Genomic analysis of genotype-environment interaction in age at first calving of Murrah buffaloes.

Age at first calving (AFC) is a measure of sexual maturity associated with the start of productive life of dairy animals. Additionally, a lower AFC reduces the generation interval and early culling of females. However, AFC has low heritability, making it a trait highly influenced by environmental factors. In this scenario, one way to improve the reproductive performance of buffalo cows is to select robust animals according to estimated breeding value (EBV) using models that include genotype-environment interaction (GEI) with the application of reaction norm models (RNMs). This can be achieved by understanding the genomic basis related to GEI of AFC. Thus, in this study, we aimed to predict EBV considering GEI via the RNM and identify candidate genes related to this component in dairy buffaloes through genome-wide association studies (GWAS). We used 1795 AFC records from three Murrah buffalo herds and formed environmental gradients (EGs) from contemporary group solutions obtained from genetic analysis of 270-day cumulative milk yield. Heritability estimates ranged from 0.15 to 0.39 along the EG. GWAS of the RNM slope parameter identified important genomic regions. The genomic window that explained the highest percentage of genetic variance of the slope (0.67%) was located on BBU1. After functional analysis, five candidate genes were detected, involved in two biological processes. The results suggested the existence of a GEI for AFC in Murrah buffaloes, with reclassification of animals when different environmental conditions were considered. The inclusion of genomic information increased the accuracy of breeding values for the intercept and slope of the reaction norm. GWAS analysis suggested that important genes associated with the AFC reaction norm slope were possibly also involved in biological processes related to lipid metabolism and immunity.

Occurrence of Aflatoxin M1 and Estimate of Dietary Exposure in Cheeses from Organic and Conventional Production Systems.

This study aimed to compare AFM1 occurrence in different cheese types produced by organic and conventional systems; and to evaluate the risk of food exposure to AFM1. A total of 176 commercial cheeses of 17 types were analyzed, 84 of organic and 92 of conventional production. Determination of AFM1 was performed by high- performance liquid chromatography (HPLC), being detected in 30.5% of samples, with 4.8% of organic cheese samples presenting quantifiable AFM1 values between 0.88 and 1.50 µg/kg. On the other hand, 4.3% of conventional cheese samples with values between 0.79 and 6.70 µg/kg. Two conventional cheese samples were above the limit of AFM1 allowed for cheeses by the Brazilian legislation. No statistical difference were found between organic and conventional cheeses regarding the occurrence (p = 0.1780) and concentration of AFM1 (p = 0.1810), according to the Chi-square and the T test, respectively. Estimated daily intake (EDI) and hazard index (HI) of dietary exposure to AFM1 were 0.26 ng/kg/day and 1.28 ng/kg/day, respectively, for conventional cheese samples, and 0.09 ng/kg/day and 0.47 ng/kg/day for organic samples, with no statistical difference for EDI (p = 0.1729) and HI (p = 0.1802) between the two production systems. Comparison between several cheese types from conventional and organic systems indicated that AFM1 is an obstacle to dairy production. Control and prevention of AFM1 contamination, as well as detoxification methods in the final products, are necessary. In the case of organic products, additional research is needed in order to determine which control and detoxification methods should be allowed in this production system.

Analysis of the population structure of buffaloes in Brazil.

The aim of this study was to evaluate the population structure of Brazilian buffaloes using of pedigree information. The pedigree used in the analyses included records of 16,915 animals. The population parameters were obtained through the ENDOG software. The estimates of mean of inbreeding (F) and average relatedness (AR) coefficients were 3.22% and 5.99%, respectively. The average generation interval was 6.39 years. The effective number of founders and ancestors was 28 and 22, respectively. In this study, we concluded that the selection of individuals with lower AR is necessary to avoid an increase in matings between inbreeding individuals in this population, in order to obtain greater genetic gain by selection.

Milk Potential of Pantaneira Cows, a Local Breed, at Organic System.

Pantaneiro cattle (Bos taurus taurus) is a breed locally adapted to the Brazilian Pantanal. Local breeds are essential for the quality production of organic systems based on planned grazing practices, because of their results in resilient and productive ecosystems, enhancing biodiversity. This study aimed to evaluate the performance of Pantaneira primiparous cows, and systems with reduced use of concentrate, simulating organic production conditions. Five animals, with an average body weight of 396.2 ± 43.5 kg, were kept in individual continuous grazing regimes and supplemented with different concentrate levels (1.2%, 0.9%, 0.6%, 0.3%, and 0.0% of body weight). The animals were allocated at random in a 5 × 5 Latin square design repeated twice during the study time. The cows had a low dry matter and nutrient intake with a reduction in concentrate level, with improvement in neutral detergent fiber digestibility and a reduction in total nutrient digestibility. No changes were observed in plasma glucose levels or urea excretion, but the plasma urea nitrogen decreased with reductions in concentrate levels. There was a reduction in milk yield, but the energy-corrected milk was not affected by the reduction in concentrate levels; furthermore, the milk yield efficiency was not affected. The milk fat content improved with the reduction in concentrate levels. The Pantaneira breed has the genetic potential for the maintenance of competitive production and quality in organic systems.

Genome-wide association studies for growth traits in buffaloes using the single step genomic BLUP.

Growth traits are important for the profitability of buffalo breeding systems, since in general, these animals are raised both for meat and milk. In this study, the single-step genomic BLUP method was employed to prospect the genomic regions' associated with weight at standard ages of 100, 210, 365, and 550 days in a buffalo population, aiming to identify genes with stronger expression for those characteristics. We found 6, 1, 2, and 5 SNPs significantly associated (p value < 10-5) with weight at 100, 210, 365, and 550 days of age, respectively, where those SNPs respectively explained 0.164, 0.040, 0.044, and 0.213% of the additive variance of each trait. SNP AX-85099682 (BBU24) was significant for weight at 100, 210, and 365 days, indicating the existence of a possible QTL affecting the initial growth rate of buffaloes. All told, eight genes (CBLB, TRNAG-UCC, GADD45B, LOC112583811, MGAT4C, KCNMA1, SLC5A2, and TGFB1I1) were identified as candidates for the growth traits of buffaloes. However, molecular and gene expression studies are necessary to validate these genes for subsequent use in programs for genetic improvement of the species.

Genetic parameters for milk, fat and protein yields in Murrah buffaloes (Bubalus bubalis Artiodactyla, Bovidae).

The objective of the present study was to estimate genetic parameters for test-day milk, fat and protein yields and 305-day-yields in Murrah buffaloes. 4,757 complete lactations of Murrah buffaloes were analyzed. Co-variance components were estimated by the restricted maximum likelihood method. The models included additive direct genetic and permanent environmental effects as random effects, and the fixed effects of contemporary group, milking number and age of the cow at calving as linear and quadratic covariables. Contemporary groups were defined by herd-year-month of test for test-day yields and by herd-year-season of calving for 305-day yields. The heritability estimates obtained by two-trait analysis ranged from 0.15 to 0.24 for milk, 0.16 to 0.23 for protein and 0.13 to 0.22 for fat, yields. Genetic and phenotypic correlations were all positive. The observed population additive genetic variation indicated that selection might be an effective tool in changing population means in milk, fat and protein yields.