Maurício Mello de Alencar

Tendência Genética dos Efeitos Direto e Materno sobre os Pesos à Desmama e Pós-Desmama de Bovinos da Raça Tabapuã no Brasil

Data related to weights of animals of the Tabapua breed, born from 1959 to 1996, in several areas of Brazil, were analyzed with the objective of evaluating the direct and maternal genetic trends, for body weights adjusted for 205 (W205), 365 (W365) and 550 (W550) days of age. The (co)variance component estimates used in the calculation of the breeding values were obtained by the restricted maximum likelihood method (REML), with a model containing the random additive direct, maternal and permanent environmental effects, and the fixed effects of contemporary group (unit of the federation, farm, sex, season and year of birth of the animal) and the covariable age of the cow at calving (linear and quadratic effects). The genetic trends of the direct and maternal genetic effects were estimated by the regression of the breeding value annual means on year of birth of the animals. The genetic trends of the direct effects were 0.134, 0.199 and 0.276 kg/year, for W205, W365 and W550, respectively. The estimates of the maternal genetic trends were, in the same order, 0.019, -0.010 and -0.022 kg/year, respectively. Due to the existing genetic variability on the traits, the genetic changes attained are bellow the possible ones.

Genome-Wide Association for Growth Traits in Canchim Beef Cattle

Studies are being conducted on the applicability of genomic data to improve the accuracy of the selection process in livestock, and genome-wide association studies (GWAS) provide valuable information to enhance the understanding on the genetics of complex traits. The aim of this study was to identify genomic regions and genes that play roles in birth weight (BW), weaning weight adjusted for 210 days of age (WW), and long-yearling weight adjusted for 420 days of age (LYW) in Canchim cattle. GWAS were performed by means of the Generalized Quasi-Likelihood Score (GQLS) method using genotypes from the BovineHD BeadChip and estimated breeding values for BW, WW, and LYW. Data consisted of 285 animals from the Canchim breed and 114 from the MA genetic group (derived from crossings between Charolais sires and ½ Canchim + ½ Zebu dams). After applying a false discovery rate correction at a 10% significance level, a total of 4, 12, and 10 SNPs were significantly associated with BW, WW, and LYW, respectively. These SNPs were surveyed to their corresponding genes or to surrounding genes within a distance of 250 kb. The genes DPP6 (dipeptidyl-peptidase 6) and CLEC3B (C-type lectin domain family 3 member B) were highlighted, considering its functions on the development of the brain and skeletal system, respectively. The GQLS method identified regions on chromosome associated with birth weight, weaning weight, and long-yearling weight in Canchim and MA animals. New candidate regions for body weight traits were detected and some of them have interesting biological functions, of which most have not been previously reported. The observation of QTL reports for body weight traits, covering areas surrounding the genes (SNPs) herein identified provides more evidence for these associations. Future studies targeting these areas could provide further knowledge to uncover the genetic architecture underlying growth traits in Canchim cattle.

Association of GH and IGF-1 polymorphisms with growth traits in a synthetic beef cattle breed

The Canchim beef cattle (5/8 Charolais + 3/8 Zebu) has been selected for meat production in Brazil since late 1950. In the present work the effects of growth hormone (GH) and insulin-like growth factor 1 (IGF-1) polymorphisms were investigated in 688 animals born between 1998 and 2000. These animals belonged to two genetic groups, i.e., traditional and new lineages. Genotype effects on expected breeding values for birth weight (BW), weaning weight (WW) and yearling weight (YW) were investigated by the least square method. Significant effects were found for GH genotype on YW (p ≤ 0.05), with positive effects associated with the LV (leucine/valine) genotype. For IGF-1 genotypes, significant effects were found on BW (p ≤ 0.01) and YW (p ≤ 0.01). Average substitution effects for IGF-1 alleles estimated by regression analysis suggested a positive effect of the IGF-1 225 bp allele on BW and of the 229 bp allele on YW.

Genome-wide association study for intramuscular fat deposition and composition in Nellore cattle

BackgroundMeat from Bos taurus and Bos indicus breeds are an important source of nutrients for humans and intramuscular fat (IMF) influences its flavor, nutritional value and impacts human health. Human consumption of fat that contains high levels of monounsaturated fatty acids (MUFA) can reduce the concentration of undesirable cholesterol (LDL) in circulating blood. Different feeding practices and genetic variation within and between breeds influences the amount of IMF and fatty acid (FA) composition in meat. However, it is difficult and costly to determine fatty acid composition, which has precluded beef cattle breeding programs from selecting for a healthier fatty acid profile. In this study, we employed a high-density single nucleotide polymorphism (SNP) chip to genotype 386 Nellore steers, a Bos indicus breed and, a Bayesian approach to identify genomic regions and putative candidate genes that could be involved with deposition and composition of IMF.ResultsTwenty-three genomic regions (1-Mb SNP windows) associated with IMF deposition and FA composition that each explain ≥ 1% of the genetic variance were identified on chromosomes 2, 3, 6, 7, 8, 9, 10, 11, 12, 17, 26 and 27. Many of these regions were not previously detected in other breeds. The genes present in these regions were identified and some can help explain the genetic basis of deposition and composition of fat in cattle.ConclusionsThe genomic regions and genes identified contribute to a better understanding of the genetic control of fatty acid deposition and can lead to DNA-based selection strategies to improve meat quality for human consumption.

Linkage disequilibrium and haplotype block structure in a composite beef cattle breed.

BackgroundThe development of linkage disequilibrium (LD) maps and the characterization of haplotype block structure at the population level are useful parameters for guiding genome wide association (GWA) studies, and for understanding the nature of non-linear association between phenotypes and genes. The elucidation of haplotype block structure can reduce the information of several single nucleotide polymorphisms (SNP) into the information of a haplotype block, reducing the number of SNPs in a coherent way for consideration in GWA and genomic selection studies.ResultsThe maximum average LD, measured by r2 varied between 0.33 to 0.40 at a distance of < 2.5 kb, and the minimum average values of r2 varied between 0.05 to 0.07 at distances ranging from 400 to 500 kb, clearly showing that the average r2 reduced with the increase in SNP pair distances. The persistence of LD phase showed higher values at shorter genomic distances, decreasing with the increase in physical distance, varying from 0.96 at a distance of < 2.5 kb to 0.66 at a distance from 400 to 500 kb. A total of 78% of all SNPs were clustered into haplotype blocks, covering 1,57 Mb of the total autosomal genome size.ConclusionsThis study presented the first high density linkage disequilibrium map and haplotype block structure for a composite beef cattle population, and indicates that the high density SNP panel over 700 k can be used for genomic selection implementation and GWA studies for Canchim beef cattle.

Estimativas de (Co)Variâncias e Tendências Genéticas para Pesos em um Rebanho Canchim

The objectives of this study were to estimate variances and covariances and to evaluate the genetic trends for body weight at birth (BW), weaning (WW) and twelve months of age (YW) in a Canchim (5/8 Charolais + 3/8 Zebu) herd. Data on 6.517 animals, born from 1953 through 1996, were used to estimate breeding values by the derivative free restricted maximum likelihood method, using a model that included the fixed effects of contemporary group (year-season of birth-sex of calf) and the covariable age of cow at calving (linear and quadratic effects), and the random additive direct, additive maternal and permanent environmental effects. Genetic trends for direct, maternal and total maternal effects were estimated by the weighed regression of the annual (generation) breeding value (direct, maternal and total maternal) means on year (generation) of birth of the animals. The direct heritability estimates were equal to 0.39, 0.48 and 0.63 for BW, WW and YW, respectively, while the maternal heritabilities were, in the same order, equal to 0.03, 0.04 and 0.05, respectively. The annual direct genetic trends were equal to 0.046, 1.336 and 1.619 kg for BW, WW and YW, respectively, corresponding to 0.13, 0.66 and 0.75% of the herd means. By generation, the genetic trends were, in the same order, 0.269, 7.715 and 9.599 kg, respectively. The maternal and total maternal genetic trends were linear and positive. The results showed that the selection criteria used resulted in genetic progress for BW, WW and YW; however, the progress obtained was much smaller than the possible one.

QTL affecting body weight in a candidate region of cattle chromosome 5

The objective of this work was to identify QTLs for liveweight in a candidate region of bovine chromosome 5. Half-sib families from two lines, one traditional and the other new, of Canchim beef cattle (5/8 Charolais + 3/8 Zebu) were genotyped for four microsatellite markers, including the microsatellite in the IGF-1 (insulin-like growth factor-1) promoter region. Significant differences in allele distribution between the two lines were found for three markers. Interval mapping analyses in this region indicated the presence of a QTL controlling birth weight (p < 0.05) and of a QTL influencing breeding value for yearling weight (p < 0.01) in the newer line of the breed. The previously identified interaction between the IGF-1 genotype and genetic group strengthens the hypothesis of a linked QTL rather than an IGF-1 effect on growth traits in the Canchim cattle.

Association of an insulin‐like growth factor 1 gene microsatellite with phenotypic variation and estimated breeding values of growth traits in Canchim cattle

A population of 1398 Canchim (CA) cattle was genotyped to assess the association of an insulin-like growth factor 1 (IGF1) gene microsatellite with phenotypic variation and estimated breeding values of pre-weaning, weaning and post-weaning growth traits. After an initial analysis, the IGF1 genotype only had a significant effect (P < 0.05) on birth weight (BW) and weaning weight adjusted to 240 days (WW240). For these two traits, direct and maternal breeding values were estimated using the restricted maximum likelihood (reml). Two analyses were carried out. In the first (Model I), all fixed effects were fitted. In the second (Model II), the fixed effect of the IGF1 genotype was omitted. The estimated genetic and phenotypic components of variance were similar for every trait in both models. For Model I, estimated direct and maternal heritabilities were 0.26 and 0.16 for BW and 0.23 and 0.14 for WW240 respectively. The genetic and phenotypic correlations between BW and WW240 were 0.38 and 0.38 (Model I) and 0.19 and 0.38 (Model II) respectively. Fifty animals were classified according to their direct and maternal breeding values for both traits. Spearman rank-order correlation between animal rankings in the two models was used to assess the effect of including the IGF1 genotype in the model. Non-significant values from this correlation were indicative of a difference in breeding value rankings between the two approaches. The IGF1 gene was found to be associated with phenotypic variation and breeding values in the early phase of growth.

Correlações genéticas entre características produtivas de fêmeas em um rebanho da raça Canchim

The objective of this study was to estimate the genetic correlations of female body weights at weaning (BWW), 12 (W12) and 18 (W18) months of age with age at first calving (AFC), body weight at first calving (WFC), adult body weight (ABW), and the parameters for mature weight (A) and maturation rate (k) obtained using the Von Bertalanffy model, in a Canchim herd. The restricted maximum likelihood method, with two-trait analyses, was used with models that included the fixed effects [...]The objective of this study was to estimate the genetic correlations of female body weights at weaning (BWW), 12 (W12) and 18 (W18) months of age with age at first calving (AFC), body weight at first calving (WFC), adult body weight (ABW), and the parameters for mature weight (A) and maturation rate (k) obtained using the Von Bertalanffy model, in a Canchim herd. The restricted maximum likelihood method, with two-trait analyses, was used with models that included the fixed effects of contemporary group and the random additive direct effect. For BWW the model also included the covariate age of cow at calving (linear and quadratic effects) and the additive maternal and the permanent environmental random effects, and for ABW the model included also the fixed effect of age of cow. The means of the heritability estimates were equal to: 0.37 (BWW), 0.31 (W12), 0.35 (W18), 0.39 (A), 0.29 (k), 0.13 (AFC), 0.39 (WFC), and 0.42 (ABW). The genetic correlations between BWW and the other traits were: 0.46 (A), 0.02 (k), -0.12 (AFC), 0.66 (WFC) and 0.42 (ABW). With W12 they were equal to 0.39 (A), 0.31 (k), -0.32 (AFC), 0.77 (WFC) and 0.66 (ABW), while with W18 they were equal to 0.21 (A), 0.42 (k), -0.29 (AFC), 0.65 (WFC) and 0.60 (ABW) These results indicate that selection to increase BWW, W12, W18, WFC, ABW, and parameters A and k should result in direct genetic responses, and that selection to increase female body weights from weaning to 18 months of age should result in favorable responses in AFC and parameter k, but in unfavorable correlated responses in WFC and ABW.

Genotype × environment interaction for long-yearling weight in Canchim cattle quantified by reaction norm analysis.

The objective of this study was to investigate the presence of genotype × environment interactions (G×E) for long-yearling weight in Canchim cattle (5/8 Charolais + 3/8 zebu) in Brazil using reaction norms (RN). The hierarchical RN model included the fixed effect of age of the animal (linear coefficient) and random effects of contemporary groups and additive animal genetic intercept and slope of the RN and contemporary group effects as random effects. Contemporary groups as the most elemental representation of management conditions in beef cattle were chosen to represent the environmental covariate of the RN. The deviance information criteria demonstrated that a homoskedastic residual RN model provided a better data fit compared with a heteroskedastic counterpart and with a traditional animal model, which had the worst fit. The environmental gradient for long-yearling weight based on contemporary group effects ranged from -105 to 150 kg. The additive direct variance and heritability estimates increased with increasing environmental gradient from 74.33 ± 22.32 to 1,922.59 ± 258.99 kg(2) and from 0.08 ± 0.02 to 0.68 ± 0.03, respectively. The high genetic correlation (0.90 ± 0.03) between the intercept and the slope of the RN shows that animals with the greatest breeding values best responded to environmental improvement, characterizing scale effect as the source of G×E for long-yearling weight. The phenotypic plasticity demonstrated by the slope of the RN of the animal indicates the possibility to change genotype expression along the environmental gradient through selection. The results demonstrate the importance of accounting for G×E in the genetic evaluation of this population.