Multiple-trait genomic evaluation for milk yield and milk quality traits using genomic and phenotypic data in buffalo in Brazil

The use of markers distributed all long the genome may increase the accuracy of the predicted additive genetic value of young animals that are candidates to be selected as reproducers. In commercial herds, due to the cost of genotyping, only some animals are genotyped and procedures, divided in two or three steps, are done in order to include these genomic data in genetic evaluation. However, genomic evaluation may be calculated using one unified step that combines phenotypic data, pedigree and genomics. The aim of the study was to compare a multiple-trait model using only pedigree information with another using pedigree and genomic data. In this study, 9,318 lactations from 3061 buffaloes were used, 384 buffaloes were genotyped using a Illumina bovine chip (Illumina Infinium (R) bovineHD BeadChip). Seven traits were analyzed milk yield (MY), fat yield (FY), protein yield (PY), lactose yield (LY), fat percentage (F%), protein percentage (P%) and somatic cell score (SCSt). Two analyses were done: one using phenotypic and pedigree information (matrix A) and in the other using a matrix based in pedigree and genomic information (one step, matrix H). The (co) variance components were estimated using multiple-trait analysis by Bayesian inference method, applying an animal model, through Gibbs sampling. The model included the fixed effects of contemporary groups (herd-year-calving season), number of milking (2 levels), and age of buffalo at calving as (co) variable (quadratic and linear effect). The additive genetic, permanent environmental, and residual effects were included as random effects in the model. The heritability estimates using matrix A were 0.25, 0.22, 0.26, 0.17, 0.37, 0.42 and 0.26 and using matrix H were 0.25, 0.24, 0.26, 0.18, 0.38, 0.46 and 0.26 for MY, FY, PY, LY, % F, % P and SCCt, respectively. The estimates of the additive genetic effect for the traits were similar in both analyses, but the accuracy were bigger using matrix H (superior to 15% for traits studied). The heritability estimates were moderated indicating genetic gain under selection. The use of genomic information in the analyses increases the accuracy. It permits a better estimation of the additive genetic value of the animals.

Occurrence of Staphylococcus aureus in raw milk produced in dairy farms in São Paulo state, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Population structure and effects of inbreeding on milk yield and quality of Murrah buffaloes

To provide data for conservation, selection, and expansion programs of buffalo herds, this study evaluated the history of a population of Murrah buffaloes based on population structure and the effect of inbreeding on accumulated 305-d milk yield (MY), fat yield (FY), protein yield (PY), mozzarella production (MProd), and somatic cell score (SCS). The usefulness of including the individual inbreeding coefficient (F) or individual increase in inbreeding coefficient (Delta F) in the model to describe inbreeding depression was evaluated. Pedigree information from 8,054 animals born between 1976 and 2008 and 4,497 lactation records obtained from 12 herds were used. The realized effective population size was 40.10 +/- 1.27, and the mean F of the entire population was 2.14%. The ratio between the number of founders and ancestors demonstrated the existence of a bottleneck in the pedigree of this population, which may contribute to a reduction of genetic diversity. The effect of F on MY, FY, PY, MProd, and SCS was -1.005 kg, -0.299 kg, -0.246 kg, -1.201 kg, and -0.002 units, and the effect of Delta F transformed to equivalent F (%) for a mean of 2.57 equivalent generations was -4.287 kg, -0.581 kg, -0.383 kg, -2.001 kg, and -0.007 units, respectively. The inbreeding depression observed may have important economic repercussions for production systems. The Delta F can be considered the better of the two indicators of inbreeding depression due to its properties that prevent underestimation of this effect. A designed mating system to avoid inbreeding may be applied to this population to maintain genetic diversity.

Genetic parameter estimates for buffalo milk yield, milk quality and mozzarella production and Bayesian inference analysis of their relationships

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Effect of lactation length adjustment procedures on genetic parameter estimates for buffalo milk yield

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Risk factors relating to helminth infections in cows during the peripartum

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Buffalos milk yield analysis using random regression models

Data comprising 1,719 milk yield records from 357 females (predominantly Murrah breed), daughters of 110 sires, with births from 1974 to 2004, obtained from the Programa de Melhoramento Genetic de Bubalinos (PROMEBUL) and from records of EMBRAPA Amazonia Oriental - EAO herd, located in Belem, Para, Brazil, were used to compare random regression models for estimating variance components and predicting breeding values of the sires. The data were analyzed by different models using the Legendre's polynomial functions from second to fourth orders. The random regression models included the effects of herd-year, month of parity date of the control; regression coefficients for age of females (in order to describe the fixed part of the lactation curve) and random regression coefficients related to the direct genetic and permanent environment effects. The comparisons among the models were based on the Akaike Infromation Criterion. The random effects regression model using third order Legendre's polynomials with four classes of the environmental effect were the one that best described the additive genetic variation in milk yield. The heritability estimates varied from 0.08 to 0.40. The genetic correlation between milk yields in younger ages was close to the unit, but in older ages it was low.

Buffalo milk production in brazil and colombia: Genotype by environment interaction

The objective of this study was to determine whether there is a genotype by environment interaction (GxE) for dairy buffaloes in Brazil and Colombia. The (co)variance components were estimated by using a bi-trait repeatability animal model with the REML method. Each trait consisted in the milk yield obtained in both countries. Contemporary group (herd, year and season of parity) and age at parity (linear and quadratic covariate) fixed effects, along with the additive genetic, permanent environment, and the residual random effects were included in the model. Genetic, permanent environmental and residual variance and heritabilities were different for both countries. The genetic correlations for milk yield between Brazil and Colombia were low (between 0.10 and 0.13), indicating a GxE interaction between both countries. Knowing that this interaction influences the genetic progress of buffalo populations in Brazil and Colombia, we recommend choosing sires tested in the country they will be used, along with conducting joint genetic evaluations that consider GxE interaction effects.

Genetic parameters for milk yield, lactation length and calving intervals of murrah buffaloes from brazil

The major objective of this study was to estimate heritability and genetic correlations between milk yield (MY) and calving interval (CI) and lactation length (LL) in Murrah buffaloes using Bayesian inference. The database used belongs to the genetic improvement program of four buffalo herds from Brazil. To obtain the estimates of variance and covariance, bivariate analyses were performed with the Gibbs sampler, using the program MTGSAM. The heritability coefficient estimates were 0.28, 0.03 and 0.15 for MY, CI and LL, respectively. The genetic correlations between MY and LL was moderate (0.48). However, the genetic correlation between MY and CI showed large HPD regions (highest posterior density interval). Milk yield was the only trait with clear potential for genetic improvement by direct mass selection. The genetic correlation between MY and LL indicates that indirect selection using milk yield is a potentially beneficialstrategy.Theinterpretation of the estimated genetic correlation between MY and CI is difficult and could be spurious. ©2013 Sociedade Brasileira de Zootecnia.

Genetic Parameters for Milk Yield and Lactation Length of Crossbred Buffaloes from Brazil by Bayesian Inference

The objective of the study was to estimate heritability and repeatability for milk yield (MY) and lactation length (LL) in buffaloes using Bayesian inference. The Brazilian genetic improvement program of buffalo provided the data that included 628 females, from four herds, born between 1980 and 2003. In order to obtain the estimates of variance, univariate analyses were performed with the Gibbs sampler, using the MTGSAM software. The model for MY and LL included direct genetic additive and permanent environment as random effects, and contemporary groups, milking frequency and calving number as fixed effects. The convergence diagnosis was performed with the Geweke method using an algorithm implemented in R software through the package Bayesian Output Analysis. Average for milk yield and lactation length was 1,546.1 +/- 483.8 kg and 252.3 +/- 42.5 days, respectively. The heritability coefficients were 0.31 (mode), 0.35 (mean) and 0.34 (median) for MY and 0.11 (mode), 0.10 (mean) and 0.10 (median) for LL. The repeatability coefficient (mode) were 0.50 and 0.15 for MY and LL, respectively. Milk yield is the only trait with clear potential for genetic improvement by direct genetic selection. The repeatability for MY indicates that selection based on the first lactation could contribute for an improvement in this trait.

Diversity of Staphylococcus species and prevalence of enterotoxin genes isolated from milk of healthy cows and cows with subclinical mastitis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Methicillin-resistant Staphylococcus aureus of lineage ST398 as cause of mastitis in cows

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Effects of rumen-protected choline supplementation on metabolic and performance responses of transition dairy cows

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Correlação entre o California Mastitis Test (CMT) e a Contagem de Células Somáticas (CCS) do leite de búfalas Murrah

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genetic parameters for body weight, carcass chemical composition and yield in a broiler-layer cross developed for QTL mapping

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)