nelore cattle raised in the Northern region of Brazil

The objective of this study was to estimate (co)variances and genetic parameters and to predict genetic trends for weight at 120 (W120), 210 (W210), 365 (W365), and 450 (W450) days of age in Nelore cattle raised in the northern region of Brazil. The database comprised records of 30,387 animals born between 2000 and 2013 in the Brazilian North. Estimates were calculated by the Restricted  Maximum Likelihood (REML) method, in single- and multi-trait analyses in an animal model. Heritability as obtained using single- and multi-trait models for W120 (0.22 and 0.31), W210 (0.20 and 0.34), W365 (0.51 and 0.51), and W450 (0.49 and 0.51) indicated moderate to high magnitudes, with the possibility of genetic selection and incorporation into the herd. Genetic correlations between growth traits were favorable, ranging from 0.78 to 0.96. Genetic trends for W120 and W210 varied largely, from -0.31 to 4.68 and -0.53 to 7.62 kg/year, respectively. Smaller fluctuations were observed in genetic trends for W365 and W450, which ranged from -1.08 to 10.90 and -1.29 to 12.51 kg/year, respectively. Selection for W365 and W450 proved to be the criterion of choice for Nelore herds raised in the region; however, it may compromise adult performance because of higher costs and time for production. A thorough analysis of mattings is recommended to allow the selection of earlier-developing animals. O presente trabalho foi delineado para estimar as (co) variâncias, parâmetros genéticos e de predizer as tendências genéticas para o peso aos 120 (W120), 210 (W210), 365 (W365) e 450 (W450) dias de idade de gado Nelore criado na região norte do Brasil. A base de dados foi constituituída por registro de 30387 animais, nascidos entre 2000 e 2013 no norte do Brasil. As estimativas foram calculadas pelo método de máxima restrição de probabilidade (REML) em um modelo animal com análises isoladas e multi variadas. A herdabilidade obtida para os modelos utilizados foi: W120 (0,22 e 0,31); W210 (0,20 e 0,34); W365 (0,51 e 0,51) e W450 (0,49 e 0,51), indicando moderada e alta magnitude com a possibilidade de seleção genética e incorporação no rebanho. As correlações genéticas entre grupos de tendências foram favoráveis variando de 0,78 a 0,96. As tendências genéticas para W120 e W210 apresentaram ampla variação de -0,31 a 4,68 e -0,53 a 7,62 kg/ano, respectivamente. Menores flutuações foram observadas nas tendências genéticas para W365 e W450, as quais variaram de -1,08 a 10,90 e -1,29 a12,51 kg/ano, respectivamente. Foi constatado que a seleção para W365 e W450 deve ser um critério de escolha para os rebanhos Nelore criados na região; contudo ela pode comprometer a performance dos adultos devido aos elevados custos e da duração da produção. Uma completa análise de cruzamentos é recomendada para possibilitar a seleção de animais jovens em desenvolvimento.

Frequências de genes candidatos e associações com características de carcaça e da carne em bovinos da raça Nelore e cruzados

The objective of this work was to estimate allelic frequencies of the polymorphisms IGF2/MboII (G > T) of the insulin‑like growth factor 2 (IGF2) gene, DQ499531.1:g.134A > T of the pro‑melanin‑concentrating hormone (PMCH) gene, and DQ667048.1:g.3290G > T of the RAR‑related orphan receptor C (RORC) gene in beef cattle of different genetic groups, and to evaluate the associations between these polymorphisms and traits related to carcass composition and meat quality. Data on carcass and meat quality of 499 animals was used: of 313 Nellore (Bos indicus) and of 186 Nellore crossed with different taurine (Bos taurus) breeds. For the IGF2/MboII polymorphism, the frequencies found for the G allele were 0.231 and 0.631 for Nellore and crossed breeds, respectively. For the DQ499531.1:g.134A > T polymorphism, the allelic frequencies of A were 0.850 for Nellore and 0.905 for crossed breeds. For the DQ667048.1:g.3290G > T polymorphism, the allelic frequencies of G were 0.797 and 0.460 for Nellore and crossed breeds, respectively. The evaluated single nucleotide polymorphisms (SNPs) are not significantly associated with carcass and meat traits (rib eye area, back fat thickness, shear force, total lipids, and myofibrillar fragmentation index), suggesting little utility of the analyzed polymorphisms of the IGF2, PMHC, and RORC  genes as selection markers in the studied cattle populations.O objetivo deste trabalho foi estimar as frequências alélicas dos polimorfismos IGF2/MboII (G > T) do gene “insulin‑like growth fator 2” (IGF2), DQ499531.1:g.134 A> T do gene “pro‑melanin‑concentrating hormone” (PMCH) e DQ667048.1:g.3290G> T do gene “RAR‑related orphan receptor C” (RORC) em bovinos de corte de diferentes grupos genéticos, e avaliar a ocorrência de associações entre esses polimorfismos e características relacionadas à composição da carcaça e à qualidade de carne. Foram utilizados dados de carcaça e qualidade de carne de 499 animais: 313 da raça Nelore (Bos indicus) e 186 provenientes de seus cruzamentos com raças taurinas (Bos taurus). Para o polimorfismo IGF2/MboII, as frequências encontradas para o alelo G foram 0,231 e 0,631 para Nelore e cruzados, respectivamente. Para o polimorfismo DQ499531.1:g.‑134A > T, as frequências alélicas de A foram 0,850 para Nelore e 0,905 para cruzados. Para o polimorfismo DQ667048.1:g.3290G > T, as frequências alélicas de G foram 0,797 e 0,460 para Nelore e cruzados, respectivamente. Os polimorfismos de nucleotídeo único (SNPs) avaliados não se relacionam significativamente com as características de carcaça e carne (área de olho de lombo, espessura de gordura subcutânea, força de cisalhamento, lipídeos totais e índice de fragmentação miofibrilar), o que sugere pouca utilidade dos polimorfismos analisados dos genes IGF2,PMHC e RORC como marcadores de seleção nas populações bovinas estudadas

Genome-wide association between single nucleotide polymorphisms with beef fatty acid profile in Nellore cattle using the single step procedure

Abstract\ud \ud Background\ud Saturated fatty acids can be detrimental to human health and have received considerable attention in recent years. Several studies using taurine breeds showed the existence of genetic variability and thus the possibility of genetic improvement of the fatty acid profile in beef. This study identified the regions of the genome associated with saturated, mono- and polyunsaturated fatty acids, and n-6 to n-3 ratios in the Longissimus thoracis of Nellore finished in feedlot, using the single-step method.\ud \ud \ud Results\ud The results showed that 115 windows explain more than 1 % of the additive genetic variance for the 22 studied fatty acids. Thirty-one genomic regions that explain more than 1 % of the additive genetic variance were observed for total saturated fatty acids, C12:0, C14:0, C16:0 and C18:0. Nineteen genomic regions, distributed in sixteen different chromosomes accounted for more than 1 % of the additive genetic variance for the monounsaturated fatty acids, such as the sum of monounsaturated fatty acids, C14:1 cis-9, C18:1 trans-11, C18:1 cis-9, and C18:1 trans-9. Forty genomic regions explained more than 1 % of the additive variance for the polyunsaturated fatty acids group, which are related to the total polyunsaturated fatty acids, C20:4 n-6, C18:2 cis-9 cis12 n-6, C18:3 n-3, C18:3 n-6, C22:6 n-3 and C20:3 n-6 cis-8 cis-11 cis-14. Twenty-one genomic regions accounted for more than 1 % of the genetic variance for the group of omega-3, omega-6 and the n-6:n-3 ratio.\ud \ud \ud Conclusions\ud The identification of such regions and the respective candidate genes, such as ELOVL5, ESSRG, PCYT1A and genes of the ABC group (ABC5, ABC6 and ABC10), should contribute to form a genetic basis of the fatty acid profile of Nellore (Bos indicus) beef, contributing to better selection of the traits associated with improving human health.MVA Lemos, (FAPESP, Fundação de Amparo à Pesquisa do Estado de São\ud Paulo). HLJ Chiaia, MP Berton, FLB Feitosa received scholarships from the\ud Coordination Office for Advancement of University-level Personnel (CAPES;\ud Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) in conjunction\ud with the Postgraduate Program on Genetics and Animal Breeding, Faculdade\ud de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (FCAV,\ud UNESP). F Baldi (FAPESP, Fundação de Amparo à Pesquisa do Estado de São\ud Paulo grant #2011/21241-0). Lucia G. Albuquerque (FAPESP, Fundação de\ud Amparo à Pesquisa do Estado de São Paulo grant #2009/16118-5)

Desequilíbrio de ligação e associação entre polimorfismos de base única com maciez da carne e espessura de gordura em bovinos Nelore utilizando painéis de alta densidade

A carne produzida no Brasil a partir de raças zebuínas possui características organolépticas que não são bem aceitas nos mercados mais exigentes. As características de carcaça e da carne, como a maciez e a espessura de gordura subcutânea podem garantir qualidade e uniformidade na produção de carne bovina, porém o melhoramento genético para essas características não tem sido praticado. Os objetivos deste estudo foram analisar o desequilíbrio de ligação entre os polimorfismos de base única (SNPs), e estudar a associação destes com a maciez da carne e espessura de gordura subcutânea no genoma de bovinos da raça Nelore utilizando um painel de SNPs de alta densidade. Foram utilizados 795 machos da raça Nelore nascidos em 2008 e 2009 e pertencentes a três programas de melhoramento genético. Um total de 117 grupos de contemporâneos foi formado, constituídos por ano de nascimento, fazenda, grupos de manejo ao nascimento, grupos de manejo à desmama e ao sobreano. Os animais foram genotipados utilizando o Illumina High-Density Bovine BeadChip com 777.962 marcadores SNPs. O DNA genômico foi extraído utilizando amostras de cinco gramas de tecido muscular retirados do Longissimus dorsi de cada animal. Foram excluídos SNPs que apresentaram MAF (alelo de menor frequência) inferior a 0,05 e Call Rate menor que 0,93, totalizando 446.986 SNPs. Os fenótipos para maciez da carne foram obtidos utilizando um equipamento de análise de textura equipado com uma sonda Warner Bratzler em amostras de 2,54 cm retiradas entre a 12ª e 13ª costelas da meiacarcaça esquerda. Na mesma amostra foi mensurada a espessura de gordura subcutânea com paquímetro, medindo a camada de gordura localizada a um ângulo de 45º a partir do centro geométrico. As análises de associação foram realizadas considerando apenas um marcador por vez...The meat produced in Brazil from Zebu breeds has organoleptic characteristics that are not well accepted in the most demanding markets. Carcass and meat traits, like tenderness and fat thickness, can ensure quality and uniformity in beef production, but genetic improvement for these traits has not been practiced. The objective of this study was analyze the linkage disequilibrium between single nucleotide polymorphisms (SNPs), and to study their association with the tenderness of meat and fat thickness in the genome of Nellore cattle using a panel of highdensity SNPs. Data from 795 Nellore cattle born in 2008 and 2009 and belonging to three breeding programs were used. A total of 117 contemporary groups were formed, constituted of year of birth, farm, management groups at birth, management groups at weaning and yearling. The animals were genotyped using Illumina High- Density Bovine BeadChip with 777,962 SNP markers. Genomic DNA was extracted with samples from five grams of tissue taken from the Longissimus dorsi muscle of each animal. SNPs that had MAF less than 0.05 and Call Rate less than 0.93 were excluded, totaling 446,986 SNPs. The phenotypes for meat tenderness were obtained using a texture analysis equipment equipped with a Warner Bratzler probe in samples of 2.54 cm taken between the 12th and 13th ribs of the left half carcass. On the same sample, it was measured the thickness of subcutaneous fat with caliper rule, measuring the fat located at an angle of 45° from the geometric center. The association analysis was performed considering only one marker at a time. The fixed effects in the model were SNP marker, contemporary group, date of slaughter and slaughter age as covariate. To estimate the effect of each SNP over the traits, the SNP marker was included as a covariate (linear effect). The average linkage disequilibrium (r²)... (Complete abstract click electronic access below

Aplicação de modelos não-lineares para descrever a evolução de características de crescimento e carcaça em bovinos da raça Hereford

Este trabalho foi desenvolvido com o objetivo de estudar a evolução das características de crescimento e carcaça em função da idade em bovinos da raça Hereford, utilizando modelos não-lineares. Foram utilizados dados de 240 bovinos machos (castrados) da raça Hereford, pertencentes à fazenda Experimental La Estanzuela do INIA, Colonia, Uruguai. As características começaram a ser mensuradas a partir da desmama de animais com aproximadamente seis meses de idade, até o abate (dois anos de idade). As medições de peso foram realizadas a cada 15±3 dias durante todo o período e sem jejum prévio. As mensurações de área de olho de lombo, obtidas por ultrassom, e altura dos animais foram obtidas a cada 90 dias, sendo que as medidas de ultrassom foram tomadas entre a 12ª e 13ª costelas. Os modelos não-lineares utilizados foram os modelos de Brody, Gompertz, Logístico e Von Bertalanffy. Para as características peso, altura e área de olho de lombo, todos os modelos avaliados atingiram a convergência. Para descrever a evolução dos dados de peso e área de olho de lombo em função da idade, o modelo de Von Bertalanffy foi o mais indicado, e os modelos de Brody e Logístico mostraram o pior ajuste, respectivamente. A evolução da altura dos animais desde o desmame até os dois anos de idade pode ser modelada através de qualquer um dos modelos não-lineares considerados neste estudo.The objective of this research was to study the evolution of growth and carcass traits as a function of age in Hereford cattle using nonlinear models. Records from 240 Hereford steers (castrated), belonging to the experimental station La Estanzuela of INIA Uruguay, were utilized. The animals were measured from weaning, approximately at 6 months of age, to slaughter (two years of age). The animals were weighed, without fasting, every 15±3 days throughout the period. The measurements of ribeye loin area (between the 12th and 13th rib) were obtained by ultrasound every 90 days. The height of the animals was obtained every 90 days. The Brody, Gompertz, Logistic and Von Bertalanffy nonlinear models were applied to describe the trajectory of weight, height and ribeye loin area along the age. For height, weight and ribeye loin area, all the models reached the convergence. To describe the evolution of weight and ribeye loin area, the Von Bertalanffy nonlinear model was the most suitable. For weight and ribeye loin area, the Brody and Logistic nonlinear models have shown the worst fit, respectively. The height trajectory from weaning until two years of age can be modeled by any of the nonlinear models considered in this research.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Sliding window haplotype approaches overcome single SNP analysis limitations in identifying genes for meat tenderness in Nelore cattle

Abstract Background Traditional single nucleotide polymorphism (SNP) genome-wide association analysis (GWAA) can be inefficient because single SNPs provide limited genetic information about genomic regions. On the other hand, using haplotypes in the statistical analysis may increase the extent of linkage disequilibrium (LD) between haplotypes and causal variants and may also potentially capture epistastic interactions between variants within a haplotyped locus, providing an increase in the power and robustness of the association studies. We performed GWAA (413,355 SNP markers) using haplotypes based on variable-sized sliding windows and compared the results to a single-SNP GWAA using Warner-Bratzler shear force measured in the longissimus thorasis muscle of 3161 Nelore bulls to ascertain the optimal window size for identifying the genomic regions that influence meat tenderness. Results The GWAA using single SNPs identified eight variants influencing meat tenderness on BTA 3, 4, 9, 10 and 11. However, thirty-three putative meat tenderness QTL were detected on BTA 1, 3, 4, 5, 8, 9, 10, 11, 15, 17, 18, 24, 25, 26 and 29 using variable-sized sliding haplotype windows. Analyses using sliding window haplotypes of 3, 5, 7, 9 and 11 SNPs identified 57, 61, 42, 39, and 21% of all thirty-three putative QTL regions, respectively; however, the analyses using the 3 and 5 SNP haplotypes, cumulatively detected 88% of the putative QTL. The genes associated with variation in meat tenderness participate in myogenesis, neurogenesis, lipid and fatty acid metabolism and skeletal muscle structure or composition processes. Conclusions GWAA using haplotypes based on variable-sized sliding windows allowed the detection of more QTL than traditional single-SNP GWAA. Analyses using smaller haplotypes (3 and 5 SNPs) detected a higher proportion of the putative QTL

Study of whole genome linkage disequilibrium in Nellore cattle

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