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.

Genetic parameters and genome-wide association studies for mozzarella and milk production traits, lactation length, and lactation persistency in Murrah buffaloes.

Genetic and genomic analyses of longitudinal traits related to milk production efficiency are paramount for optimizing water buffaloes breeding schemes. Therefore, this study aimed to (1) compare single-trait random regression models under a single-step genomic BLUP setting based on alternative covariance functions (i.e.

Random regression models using B-splines functions provide more accurate genomic breeding values for milk yield and lactation persistence in Murrah buffaloes.

There is a great worldwide demand for cheese made with buffalo milk, due to its flavour and nutritional properties. In this context, there is a need for increasing the efficiency of buffalo milk production (including lactation persistence), which can be achieved through genomic selection. The most used methods for the genetic evaluation of longitudinal data, such as milk-related traits, are based on random regression models (RRM).

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.

Genetics of tolerance to heat stress in milk yield of dairy buffaloes assessed by a reaction norm model.

The objectives of this study were to assess the effects of heat stress on the milk yield and investigate the presence of genotype × environment interaction (G × E) in Brazilian Murrah buffaloes reared under tropical conditions. With this, 58,070 test-day (TD) records for milk yield from 3,459 first lactations of buffaloes collected between 1987 and 2018 were evaluated. A mixed model considering days in milk (DIM) and temperature-humidity index (THI) was applied to quantify milk yield losses due to heat stress.

Genomic studies of milk-related traits in water buffalo (Bubalus bubalis) based on single-step genomic best linear unbiased prediction and random regression models.

Genomic selection has been widely implemented in many livestock breeding programs, but it remains incipient in buffalo. Therefore, this study aimed to (1) estimate variance components incorporating genomic information in Murrah buffalo; (2) evaluate the performance of genomic prediction for milk-related traits using single- and multitrait random regression models (RRM) and the single-step genomic best linear unbiased prediction approach; and (3) estimate longitudinal SNP effects and candidate genes potentially associated with time-dependent variation in milk, fat, and protein yields, as well as somatic cell score (SCS) in multiple parities. The data used to estimate the genetic parameters consisted of a total of 323,140 test-day records.

Water buffaloes (Bubalus bubalis) only have A2A2 genotype for beta-casein.

Beta-casein is a milk protein that has two variants: A1 and A2. Some individuals have difficulties digesting beta-casein A1, which can cause gastrointestinal disorders. A2 milk has emerged as an alternative.

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

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.

Publisher Correction: Uncovering Sub-Structure and Genomic Profiles in Across-Countries Subpopulations of Angus Cattle.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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.

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.

Uncovering Sub-Structure and Genomic Profiles in Across-Countries Subpopulations of Angus Cattle.

Highlighting genomic profiles for geographically distinct subpopulations of the same breed may provide insights into adaptation mechanisms to different environments, reveal genomic regions divergently selected, and offer initial guidance to joint genomic analysis. Here, we characterized similarities and differences between the genomic patterns of Angus subpopulations, born and raised in Canada (N = 382) and Brazil (N = 566). Furthermore, we systematically scanned for selection signatures based on the detection of autozygosity islands common between the two subpopulations, and signals of divergent selection, via F and varLD tests.

Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species.

The aim of this study was to analyze the genomic homology between cattle () and buffaloes () and to propose a rearrangement of the buffalo genome through linkage disequilibrium analyses of buffalo SNP markers referenced in the cattle genome assembly and also compare it to the buffalo genome assembly. A panel of bovine SNPs (single nucleotide polymorphisms) was used for hierarchical, non-hierarchical and admixture cluster analyses. Thus, the linkage disequilibrium information between markers of a specific panel of buffalo was used to infer chromosomal rearrangement.

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.

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.

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) with weight at 100, 210, 365, and 550 days of age, respectively, where those SNPs respectively explained 0.

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.

Genetic parameters for tonic immobility, body weight, and morphological traits of the red-winged tinamou (Rhynchotus rufescens).

This study was carried out to estimate genetic parameters for morphology, body weight, and tonic immobility traits in the red-winged tinamou (Rhynchotus rufescens). Information on 690 birds was used and genetic parameters were estimated using Bayesian methods under a multi-trait animal model. The following traits were considered in this study: tarsal length (TL), bill length (BL), wing length (WL), head width (HW), bill width (BW), mature weight (MW), weight at 90 days (W90), and tonic immobility (TI).

Twinning rate in buffaloes: A case report.

The information of twin pregnancy frequencies in buffaloes is scarce in the literature. Evidence even indicates that twin pregnancies are not carried to term, but it does not seem to be the case. In this case report, the event of twin pregnancy in buffaloes is reported as well as its frequency.

Genotype-environment interaction for age at first calving in buffaloes, using the reaction norm model.

The objective of this study was to evaluate the genotype-environment interaction effect on age at first calving in buffaloes. The records were analysed using two approaches: (a) standard animal model and (b) reaction norm model. For the reaction norm analysis, two environmental gradients were formed, using age of first calving or milk yield group contemporary average.

Use of single-step genome-wide association studies for prospecting genomic regions related to milk production and milk quality of buffalo.

The aim of this research communication was to identify chromosome regions and genes that could be related to milk yield (MY), milk fat (%F) and protein percentage (%P) in Brazilian buffalo cows using information from genotyped and non-genotyped animals. We used the 90 K Axiom® Buffalo Genotyping array. A repeatability model was used.

Prediction of genomic breeding values for reproductive traits in Nellore heifers.

The objective of this study was to assess the accuracy of genomic predictions for female reproductive traits in Nellore cattle. A total of 1853 genotyped cows and 305,348 SNPs were used for genomic selection analyses. GBLUP, BAYESCπ, and IBLASSO were applied to estimate SNP effects.

Genomic prediction ability for beef fatty acid profile in Nelore cattle using different pseudo-phenotypes.

The aim of the present study was to compare the predictive ability of SNP-BLUP model using different pseudo-phenotypes such as phenotype adjusted for fixed effects, estimated breeding value, and genomic estimated breeding value, using simulated and real data for beef FA profile of Nelore cattle finished in feedlot. A pedigree with phenotypes and genotypes of 10,000 animals were simulated, considering 50% of multiple sires in the pedigree. Regarding to phenotypes, two traits were simulated, one with high heritability (0.

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.

Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle.

Background: This study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that have undergone recent selection. We used a sample of 763 animals genotyped with the Illumina BovineHD BeadChip, among which 674 animals originated from two lines that are maintained under directional selection for increased yearling body weight and 89 animals from a control line that is maintained under stabilizing selection.

Results: Multidimensional analysis of the genomic dissimilarity matrix and admixture analysis revealed a substantial level of population stratification between the directional selection lines and the stabilizing selection control line.