Genetic parameters, genomic prediction, and identification of regulatory regions located on chromosome 14 for weight traits in Nellore cattle.

This study aimed to investigate functional variants in chromosome 14 (BTA14) and its impact in genomic selection for birth weight (BW), weaning weight (WW), and yearling weight (YW) in Nellore cattle. Genetic parameter estimation and the weighted single-step genomic best linear unbiased prediction (WssGBLUP) analyses were performed. Direct additive heritability estimates were high for WW and YW, and moderate for BW. Trait-associated variants distributed across multiple regions on BTA14 were observed in the weighted single-step genome-wide association studies (WssGWAS) results, implying a polygenic genetic architecture for weight in different ages. Several genes have been found in association with the weight traits, including the CUB And Sushi multiple domains 3 (CSMD3), thyroglobulin (TG), and diacylglycerol O-acyltransferase 1 (DGAT1) genes. The variance explained per SNP was higher in six functional classes of gene regulatory regions (5UTR, CpG islands, downstream, upstream, long non-coding RNA, and transcription factor binding sites (TFBS)), highlighting their importance for weight traits in Nellore cattle. A marginal increase in accuracy was observed when the selected functional variants (SV) information was considered in the WssGBLUP method, probably because of the small number of SV available on BTA14. The identified genes, pathways, and functions contribute to a better understanding of the genetic and physiological mechanisms regulating weight traits in the Nellore breed.

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.

Signatures of selection in Nelore cattle revealed by whole-genome sequencing data.

Nelore cattle breed was farmed worldwide due to its economic importance in the beef market and adaptation to the tropics. In Brazil, purebred Nelore animals (PO) receive a certificate from the breeders' association based on the animal's genealogy and morphological characterization. The top 20 to 30% of the superior animals are eligible to receive the Special Certificate of Identification and Production (CEIP), meaning animals from this category were selected and evaluated in a breeding program to improve economically important traits. We used whole-genome sequencing and approaches based on haplotype differentiation and allelic differentiation to detect regions of selection signatures in Nelore cattle by comparing animals from PO and CEIP categories. From a total of 150 animals, a hierarchical clustering analysis was performed to choose the more unrelated animals from each category (16 PO and 40 CEIP). The hapFLK statistic was performed, and extensions of hapFLK values were investigated considering continuous regions with significant q-values. The Weir and Cockerham's Fst estimator (wcFst) was computed using the GPAT++ software library. The total of 82,326 SNPs with hapFLK values passed the FDR control (q-value<0.05), and 718 segments were target as signatures of selection. A total of 1713 highly differentiated genomic regions were identified based on the segmentFst approach. The signatures of selection were spread across the genome. Annotation of overlapping selection signature regions between the two methods revealed 118 genes in common. A variant located within the 3' region of the BOLA-DRB3 gene was found as a promising candidate polymorphism. Within genomic regions that deserves attention, we found genes previously associated with adaptation to tropical environments (HELB), growth and navel size (HMGA2), fat deposition and domestication (IRAK3), and feed efficiency and postmortem carcass traits (GABRG3). The genes BOLA-DQA2, BOLA-DQB, BOLA-DQA5, BOLA-DQA1, BOLA-DRB3, ENSBTAG00000038397 on chromosome 23 are part of the Bovine Major Histocompatibility Complex (MHC) Class II gene family, representing good candidates for immune response and adaptation to tropical conditions. The BoLA family genes and the interaction of ROBO1 with SLIT genes appeared in the enrichment results. Genomic regions located in intronic regions were also identified and might play a regulatory role in traits under selection in PO and CEIP subpopulations. The regions here identified contribute to our knowledge regarding genes and variants that have an important role in complex traits selected in this breed.

Natural levels of Rhipicephalus microplus infestation and Anaplasma marginale infection in Angus and Ultrablack calves.

Infections by Anaplasma marginale and infestations by Rhipicephalus microplus occur endemically in Brazil, representing an obstacle to expanding the use of taurine breeds, which are more susceptible. In this study, the levels of infection by A. marginale and infestation by R. microplus were monitored in 31 calves that were either purebred or had a high degree of taurine blood: 17 Angus (100% taurine) and 14 Ultrablack (ca. 82% taurine and 18% Zebu). The animals were evaluated on 13 occasions at 12-day intervals. The levels of A. marginale infection were determined by quantification of DNA copy number (CN) by qPCR, and ticks were monitored by two methods: counting adult females (≥ 4.5 mm) and scoring the level of tick infestation considering all visible instars in the animals' bodies. No significant effects were observed between the means of CN of A. marginale, tick counts and scores among Angus and Ultrablack animals. The repeatability estimates for CN of A. marginale, tick counts and tick scores were 0.53, 0.12 and 0.16, respectively. The correlations between CN and tick counts and scores were close to zero, whereas the correlations between tick assessment methods were 0.57. The absence of differences between the two genetic groups indicates, under the conditions of the present study, that the low degree of Zebu blood did not influence the levels of infection by A. marginale or infestation by R. microplus. The results also suggest that the evaluation of the levels of infestation by ticks using scores can provide information closer to the real infestation rate considering that it uses all the visible instars of the parasites.

Estimation of genetic parameters for the tick and hemoparasite burden in Angus cattle.

The study was conducted with the objective of estimating genetic and phenotypic parameters for tick (CRM) and Babesia bigemina (IBBi), Babesia bovis (IBBo), and Anaplasma marginale (IAM) burden in Angus female breed in Brazil. The sample group was composed of Angus females raised in herds located in a region of endemic instability for cattle tick fever in the state of Rio Grande Sul (RS), Brazil. The variance components were estimated using Bayesian inference and Gibbs sampling algorithm, considering a multi-trait animal model. Heritability estimates showed values of low magnitude, ranging from 0.03 (IBBo) to 0.16 (CRM), while repeatability estimates ranged between 0.07 (IBBo) and 0.21 (CRM). Regarding the genetic correlation estimates, the values showed low (-0.01 for IBBo × IAM) to moderate (0.55 between IBBi × IAM) magnitudes. The results indicate that it is possible to use tick count and hemoparasite infection levels as selection criteria, with small genetic gains.

How long does the mRNA remains stable in untreated whole bovine blood?

BACKGROUND: High quality and quantity of messenger RNA (mRNA) are required for accuracy of gene expression studies and other RNA-based downstream applications. Since RNA is considered a labile macromolecular prone to degradation, which may result in falsely altered gene expression patterns, several commercial stabilizing reagents have been developed aiming to keep RNA stable for long period. However, for studies involving large number of experimental samples, the high costs related to these specific reagents may constitute a barrier. METHODS AND RESULTS: In this context the present study was designed aiming to evaluate the stability of mRNA in whole bovine blood collected in EDTA tubes during storage at common fridge (4 °C). Whole blood samples were collected from six Holstein calves and submitted to RNA extraction in each different interval: immediately after blood sampling (< 2 h), at 1-day post-sampling (dps), 2 dps, 3 dps, 7 dps and 14dps intervals. RNA integrity and purity were evaluated, and RT-qPCR assays were run using seven different genes (B2M, ACTB, PPIA, GAPDH, YWHAZ, CD4 and IFN-γ) aiming to evaluate the presence of altered gene transcription during storage. All extracted RNA samples presented high purity, while optimal integrity and unaltered gene expression were observed in whole experimental group up to 3 days of storage. CONCLUSION: Bovine blood RNA remained stable in K3EDTA tubes for 3 days stored at common fridge and can be successfully and accurately used for gene expression studies.

Selection effect for growth traits on energy requirements in beef Nelore steers.

Growth data of 77,372 Nelore steers were used to estimate the selection effect on energy requirements considering two beef production systems: cow-calf and slaughter cycles. All the animals had measures from 120 days to 7 years old. The parameters necessary to evaluate the selection effect on energy requirements were obtained by random regression analysis using Legendre polynomials. The models included additive direct and maternal effects, and animal and maternal permanent environmental effects as random terms. Contemporary group and dam age at calving (linear and quadratic effect) were included as fixed effects, and orthogonal Legendre polynomials of animal age (cubic regression) were considered random covariables. The coefficients from the model M3353_5 were used to calculate the genetic gains necessary to predict the increase in phenotypes. The selection was simulated for body weight (BW) and weight gain (WG) at different ages and energy requirements were calculated using NRC equations. The cost of feed was calculated for a cow-calf and slaughter cycle of production considering a system of Brachiaria decumbens pasture without supplementation. In slaughter system, the selection for weight of 365 days of age is the best option. In cow-calf systems, the selection W120 is the best choice.

Resting egg banks can facilitate recovery of zooplankton communities after short exposure to glyphosate.

We assessed the short-term viability and recovery of zooplankton communities after exposure to glyphosate (active ingredient-a.i.). We conducted a hatching experiment in two steps: Step 1-natural lake sediments containing resting egg banks were placed into individual trays and exposed to a solution medium of glyphosate at three different treatments (LD = Values below the detection limits, LD < 0.05, 0.44, and 0.89 mg a.i./L) for 14 days; and Step 2-we replaced the exposure solution of glyphosate with distilled freshwater, keeping them all trays under freshwater conditions for another 14 day. The results from Step 1 showed significant effects of glyphosate on the emergence patterns of resting eggs, with a reduction in hatching of rotifers, mainly at concentrations of 0.44 and 0.89 mg a.i./L. On the other hand, the results from Step 2 showed an increase in the emergence of viable eggs for rotifers after restoration of freshwater conditions in all treatments; there was no effect for total zooplankton and microcrustaceans. These findings suggest that (i) glyphosate may, effectively, impair zooplankton hatching from resting egg banks; (ii) the magnitude of the negative effects depends on the the zooplanktonic group considered; and (iii) the restoration of freshwater conditions may, in some way, allow the recovery of the zooplankton community from viable egg banks. Our results can be useful in predicting the influence of glyphosate on the distribution patterns of freshwater zooplankton, which can represent vital information for environmental managers.

Comparison of methods for predicting genomic breeding values for growth traits in Nellore cattle.

The objective of this study was to evaluate the accuracy of genomic predictions of growth traits in Nellore cattle. Data from 5064 animals belonging to farms that participate in the Conexão DeltaGen and PAINT breeding programs were used. Genotyping was performed with the Illumina BovineHD BeadChip (777,962 SNPs). After quality control of the genomic data, 412,993 SNPs were used. Deregressed EBVs (DEBVs) were calculated using the estimated breeding values (EBVs) and accuracies of birth weight (BW), weight gain from birth to weaning (GBW), postweaning weight gain (PWG), yearling height (YH), and cow weight (CW) provided by GenSys. Three models were used to estimate marker effects: genomic best linear unbiased prediction (GBLUP), BayesCπ, and improved Bayesian least absolute shrinkage and selection operator (IBLASSO). The prediction ability of genomic estimated breeding value (GEBVs) was estimated by the average Pearson correlation between DEBVs and GEBVs, predicted with the different methodologies in the validation populations. The regression coefficients of DEBVs on GEBVs in the validation population were calculated and used as indicators of prediction bias of GEBV. In general, the Bayesian methods provided slightly more accurate predictions of genomic breeding values than GBLUP. The BayesCπ and IBLASSO were similar for all traits (BW, GBW, PWG, and YH), except for CW. Thus, there does not seem to be a more suitable method for the estimation of SNP effects and genomic breeding values. Bayesian regression models are of interest for future applications of genomic selection in this population, but further improvements are needed to reduce deflation of their predictions.

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.

Correlations and repeatability between Babesia spp. infection levels using two dairy cattle breeding systems.

Babesia bovis and Babesia bigemina are tick-transmitted piroplasms that cause severe damage to the livestock industry in tropical regions of the world. Recent studies demonstrated differences in infection levels of these haemoparasites among bovine breeds and variation between individual cows regarding resistance to these diseases. This study aimed to estimate the repeatability and correlations between B. bovis and B. bigemina using two cattle breeding systems, an individual system (IS) and a collective paddock system (CPS). All animals were Holstein breed, and the levels of B. bovis and B. bigemina in blood samples were estimated by quantitative polymerase chain reaction (qPCR). The estimated correlations for the B. bigemina and B. bovis DNA copy number for IS and CPS were moderate and high, respectively, whereas repeatability estimates for both systems and both Babesia species were moderate. Although we cannot infer that the type of rearing system directly influenced the correlation and repeatability coefficients, it appears that the bovine parasitemia burden may be dependent on (or determine) the parasitemia burden on ticks because the bovines remained in the same place for a longer time in both systems. Thus, the babesiosis infection levels of the ticks may have been uniform, a phenomenon that also ensures greater uniformity in cattle infection. This factor may have favored the occurrence of infected ticks leading to higher repeatability estimates and correlations. Our study confirms high variability in resistance/susceptibility between breeds, and the high correlations found may be linked to this characteristic and the most intensive breeding type of dairy cattle. Besides, under the present study conditions, the estimated correlations suggest that measuring an infection level of one Babesia species can predict the level of infection of the other.

Population structure of Simmental beef cattle using pedigree analysis.

The purpose of this study was to estimate parameters related to the population structure and genetic diversity in the Simental breed based on the pedigree information of 77,553 animals. The individual coefficients of inbreeding and average relatedness, number of complete generations, coefficient of change of inbreeding, effective size, effective number of founders, number of ancestors and generation interval were calculated. Using the Simmental cattle information, the mean inbreeding and average relatedness coefficients were 1.49% and 0.99%, respectively. The effective number of founders and ancestors was 163 and 132, respectively, and the effective population size was 48.03. Despite the relatively small inbreeding coefficient, some of the estimated population parameters indicated the need to adopt measures to maintain the genetic variability of the population.

Development of a loop-mediated isothermal amplification (LAMP) assay for the detection of Anaplasma marginale.

Parasitemia generated by Anaplasma marginale causes significant losses in the cattle industry. A major constraint to the effective control and management of anaplasmosis in livestock is the lack of a rapid and reliable diagnostic test to identify the parasite and allow for immediate therapy. In the present study, we developed a novel DNA-based assay for the detection of A. marginale in bovine blood samples, using loop-mediated isothermal amplification (LAMP). DNA from six cattle and hemoparasite samples (Babesia bovis, Babesia bigemina, Anaplasma centrale and A. marginale) were tested for specificity, sensitivity and cross-reactions. The developed LAMP procedures were also confirmed and compared with the qPCR method. The same gene sequence (major surface protein 1b, msp1b) of A. marginale was used to design a set of primers for the LAMP and qPCR assays. The results showed that LAMP is specific, as no positive signal was observed for the other tested hemoparasites. However, the sensitivity of the qPCR assay was ten times higher than LAMP. Our findings indicate that this LAMP method has a good sensitivity and high specificity for the detection of A. marginale and may have a potential application in the detection and differentiation of bovine anaplasmosis.

Comparative evaluation of DNA extraction kit, matrix sample and qPCR assays for bovine babesiosis monitoring.

Bovine babesiosis caused by protozoan parasites Babesia bovis and B. bigemina is one of the most important causes of losses for the livestock industry in tropical and subtropical regions of the world. Therefore, highly sensitive and specific tools for these hemoparasites detection and monitoring are required, especially in carrier animals, in which low parasite levels were usually present. In this context, qPCR assays have been successfully and fairly used in last years. Aiming to improve the performance of Babesia levels monitoring by qPCR, some of main aspects of this methodology that may influence results were tested: DNA extraction kits, whole blood EDTA pre-treatment, blood source (tip of tail or jugular vein), erythrocytes isolation, FTA card interference and qPCR system of detection. Under our experimental conditions, both EDTA pre-treatment and FTA card application have no influence on the sensitivity of detection, and two DNA extraction kits provided higher sensitivity compared to others. As expected, blood samples collected from the tip of tail vessels presented higher levels of B. bovis DNA compared to those obtained from the jugular vein, and erythrocytes processed isolated has also improved the sensitivity compared to whole blood. Moreover, both qPCR assays here developed using hydrolysis probes for B. bovis and B. bigemina detection, presented enhanced reproducibility compared to qPCR assays using intercalating dye system. Even, qPCR for B. bigemina using hydrolysis probe here developed presented higher sensitivity compared to intercalating dye system. This study has contributed to the improvement of molecular diagnosis of bovine babesiosis, which may improve epidemiological studies related to these pathogens.

Genomic selection in dairy cattle simulated populations.

Genomic selection is arguably the most promising tool for improving genetic gain in domestic animals to emerge in the last few decades, but is an expensive process. The aim of this study was to evaluate the economic impact related to the implementation of genomic selection in a simulated dairy cattle population. The software QMSim was used to simulate genomic and phenotypic data. The simulated genome contained 30 chromosomes with 100 cm each, 1666 SNPs markers equally spread and 266 QTLs randomly designated for each chromosome. The numbers of markers and QTLs were designated according to information available from Animal QTL (http://www.animalgenome.org/QTLdb) and Bovine QTL (http://bovineqtl.tamu.edu/). The allelic frequency changes were assigned in a gamma distribution with alpha parameters equal to 0·4. Recurrent mutation rates of 1·0e-4 were assumed to apply to markers and QTLs. A historic population of 1000 individuals was generated and the total number of animals was reduced gradually along 850 generations until we obtained a number of 200 animals in the last generation, characterizing a bottleneck effect. Progenies were created along generations from random mating of the male and female gametes, assuming the same proportion of both genders. Than the population was extended for another 150 generations until we obtained 17 000 animals, with only 320 male individuals in the last generation. After this period a 25 year of selection was simulated taking into account a trait limited by sex with heritability of 0·30 (i.e. milk yield), one progeny/cow/year and variance equal to 1·0. Annually, 320 bulls were mated with 16 000 dams, assuming a replacement rate of 60 and 40% for males and females, respectively. Selection and discard criteria were based in four strategies to obtain the EBVs assuming as breeding objective to maximize milk yield. The progeny replaced the discarded animals creating an overlapping generation structure. The selection strategies were: RS is selection based on random values; PS is selection based on phenotypic values; Blup is selection based on EBVs estimated by BLUP; and GEBV is selection based on genomic estimated breeding values in one step, using high (GBlup) and low (GBlupi) density panels. Results indicated that the genetic evaluation using the aid of genomic information could provide better genetic gain rates in dairy cattle breeding programs as well as reduce the average inbreeding coefficient in the population. The economic viability indicators showed that only Blup and GBlup/GBlupi strategies, the ones that used milk control and genetic evaluation were economic viable, considering a discount rate of 6·32% per year.

qPCR estimates of Babesia bovis and Babesia bigemina infection levels in beef cattle and Rhipicephalus microplus larvae.

Babesia spp. are tick-transmitted intraerythrocytic apicomplexan parasites that infect wild and domestic animals. Babesia bovis and B. bigemina are endemic and responsible for enormous economic losses to the livestock industry in most of the Brazilian territory, wherein the tick Rhipicephalus microplus is the unique vector. Better understanding of epidemiology and parasite-host interactions may improve the tools for disease control and genetic management for selection of resistant animals. This study aimed to detect, quantify and measure the correlation between B. bigemina and B. bovis infection levels in bovine blood and into tick, by absolute quantification of hemoparasite DNA using qPCR. Blood bovine samples and larvae pools from 10 engorged R. microplus females were collected from each Canchim heifers (5/8 Charolais + 3/8 zebu, n = 36). All evaluated samples were positive for both Babesia species tested. Correlations of B. bovis and B. bigemina levels between cattle and tick host were 0.58 and 0.66, respectively. These high positive correlation coefficients indicate that parasitemia load in the bovine may be dependent on or may determine the parasitemia load in the ticks.

Genome-wide association between single nucleotide polymorphisms with beef fatty acid profile in Nellore cattle using the single step procedure.

BACKGROUND: Saturated fatty acids can be detrimental to human health and have received considerable attention in recent years. Several studies using taurine breeds showed the existence of genetic variability and thus the possibility of genetic improvement of the fatty acid profile in beef. This study identified the regions of the genome associated with saturated, mono- and polyunsaturated fatty acids, and n-6 to n-3 ratios in the Longissimus thoracis of Nellore finished in feedlot, using the single-step method. RESULTS: The results showed that 115 windows explain more than 1 % of the additive genetic variance for the 22 studied fatty acids. Thirty-one genomic regions that explain more than 1 % of the additive genetic variance were observed for total saturated fatty acids, C12:0, C14:0, C16:0 and C18:0. Nineteen genomic regions, distributed in sixteen different chromosomes accounted for more than 1 % of the additive genetic variance for the monounsaturated fatty acids, such as the sum of monounsaturated fatty acids, C14:1 cis-9, C18:1 trans-11, C18:1 cis-9, and C18:1 trans-9. Forty genomic regions explained more than 1 % of the additive variance for the polyunsaturated fatty acids group, which are related to the total polyunsaturated fatty acids, C20:4 n-6, C18:2 cis-9 cis12 n-6, C18:3 n-3, C18:3 n-6, C22:6 n-3 and C20:3 n-6 cis-8 cis-11 cis-14. Twenty-one genomic regions accounted for more than 1 % of the genetic variance for the group of omega-3, omega-6 and the n-6:n-3 ratio. CONCLUSIONS: The identification of such regions and the respective candidate genes, such as ELOVL5, ESSRG, PCYT1A and genes of the ABC group (ABC5, ABC6 and ABC10), should contribute to form a genetic basis of the fatty acid profile of Nellore (Bos indicus) beef, contributing to better selection of the traits associated with improving human health.

A small proportion of Zebu genetic background in crossbred calves may not be enough to improve resistance against natural bovine Babesia spp. infections.

The main objective of cattle breeders in tropical and subtropical regions is to acquire animals with taurine-productive traits adapted to the broad weather range of these regions. However, one of the main challenges on using taurine genetics in these areas is the high susceptibility of these animals to tick-borne diseases. Consequently, the present study evaluated from 10 November 2021-19 April 2022, the over 13 assessments, the Babesia bovis and Babesia bigemina DNA loads and the IgG anti-B. bovis and anti-B. bigemina levels in Angus (n = 17, 100% Taurine) and Ultrablack (n = 14, ∼82% taurine and 18% Zebu) calves. Data were analyzed using a multivariate mixed model with repeated measures of the same animal including the fixed effects of evaluation, genetic group, sex, Babesia spp., and their interactions. The repeatability values were estimated from the (co)variances matrix and expressed for each species. The correlations between the DNA loads (CNlog) and IgG titers (S/P) values for the two species were also estimated using the same model. Regarding the specific IgG antibody titers for both Babesia spp., no significant differences were observed between the two genetic groups. However, for B. bovis and B. bigemina DNA loads, Ultrablack calves presented significantly higher values than Angus calves. Under the conditions evaluated in this study, our findings suggest that the low percentage of Zebu genetic in the Ultrablack breed was insufficient to improve resistance against babesiosis. Further studies must demonstrate if the low percentages of Zebu genetics in Taurine breeds can modify the susceptibility to babesiosis infections.

Identification of candidate lethal haplotypes and genomic association with post-natal mortality and reproductive traits in Nellore cattle.

The wide use of genomic information has enabled the identification of lethal recessive alleles that are the major genetic causes of reduced conception rates, longer calving intervals, or lower survival for live-born animals. This study was carried out to screen the Nellore cattle genome for lethal recessive haplotypes based on deviation from the expected population homozygosity, and to test SNP markers surrounding the lethal haplotypes region for association with heifer rebreeding (HR), post-natal mortality (PNM) and stayability (STAY). This approach requires genotypes only from apparently normal individuals and not from affected embryos. A total of 62,022 animals were genotyped and imputed to a high-density panel (777,962 SNP markers). Expected numbers of homozygous individuals were calculated, and the probabilities of observing 0 homozygotes was obtained. Deregressed genomic breeding values [(G)EBVs] were used in a GWAS to identify candidate genes and biological mechanisms affecting HR, STAY and PNM. In the functional analyses, genes within 100 kb down and upstream of each significant SNP marker, were researched. Thirty haplotypes had high expected frequency, while no homozygotes were observed. Most of the alleles present in these haplotypes had a negative mean effect for PNM, HR and STAY. The GWAS revealed significant SNP markers involved in different physiological mechanisms, leading to harmful effect on the three traits. The functional analysis revealed 26 genes enriched for 19 GO terms. Most of the GO terms found for biological processes, molecular functions and pathways were related to tissue development and the immune system. More phenotypes underlying these putative regions in this population could be the subject of future investigation. Tests to find putative lethal haplotype carriers could help breeders to eliminate them from the population or manage matings in order to avoid homozygous.

A nonsense mutation in the tyrosinase gene causes albinism in water buffalo.

BACKGROUND: Oculocutaneous albinism (OCA) is an autosomal recessive hereditary pigmentation disorder affecting humans and several other animal species. Oculocutaneous albinism was studied in a herd of Murrah buffalo to determine the clinical presentation and genetic basis of albinism in this species. RESULTS: Clinical examinations and pedigree analysis were performed in an affected herd, and wild-type and OCA tyrosinase mRNA sequences were obtained. The main clinical findings were photophobia and a lack of pigmentation of the hair, skin, horns, hooves, mucosa, and iris. The results of segregation analysis suggest that this disease is acquired through recessive inheritance. In the OCA buffalo, a single-base substitution was detected at nucleotide 1,431 (G to A), which leads to the conversion of tryptophan into a stop codon at residue 477. CONCLUSION: This premature stop codon produces an inactive protein, which is responsible for the OCA buffalo phenotype. These findings will be useful for future studies of albinism in buffalo and as a possible model to study diseases caused by a premature stop codon.