Resequencing of Brazilian locally adapted cattle breeds revealed variants in candidate genes and transcription factors for meat fatty acid profile.

The beef cattle industry has experienced a shift driven by a market demand for healthier meat, cost efficiency and environmental sustainability in recent years. Consequently, there has been a growing focus on the fatty acids content and functions of meat in cattle breeding programmes. Besides, a deeper understanding of the biological mechanisms influencing the expression of different phenotypes related to fatty acid profiles is crucial. In this study, we aimed to identify Single-Nucleotide Variants (SNV) and Insertion/Deletion (InDels) DNA variants in candidate genes related to fatty acid profiles described in genomic, transcriptomic and proteomic studies conducted in beef cattle breeds. Utilizing whole-genome re-sequencing data from Brazilian locally adapted bovine breeds, namely Caracu and Pantaneiro, we identified SNVs and InDels associated with 23,947 genes. From these, we identified 318 candidate genes related to fatty acid profiles that contain variants. Subsequently, we select only genes with SNVs and InDels in their promoter, 5' UTR and coding region. Through the gene-biological process network, approximately 19 genes were highlighted. Furthermore, considering the studied trait and a literature review, we selected the main transcription factors (TF). Functional analysis via gene-TF network allowed us to identify the 30 most likely candidate genes for meat fatty acid profile in cattle. LIPE, MFSD2A and SREBF1 genes were highlighted in networks due to their biological importance. Further dissection of these genes revealed 15 new variants found in promoter regions of Caracu and Pantaneiro sequences. The gene networks facilitated a better functional understanding of genes and TF, enabling the identification of variants potentially related to the expression of candidate genes for meat fatty acid profiles in cattle.

Heterogeneity of variance and genetic parameters for milk production in cattle, using Bayesian inference.

The goal of this study was to verify the effect of heterogeneity of variance (HV) on milk production in up to 305 days of lactation (L305) of daughters of Girolando, Gir and Holstein sires, as well as in the genetic evaluation of these sires and their progenies. in Brazil. The model included contemporary groups (consisting of herd, year and calving season) as a fixed effect, cow age at calving (linear and quadratic effects) and heterozygosity (linear effect) as covariates, in addition to the random effects of direct additive genetic and environmental, permanent and residual. The first analysis consisted of the single-trait animal model, with L305 records (disregarding HV). The second considered classes of standard deviations (SD): two-trait model including low and high classes (considering HV), according to the standardized means of L305 for herd-year of calving. The low SD class was composed of herds with SD equal to or less than zero and the high class with positive SD values. Estimates of (co)variance components and breeding values were obtained separately for each scenario using Bayesian inference via Gibbs sampling. Different heritability was estimated. Higher for the high DP class in the Gir (0.20) and Holstein (0.15) breeds, not occurring the same in the Girolando breed, with a lower value among the classes for the high DP (0.10). High values of genetic correlations were also found between low and high SD classes (0.88; 0.85 and 0.79) for the Girolando, Gir and Holstein breeds, respectively. Like the order correlations (Spearman) which were also high for the three breeds analyzed (equal to or above 0.92). Thus, the presence of HV had a smaller impact for L305 and did not affect the genetic evaluation of sires.

Assessment of copy number variants in three Brazilian locally adapted cattle breeds using whole-genome re-sequencing data.

Further characterization of genetic structural variations should strongly focus on small and endangered local breeds given their role in unraveling genes and structural variants underlying selective pressures and phenotype variation. A comprehensive genome-wide assessment of copy number variations (CNVs) based on whole-genome re-sequencing data was performed on three Brazilian locally adapted cattle breeds (Caracu Caldeano, Crioulo Lageano, and Pantaneiro) using the ARS-UCD1.2 genome assembly. Data from 36 individuals with an average coverage depth of 14.07× per individual was used. A total of 24 945 CNVs were identified distributed among the breeds (Caracu Caldeano = 7285, Crioulo Lageano = 7297, and Pantaneiro = 10 363). Deletion events were 1.75-2.07-fold higher than duplications, and the total length of CNVs is composed mostly of a high number of segments between 10 and 30 kb. CNV regions (CNVRs) are not uniformly scattered throughout the genomes (n = 463), and 105 CNVRs were found overlapping among the studied breeds. Functional annotation of the CNVRs revealed variants with high consequence on protein sequence harboring relevant genes, in which we highlighted the BOLA-DQB, BOLA-DQA5, CD1A, ß-defensins, PRG3, and ULBP21 genes. Enrichment analysis based on the gene list retrieved from the CNVRs disclosed over-represented terms (p < 0.01) strongly associated with immunity and cattle resilience to harsh environments. Additionally, QTL associated with body conformation and dairy-related traits were also unveiled within the CNVRs. These results provide better understanding of the selective forces shaping the genome of such cattle breeds and identify traces of natural selection pressures by which these populations have been exposed to challenging environmental conditions.

Genetic parameters for body weight and milk production of dairy Gyr herds.

The aim of this study was to estimate genetic parameters for cow weight at calving (CW) and cumulative 305-day milk yield (MY305) in dairy Gyr cattle by two-trait analysis. The study used 1,847 CW records, in which 418 females presented more than one measure, and 4,048 MY305 records, wherein 1068 females provided repeated measures, from 2,339 females belonging to three herds, which calved between 1986 and 2019. Variance components were estimated by the restricted maximum likelihood method (REML) using a two-trait animal model. The model included direct additive genetic, permanent environmental and residual effects as random effects and the fixed effects of contemporary group, formed by animals that had calved on the same farm year and season, and age of cow at calving as covariates (fitted as linear and quadratic effect). The heritability estimates for CW and MY305 were 0.21 ± 0.06 and 0.29 ± 0.04, respectively, and repeatability estimates were 0.49 ± 0.03 and 0.49 ± 0.02. The genetic correlation between CW and MY305 was positive and of low magnitude (0.33 ± 0.18), indicating that selection for MY305 will cause little genetic change in the weights of dairy Gyr animals. The genetic trends of breeding values of analyzed traits showed marked genetic gains in MY305, with little changes in CW of dairy Gyr cows over the years in the herds studied, which is an important result considering the production systems adopted in the tropics.

Genome-Wide Analyses Reveal the Genetic Architecture and Candidate Genes of Indicine, Taurine, Synthetic Crossbreds, and Locally Adapted Cattle in Brazil.

Cattle population history, breeding systems, and geographic subdivision may be reflected in runs of homozygosity (ROH), effective population size (N e), and linkage disequilibrium (LD) patterns. Thus, the assessment of this information has become essential to the implementation of genomic selection on purebred and crossbred cattle breeding programs. In this way, we assessed the genotype of 19 cattle breeds raised in Brazil belonging to taurine, indicine, synthetic crossbreds, and Iberian-derived locally adapted ancestries to evaluate the overall LD decay patterns, N e, ROH, and breed composition. We were able to obtain a general overview of the genomic architecture of cattle breeds currently raised in Brazil and other tropical countries. We found that, among the evaluated breeds, different marker densities should be used to improve the genomic prediction accuracy and power of genome-wide association studies. Breeds showing low N e values indicate a recent inbreeding, also reflected by the occurrence of longer ROH, which demand special attention in the matting schemes to avoid extensive inbreeding. Candidate genes (e.g., ABCA7, PENK, SPP1, IFNAR1, IFNAR2, SPEF2, PRLR, LRRTM1, and LRRTM4) located in the identified ROH islands were evaluated, highlighting biological processes involved with milk production, behavior, rusticity, and fertility. Furthermore, we were successful in obtaining the breed composition regarding the taurine and indicine composition using single-nucleotide polymorphism (SNP) data. Our results were able to observe in detail the genomic backgrounds that are present in each breed and allowed to better understand the various contributions of ancestor breeds to the modern breed composition to the Brazilian cattle.

Genetic Characterization of Indubrasil Cattle Breed Population.

The Indubrasil breed was developed in the Brazilian region called Triângulo Mineiro as a result of a cross between zebu cattle. Initially, it was used as a terminal cross and currently it represents approximately 4.45% of all the Brazilian zebu cattle. Studies were conducted to estimate genetic parameters in the Indubrasil using pedigree information, however, until now, no study has been developed using large-scale genomic markers in this breed. Pedigree information are widely used to investigate population parameters; however, they can neglect some estimates when compared to the use of genomic markers. Therefore, the objective of this study was to investigate the population structure and the genetic diversity of Indubrasil cattle using a high-density Single Nucleotide Polymorphism (SNP) panel (Illumina BovineHD BeadChip 700k). Levels of genomic homozygosity were evaluated using three different approaches: Runs of homozygosity (FROH), % of homozygosis (FSNP), and inbreeding coefficient (Fx). Further, Runs of Homozygosity (ROH) segments conserved among the animals were investigated to identify possible regions associated with the breed characteristics. Our results indicate that even the Indubrasil breed having a small effective population size, the levels of homozygosity (FROH = 0.046) are still small. This was possibly caused by the cross conducted among different breeds for its development. It suggests no immediate risks associated with loss of genetic variation. This information might be used in breeding programs, for the breed conservation and for the expansion of the Indubrasil breed.