Identification of genomic regions and pathways associated with traits related to rumen acidosis in feedlot Nellore cattle.

There may be an increased risk of metabolic disorders, such as rumen acidosis, in cattle fed high-concentrate diets, particularly those from Bos taurus indicus genotypes, which have shown to be more sensitive to ruminal acidification. Therefore, this study aimed to estimate (co)variance components and identify genomic regions and pathways associated with ruminal acidosis in feedlot Nellore cattle fed high-concentrate diets. It was utilized a dataset containing a total of 642 Nellore bulls that were genotyped from seven feedlot nutrition studies. The GGP Indicus 35k panel was used with the single step genome-wide association study methodology in which the effects of the markers were obtained from the genomic values estimated by the GBLUP model. A bivariate model to estimate genetic correlations between the economically important traits and indicator traits for acidosis was used. The traits evaluated in this study that were nutritionally related to rumen acidosis included average daily gain (ADG), final body weight, time spent eating (TSE), time spent ruminating, rumenitis score (RUM), rumen absorptive surface area (ASA), rumen keratinized layer thickness (KER) and hot carcass weight (HCW). The identified candidate genes were mainly involved in the negative or non-regulation of the apoptotic process, salivary secretion, and transmembrane transport. The genetic correlation between HCW and ASA was low positive (0.27 ± 0.23), and between ADG and ASA was high moderate (0.58 ± 0.59). A positive genetic correlation between RUM and all performance traits was observed, and TSE correlated negatively with HCW (-0.33 ± 0.21), ASA (-0.75 ± 0.48), and KER (-0.40 ± 0.27). The genetic association between economically important traits and indicator traits for acidosis suggested that Nellore cattle may be more sensitive to acidosis in feedlot systems.

Image analysis to automatically classify anemia based on Famacha score in sheep using ocular conjunctiva images.

Haemonchus contortus is the most pathogenic blood-feeding parasitic in sheep, causing anemia and consequently changes in the color of the ocular conjunctiva, from the deep red of healthy sheep to shades of pink to practically white of non-healthy sheep. In this context, the Famacha method has been created for detecting sheep unable to cope with the infection by H. contortus, through visual assessment of ocular conjunctiva coloration. Thus, the objectives of this study were (1) to extract ocular conjunctiva image features to automatically classify Famacha score and compare two classification models (multinomial logistic regression-MLR and random forest-RF) and (2) to evaluate the applicability of the best classification model on three sheep farms. The dataset consisted of 1,156 ocular conjunctiva images from 422 animals. RF model was used to segment the images, i.e., to select the pixels that belong to the ocular conjunctiva. After segmentation, the quantiles (1%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, and 99%) of color intensity in each image channel (red, blue, and green) were determined and used as explanatory variables in the classification models, and the Famacha scores 1 (non-anemic) to 5 (severely anemic) were the target classes to be predicted (scores 1 to 5, with 162, 255, 443, 266, and 30 images, respectively). For objective 1, the performance metrics (precision and sensitivity) were obtained using MLR and RF models considering data from all farms randomly split. For objective 2, a leave-one-farm-out cross-validation technique was used to assess prediction quality across three farms (farms A, B, and C, with 726, 205, and 225 images, respectively). The RF provided the best performances in predicting anemic animals, as indicated by the high values of sensitivity for Famacha score 3 (80.9%), 4 (46.2%), and 5 (60%) compared to the MLR model. The precision of the RF was 72.7% for Famacha score 1 and 62.5% for Famacha score 2. These results indicate that is possible to successfully predict Famacha score, especially for scores 2 to 4, in sheep via image analysis and RF model using ocular conjunctiva images collected in farm conditions. As expected, model validation excluding entire farms in cross-validation presented a lower prediction quality. Nonetheless, this setup is closer to reality because the developed models are supposed to be used across farms, including new ones, and with different environments and management conditions.

Classification Performance of Machine Learning Methods for Identifying Resistance, Resilience, and Susceptibility to Haemonchus contortus Infections in Sheep.

This study investigated the feasibility of using easy-to-measure phenotypic traits to predict sheep resistant, resilient, and susceptible to gastrointestinal nematodes, compared the classification performance of multinomial logistic regression (MLR), linear discriminant analysis (LDA), random forest (RF), and artificial neural network (ANN) methods, and evaluated the applicability of the best classification model on each farm. The database comprised 3654 records of 1250 Santa Inês sheep from 6 farms. The animals were classified into resistant (2605 records), resilient (939 records), and susceptible (110 records) according to fecal egg count and packed cell volume. A random oversampling method was performed to balance the dataset. The classification methods were fitted using the information of age class, the month of record, farm, sex, Famacha© degree, body weight, and body condition score as predictors, and the resistance, resilience, and susceptibility to gastrointestinal nematodes as the target classes to be predicted considering data from all farms randomly. An additional leave-one-farm-out cross-validation technique was used to assess prediction quality across farms. The MLR and LDA models presented good performances in predicting susceptible and resistant animals. The results suggest that the use of readily available records and easily measurable traits may provide useful information for supporting management decisions at the farm level.

Effect of Thermal Stress on Thermoregulation, Hematological and Hormonal Characteristics of Caracu Beef Cattle.

This study evaluated the influence of environmental temperature on thermoregulation, hormonal, and hematological characteristics in Caracu cattle. Blood samples, hair length, coat and muzzle colors, rectal (RT), and surface temperatures were collected from 48 males and 43 females before (morning) and after sun exposure for eight hours (afternoon). Infrared thermography (IRT) was used to identify superficial temperature that exhibits a high correlation with RT. Hematological parameters, hormone concentrations, RT, and the superficial temperature obtained by IRT that exhibited the highest correlation with RT were evaluated by variance analysis. Regarding IRT, the lower left side of the body (LS) showed the highest correlation with the RT. Interaction between period and sex was observed for LS, cortisol, and eosinophils. Cortisone, progesterone, and RT were influenced by period and sex. Neutrophils and segmented neutrophils were influenced by the period, which showed the highest concentrations after sun exposure. Platelets, leukocytes, lymphocytes, and monocytes were influenced by sex. Heat stress changes several physiological characteristics where males and females exhibited differences in their responses to heat stress. Furthermore, most characteristics evaluated remained within the regular values observed for taurine Creole breeds, showing that Caracu is adapted to tropical climates.

Effects of Feeding and Drinking Behavior on Performance and Carcass Traits in Beef Cattle.

Feed and water efficiency are important traits to improve beef cattle production's economic and environmental sustainability. This study evaluated residual feed intake (RFI) and residual water intake (RWI) and their relationship with performance, ingestive behavior, and carcass traits in Caracu beef cattle. The data were analyzed using a generalized linear model with least squares means. The ingestive behavior, performance, and carcass traits were influenced by sex (p < 0.05). Males showed higher dry matter intake (DMI), average daily gain (ADG), mid-test metabolic weight (BW0.75), rib eye area, and rump fat thickness than females, besides spending more time drinking and eating. Low RFI animals exhibited higher DMI than high RFI animals. Low RWI animals ingested 3.89 L/d of water further than high RWI animals. The interaction between sex and RWI influenced the DMI, BW0.75, and backfat thickness. The ingestive behavior of low and high RFI animals was similar, although high RWI animals visited a smaller number of drinkers than low RWI animals. Water intake positively affects productive efficiency, and the combined use of RWI and RFI may help improve the selection of more efficient animals contributing to reducing the costs of beef cattle production and improving environmental sustainability.

Weighted single-step genome-wide association study and pathway analyses for feed efficiency traits in Nellore cattle.

The aim was to conduct a weighted single-step genome-wide association study to detect genomic regions and putative candidate genes related to residual feed intake, dry matter intake, feed efficiency (FE), feed conversion ratio, residual body weight gain, residual intake and weight gain in Nellore cattle. Several protein-coding genes were identified within the genomic regions that explain more than 0.5% of the additive genetic variance for these traits. These genes were associated with insulin, leptin, glucose, protein and lipid metabolisms; energy balance; heat and oxidative stress; bile secretion; satiety; feed behaviour; salivation; digestion; and nutrient absorption. Enrichment analysis revealed functional pathways (p-value < .05) such as neuropeptide signalling (GO:0007218), negative regulation of canonical Wingless/Int-1 (Wnt) signalling (GO:0090090), bitter taste receptor activity (GO:0033038), neuropeptide hormone activity (GO:0005184), bile secretion (bta04976), taste transduction (bta0742) and glucagon signalling pathway (bta04922). The identification of these genes, pathways and their respective functions should contribute to a better understanding of the genetic and physiological mechanisms regulating Nellore FE-related traits.

Short communication: Characterization of the milk protein expression profiles in dairy buffaloes with and without subclinical mastitis.

The aim of this study was to characterize the proteins present in milk whey from buffaloes with and without subclinical mastitis using a proteomic approach to identify differentially expressed proteins as potential biomarkers for this disease. Whey from Murrah buffaloes with subclinical mastitis was compared with whey from healthy animals using liquid chromatography-tandem mass spectrometry. The annotated protein databases for Bubalus bubalis and Bos taurus were used in the analysis, and the gene annotations from the buffalo and bovine reference assemblies were also used. After integrating gene annotations from both buffaloes and bovines, a total of 1,033 proteins were identified, of which 156 were differentially expressed. Eighteen biological processes were annotated with Gene Ontology. Cathelicidin-3 was identified as a potential biomarker for subclinical mastitis. These results are important to the characterization of mastitis in the buffalo mammary gland and may aid in the development of tools for early diagnosis.

Polymorphisms in major histocompatibility complex genes and its associations with milk quality in Murrah buffaloes.

Animal breeding programs have used molecular genetic tools as an auxiliary method to identify and select animals with superior genetic merit for milk production and milk quality traits as well as disease resistance. Genes of the major histocompatibility complex (MHC) are important molecular markers for disease resistance that could be applied for genetic selection. The aim of this study was to identify single nucleotide polymorphisms (SNPs) and haplotypes in DRB2, DRB3, DMA, and DMB genes in Murrah breed and to analyze the association between molecular markers and milk, fat, protein and mozzarella production, fat and protein percentage, and somatic cell count. Two hundred DNA samples from Murrah buffaloes were used. The target regions of candidate genes were amplified by polymerase chain reaction (PCR) followed by sequencing and identification of polymorphisms. Allele and genotype frequencies, as well as linkage disequilibrium between SNPs, were calculated. Genotypes were used in association analyses with milk production and quality traits. Except for the DMA gene, identified as monomorphic, the other genes presented several polymorphisms. The DMB, DRB2, and DRB3 genes presented two, six, and seven SNPs, respectively. Fifty-seven haplotype blocks were constructed from 15 SNPs identified, which was used in association analyses. All the studied traits had at least one associated haplotype. In conclusion, it is suggested that the haplotypes found herein can be associated with important traits related to milk production and quality.

Gene expression profile of intramuscular muscle in Nellore cattle with extreme values of fatty acid.

BACKGROUND: Fatty acid type in beef can be detrimental to human health and has received considerable attention in recent years. The aim of this study was to identify differentially expressed genes in longissimus thoracis muscle of 48 Nellore young bulls with extreme phenotypes for fatty acid composition of intramuscular fat by RNA-seq technique. RESULTS: Differential expression analyses between animals with extreme phenotype for fatty acid composition showed a total of 13 differentially expressed genes for myristic (C14:0), 35 for palmitic (C16:0), 187 for stearic (C18:0), 371 for oleic (C18:1, cis-9), 24 for conjugated linoleic (C18:2 cis-9, trans11, CLA), 89 for linoleic (C18:2 cis-9,12 n6), and 110 genes for α-linolenic (C18:3 n3) fatty acids. For the respective sums of the individual fatty acids, 51 differentially expressed genes for saturated fatty acids (SFA), 336 for monounsaturated (MUFA), 131 for polyunsaturated (PUFA), 92 for PUFA/SFA ratio, 55 for ω3, 627 for ω6, and 22 for ω6/ω3 ratio were identified. Functional annotation analyses identified several genes associated with fatty acid metabolism, such as those involved in intra and extra-cellular transport of fatty acid synthesis precursors in intramuscular fat of longissimus thoracis muscle. Some of them must be highlighted, such as: ACSM3 and ACSS1 genes, which work as a precursor in fatty acid synthesis; DGAT2 gene that acts in the deposition of saturated fat in the adipose tissue; GPP and LPL genes that support the synthesis of insulin, stimulating both the glucose synthesis and the amino acids entry into the cells; and the BDH1 gene, which is responsible for the synthesis and degradation of ketone bodies used in the synthesis of ATP. CONCLUSION: Several genes related to lipid metabolism and fatty acid composition were identified. These findings must contribute to the elucidation of the genetic basis to improve Nellore meat quality traits, with emphasis on human health. Additionally, it can also contribute to improve the knowledge of fatty acid biosynthesis and the selection of animals with better nutritional quality.

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

BACKGROUND: The 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. RESULTS: A 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 >or= 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 >or= 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). CONCLUSION: We 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.