Genomic study of the resilience of buffalo cows to a negative energy balance.

The research article was carried out with the objective of studying the genetic variation on the resilience of buffaloes to negative energy balance-NEB (measured by changes in body weight in early lactation)-as well as investigating genomic regions of interest for this trait. A model of reaction norms was used, considering milk production as the trait to be analyzed and solutions of the contemporary groups to weight changes as environmental gradient. In this methodology, the genetic value of the slope represents the measure of resilience of the animals. After the estimation step, a genome-wide association analysis was performed for the slope of the reaction norms model, to obtain a list of windows and associated genes. The heritability estimates for milk production over the resilience gradient ranged from 0.13 to 0.28, with lower values in the intermediate environmental groups. Regarding the productive resilience of dairy buffalo cows to NEB, the genomic windows with the highest contribution to the genetic variance were detected on chromosomes BBU 1, 2, 3, 4, 9, 12, 19, and 21. A functional analysis of the genes described in the selected windows indicated association with metabolic routes related to growth and immunity of the animals, with an emphasis on the STAT6 gene. The results presented indicate that there is for this trait genetic variation to be used as selection criteria, in addition to genomic regions that can increase the precision of the selection.

Prediction of genomic breeding values of milk traits in Brazilian Saanen goats.

The study's objective was to compare the genomic prediction ability methods for the traits milk yield, milk composition and somatic cell count of Saanen Brazilian goats. Nine hundred forty goats, genotyped with an Axiom_OviCap (Caprine) panel, Affimetrix customized array with 62,557 single nucleotide polymorphisms (SNPs), were used for the genomic selection analyses. The genomic methods studied to estimate the effects of SNPs and direct genomic values (DGV) were as follows: (a) genomic BLUP (GBLUP), (b) Bayes Cπ and (c) Bayesian Lasso (BLASSO). Estimated breeding values (EBV) and deregressed estimated breeding values (dEBV) were used as response variables for the genomic predictions. The prediction ability was assessed by Pearson's correlation between DGV and response variables (EBV and dEBV). Regression coefficients of the response variables on the DGV were obtained to verify if the genomic predictions were biased. In addition, the mean square error of prediction (MSE) was used as a measure of verification of model fit to the data. The means of prediction accuracy, when EBV was used as a response variable, were 0.68, 0.68 and 0.67 for GBLUP, Bayes Cπ and BLASSO, respectively. With dEBV, the mean prediction accuracy was 0.50 for all models. The averages of the EBV regression coefficients on DGV were 1.08 for all models (GBLUP, Bayes Cπ and BLASSO), higher than those obtained for the regression coefficient of dEBV on DGV, which presented values of 1.05, 1.05 and 1.08 for GBLUP, Bayes Cπ and BLASSO, respectively. None of the methods stood out in terms of prediction ability; however, the GBLUP method was the most appropriate for estimating the DGV, in a slightly more reliable and less biased way, besides presenting the lowest computational cost. In the context of the present study, EBV was the preferred response variables considering the genomic prediction accuracy despite dEBV also presented lower bias.

Polymorphisms in TLR4 Gene Associated With Somatic Cell Score in Water Buffaloes (Bubalus bubalis).

Considering the importance of the diseases affecting the productive performance of animals in the dairy industry worldwide, it is necessary to implement tools that help to control and limit the occurrence of such diseases. As the increased somatic cell counts (SCC) are a direct expression of the inflammatory process, they are candidates to become the usual parameter for assessing udder health regarding milk quality and for monitoring mastitis incidences. Toll-Like Receptors are membrane proteins that play a key role in immunity, recognizing pathogens and, subsequently, activating immune responses. The present study was conducted to identify single nucleotide polymorphisms in the TLR4 gene of buffaloes and to analyze its associations with somatic cell counts. DNA samples of 120 Murrah buffaloes were used. The whole coding region of the TLR4 gene was amplified by polymerase chain reaction reactions and sequenced for polymorphism scanning. A total of 13 polymorphisms were identified for the sequenced regions of the TLR4, most of which are in the coding region. The association with the somatic cell score was highly significant (p < 0.001) for all identified polymorphisms of TLR4 gene (g.54621T>A, g.54429G>T, g.54407T>A, g.46616C>A, g.46613T>G, g.46612A>G, g.46611C>A, g.46609T>G, g.46541C>G, g.46526C>A, g.46516T>C, g.46376C>T, g.46372T>C). Therefore, it is suggested that the markers of the TLR4 gene can be used as molecular markers for mastitis resistance in buffaloes, due to their association with somatic cell counts.

Identification of genomic regions related to age at first calving and first calving interval in water buffalo using single-step GBLUP.

In Brazil, water buffaloes have been used to produce milk for mozzarella cheese production. Consequently, the main selection criterion applied for the buffalo genetic improvement is the estimated mozzarella yield as a function of milk, fat and protein production. However, given the importance of reproductive traits in production systems, this study aimed to use techniques for identifying genomic regions that affect the age at first calving (AFC) and first calving interval (FCI) in buffalo cows and to select candidate genes for the identification of QTL and gene expression studies. The single-step GBLUP method was used for the identification of genomic regions. Windows of 1 Mb containing single-nucleotide polymorphisms were constructed and the 10 windows that explained the greatest proportion of genetic variance were considered candidate regions for each trait. Genes present into the selected windows were identified using the UOA_WB_1 assembly as the reference, and their ontology was defined with the Panther tool. Candidate regions for both traits were identified on BBU 3, 12, 21 and 22; for AFC, candidates were detected on BBU 6, 7, 8, 9 and 15 and for first calving interval on BBU 4, 14 and 19. This study identified regions with great contribution to the additive genetic variance of age at first calving and first calving interval in the population of buffalo cows studied. The ROCK2, PMVK, ADCY2, MAP2K6, BMP10 and GFPT1 genes are main candidates for reproductive traits in water dairy buffaloes, and these results may have future applications in animal breeding programs or in gene expression studies of the species.

Genome-wide association study applied to type traits related to milk yield in water buffaloes (Bubalus bubalis).

This research aimed to estimate genetic parameters for milk yield and type traits [withers height (WH), croup height (CH), body length (BL), croup length (CL), iliac width (ILW), ischial width (ISW), and thoracic circumference] in Murrah buffaloes and to identify genomic regions related to type traits by applying a single-step genome-wide association study. Data used to estimate the genetic parameters consisted of 601 records of milk yield in the first lactation and the aforementioned type traits. For the single-step genome-wide association study, 322 samples genotyped with a 90K Axiom Buffalo Genotyping array (Thermo Fisher Scientific, Santa Clara, CA) were used. Bivariate analysis revealed that heritability for milk yield (kg) at 305 d was 0.31 ± 0.11, whereas it ranged from 0.22 ± 0.07 to 0.34 ± 0.09 for the studied conformation traits. Based on the percentages of genetic variance explained by windows of 10 markers, there were 16 genomic regions explaining more than 0.5% of the variance for WH, CH, BL, CL, ILW, ISW, and thoracic circumference. Between those regions, 4 were associated with more than 1 trait, suggesting pleiotropic roles for some genes of Bos taurus autosome (BTA) 12 on CL and WH, BTA13 on ISW and ILW, BTA23 on CH and BL, and BTA28 on ISW and BL. Most of these regions coincide with known quantitative trait loci for milk traits. Thus, further studies based on sequence data will help to validate the association of this region with type traits and likely identify the causal mutations.

Expression profile of the CSF3 and LPO genes in milk from buffalo (Bubalus bubalis) with and without mastitis.

This study compared the expression profile of the candidate genes, CSF3 and LPO, by investigating the immune response mechanisms involved in the phenotype of resistance and susceptibility to mastitis of healthy and infected buffaloes. The Granulocyte Colony Stimulating Factor 3 (CSF3) and Lactoperoxidase (LPO) genes expression profiles were determined in 24 milk samples from buffaloes with (N = 12) and without (N = 12) mastitis, using the quantitative real-time PCR (qRT-PCR) technique. CSF3 and LPO expressions were 5.14 (P = 0.001) and 2.41 (P = 0.097) times higher in animals with mastitis compared to healthy animals, respectively, evidencing a trend toward different expressions of this gene in the studied groups. Our finding suggests that LPO and CSF3 genes are an important defense mechanism against mastitis in dairy buffaloes, and may be putative genes for selecting healthier animals in buffalo breeding programs.