Humberto Tonhati

A first generation whole genome RH map of the river buffalo with comparison to domestic cattle

BackgroundThe recently constructed river buffalo whole-genome radiation hybrid panel (BBURH5000) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species.ResultsA total of 3990 markers were typed on the BBURH5000 panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD ≥ 8. The estimated total length of the WG-RH map is 36,933 cR5000. Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score ≥ 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0).ConclusionWe obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome.

Análise da variabilidade genética aditiva de características de crescimento na raça Nelore

The data were obtained from 51 herds to participate in the Nelore Catttle Breeding Program (NCBP) from the states of Goias (GO), Mato Grosso do Sul (MS), Mato Grosso (MT), Minas Gerais (MG), Sao Paulo (SP), Maranhao (MA) and Bahia (BA). Were used to estimative genetic parameters for standardized weights at 120 (P120), 455 (P455) and 550 (550) days of age. Univariate and bivariate analysis were performed by animal model using MTDFREML program. For P120 was used a model that included contemporary groups and cow age at calving as fixed effects, and direct genetic, maternal genetic and permanent environment effects as random effects. For P455 and P550 were utilized the same model but without maternal direct and permanent environment effects. The estimates of heritability direct from univariate analysis were: 0.29, 0.51 and 0.47 for P120, P455 and P550, respectively. In the bivariate analyses the direct heritability values were of high magnitude. The genetic correlation between P120 and P455, P120 and P550 and P455 and P550 were 0.92, 0.93 and 0.96, respectively. The values of the heritability coefficients estimated for the trait P455 and genetic correlation that characteristic with others indicate that the genetic evaluation could be made at the 15 months of age.

Repeatability and heritability of response to superovulation in Holstein cows.

The objective of this study was to estimate the relative effects of genetic and phenotypic factors on the efficacy and efficiency of superovulation for Holstein-Friesian cows reared in Brazil. A database, established by the Associacao Brasileira de Criadores de Bovinos da Raca Holandesa, consisting of a total of 5387 superovulations of 2941 cows distributed over 473 herds and sired by 690 bulls was used for the analysis. The records were analyzed by MTDFREML (Multiple Trait Derivative-Free Restricted Maximum Likelihood), using a repeatability animal model. The fixed effects included in the model were contemporaneous group (veterinarian, herd, year and season of the superovulation); number of semen doses; cow age; and superovulation order. The estimated repeatability of the number of the transferable embryos was low (0.13), and the estimated heritability was 0.03. These results indicate that environmental factors play a critical role in the response of a cow to a superovulation treatment. There is little evidence that future responses to superovulation by individual females can be predicted by previous treatment(s) or that superovulation response is an heritable trait.

Estimação de parâmetros genéticos para peso do nascimento aos 550 dias de idade para animais da raça Tabapuã utilizando-se modelos de regressão aleatória

Data provided by the Brazilian Zebu Breeders Association (ABCZ), consisting of 21,762 records from 4,221 animals of Tabapua cattle, weighted from birth to 550 days of age, were used to estimate covariance functions by random regression models using Legendre polynomials of order two to five. Models included the direct and maternal genetic, animal and maternal permanent environmental random effects and compared by Schwarz´s Bayesian information criteria (BIC) and Akaike´s information criteria (AIC). Both criterions suggested the model including direct genetic, maternal genetic, animal permanent and maternal permanent environmental effects respectively adjusted by cubic, quadratic, fourth order and linear polynomials, and residual variances adjusted by fifth order variance function as the best one to describe the covariance structure of the used database. Direct heritability estimates were higher at the beginning and at the end of the growth trajectory. Maternal heritability estimates increased from birth to 160 days of age and decreased thereafter. In general, genetic correlation estimates decreased as age between weights increased. Efficiency of selection may be improved by using weights of the post weaning period because of their higher genetic variance and heritability estimates.

Test-day milk yield as a selection criterion for dairy buffaloes (Bubalus bubalis Artiodactyla, Bovidae)

Due to the great demand for buffalo milk by-products the interest in technical-scientific information about this species is increasing. Our objective was to propose selection criteria for milk yield in buffaloes based on total milk yield, 305-day milk yield (M305), and test-day milk yield. A total of 3,888 lactations from 1,630 Murrah (Bubalus bubalis) cows recorded between 1987 and 2001, from 10 herds in the State of Sao Paulo, Brazil, were analyzed. Covariance components were obtained using the restricted maximum likelihood method applied to a bivariate animal model. Additive genetic and permanent environmental effects were considered as random, and contemporary group and lactation order as fixed effects. The heritability estimates were 0.22 for total milk yield and 0.19 for M305. For test-day yields, the heritability estimates ranged from 0.12 to 0.30, with the highest values being observed up to the third test month, followed by a decline until the end of lactation. The present results show that test-day milk yield, mainly during the first six months of lactation, could be adopted as a selection criterion to increase total milk yield.

Genetic associations of sexual precocity with growth traits and visual scores of conformation, finishing, and muscling in Nelore cattle.

The objective of this study was to determine the possible use of heifer pregnancy at 16 mo as a selection criterion and its possible genetic associations with hip height, yearling weight, and visual scores of conformation, finishing, and muscling. The data set contained records of 56,458 Nelore yearlings for the traits described above. Covariance components were estimated by bivariate animal models assuming a linear model for hip height, yearling weight and conformation, and finishing and muscling scores, and a nonlinear (threshold) model for heifer pregnancy. Variance components were estimated using Bayesian inference. Flat distributions were used for all (co)variance components and genetic correlations. The first 5,000 rounds were considered as the burn-in period and discarded. The heritability estimate of heifer pregnancy indicates that the trait can be used as a selection criterion. Long-term selection for heifer pregnancy will result in a reduction of animal height. However, selection for increasing yearling weight should be possible in this population of Nelore cattle without having major effects on fertility. Selection for increasing visual scores of conformation, finishing, and muscling will result in small or no response in heifer pregnancy at 16 mo.

Kappa-casein gene study with molecular markers in female buffaloes (Bubalus bubalis)

Caseins comprise make up about 80% of the total protein content of milk and present polymorphism with changes in the amino acid sequence. Within this abundance of proteins, kappa-casein is noteworthy, since it has been associated with differences in milk yield, composition and processing. The objective of this study was to observe the existence of polymorphism in the kappa-casein gene in female buffaloes. For this purpose, blood samples from 115 female buffaloes, collected with vacutainer by needle punctionure of the jugular vein, were used. for genomic DNA extraction was done from blood samples. The PCR-RFLP and SSCP techniques demonstrated that the studied animals were monomorphic for the kappa-casein gene. Only allele B was observed in these animals, which was present in homozygosis. Therefore, it was not possible to quantify the gene action on milk yield and its constituents. The monomorphism observed in the population studied would allow the development of a method to identify mixtures of cow and buffalo milk in mozzarella cheese production, especially because, in cattle, the kappa-casein gene is polymorphic.

Estimativas de tendências e parâmetros genéticos do peso padronizado aos 378 dias de idade, medidas corporais e perímetro escrotal de machos Nelore de Sertãozinho, SP

The objectives of this study were to estimate the genetic trends and also the genetic and phenotypic parameters for body weight at 378 days (W378), body measurements and scrotal circumferences of Nellore males from selected and control populations of the Estacao Experimental de Zootecnia de Sertaozinho (SP), Brazil. The heritability estimates, considering sire and animal model were, respectively, 0.53± 0.12 and 0.36 for W378 days; 0.38±0.11 and 0.58 for hip height; 0.31±0.10 and 0.10 for chest girth; 0.40± 0.11 and 0.13 for body length; 0.39± 0.11 and 0.30 for dorsal line length; 0.33± 0.10 and 0.12 for rump length; 0.08 ± 0.07 and 0.14 for distance between pin bones; 0.23± 0.09 and 0.08 for distance between hip bones and 0.57± 0.13 and 0.44 for scrotal circumference. The highest genetic correlation between W378 and body measurements was found for chest girth (0.86 ± 0.08), and the others ranged from 0.46 to 0.72. Based on the median to high heritability values found for the majority of traits, it is expected to exist a good amount of additive genetic variability controlling their variation. In addition, due to the highest correlation between W378 and most of the traits, it is probable that most part of the genes that control post-weaning weight might control the growth of different regions of animal body. The good values for the genetic correlation and heritability explain the positive genetic trends for direct and secondary traits in the selection for W378.

Assessment of DGAT1 and LEP gene polymorphisms in three Nelore (Bos indicus) lines selected for growth and their relationship with growth and carcass traits.

The aim of this study was to analyze LEP and DGAT1 gene polymorphisms in 3 Nelore lines selected for growth and to evaluate their effects on growth and carcass traits. Traits analyzed were birth, weaning, and yearling weight, rump height, LM area, backfat thickness, and rump fat thickness obtained by ultrasound. Two SNP in the LEP gene [LEP 1620(A/G) and LEP 305(T/C)] and the K232A mutation in the DGAT1 gene were analyzed. The sample consisted of 357 Nelore heifers from 2 lines selected for yearling weight and a control line, established in 1980, at the Estação Experimental de Zootecnia de Sertãozinho (Sertãozinho, Brazil). Three genotypes were obtained for each marker. Differences in allele frequencies among the 3 lines were only observed for the DGAT1 K232A polymorphism, with the frequency of the A allele being greater in the control line than in the selected lines. The DGAT1 K232A mutation was associated only with rump height, whereas LEP 1620(A/G) was associated with weaning weight and LEP 305(T/C) with birth weight and backfat thickness. However, more studies, with larger data sets, are necessary before these makers can be used for marker-assisted selection.

Estimação de parâmetros genéticos para peso em diferentes idades para animais da raça Tabapuã

Weight records of 35.308 Tabapua animals born between 1975 and 2000, made available by the Brazilian Zebu Breeders Association (ABCZ), were used to estimate genetic parameters for growth from birth to 570 days of age. Univariate analyses were used to fit three different models including fixed effects of contemporary group (owner, herd, sex, breeding management, year-month of birth and year-month of weight) and age of calf and age of dam (linear and quadratic) as covariates. Model 1 included only the direct genetic additive random effect; Model 2 considered both direct genetic additive and maternal permanent environmental random effects and Model 3 included the direct genetic additive, maternal, maternal permanent environmental random effects. The likelihood ratio test indicated Model 3 best fitted the data. Heritability estimates for direct genetic effects ranged between 0.08 and 0.26, decreasing after birth along the growth period, but high heritability values were observed at 90, 180 and 345 days of age, and slight changes thereafter. In general, maternal heritability estimates were low, with higher values at the weaning age.