Genome-Wide Association (GWAS) Applied to Carcass and Meat Traits of Nellore Cattle.

The meat market has enormous importance for the world economy, and the quality of the product offered to the consumer is fundamental for the success of the sector. In this study, we analyzed a database which contained information on 2470 animals from a commercial farm in the state of São Paulo, Brazil. Of this total, 2181 animals were genotyped, using 777,962 single-nucleotide polymorphisms (SNPs).

Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattle.

This study aimed to integrate analyses of structural variations and differentially expressed genes (DEGs) associated with the beef fatty acid (FA) profile in Nellore cattle. Copy numbers variation (CNV) detection was performed using the penncnv algorithm and CNVRuler software in 3794 genotyped animals through the High-Density Bovine BeadChip. In order to perform the genomic wide association study (GWAS), a total of 963 genotyped animals were selected to obtain the intramuscular lipid concentration and quantify the beef FA profile.

Genomic integration to identify molecular biomarkers associated with indicator traits of gastrointestinal nematode resistance in sheep.

This study aimed to integrate GWAS and structural variants to propose possible molecular biomarkers related to gastrointestinal nematode resistance traits in Santa Inês sheep. The phenotypic records FAMACHA, haematocrit, white blood cell count, red blood cell count, haemoglobin, platelets and egg counts per gram of faeces were collected from 700 naturally infected animals, belonging to four Brazilian flocks. A total of 576 animals were genotyped using the Ovine SNP12k BeadChip and were imputed using a reference population with Ovine SNP50 BeadChip.

Genetic parameter estimates for gastrointestinal nematode parasite resistance and maternal efficiency indicator traits in Santa Inês breed.

Infection with Haemonchus contortus is the most economically important gastrointestinal nematode parasitosis and the most important cause of mortality in sheep production. The aim of this study was to estimate variance components of gastrointestinal parasite resistance traits, maternal efficiency (ME) and ewe adult weight (AW) in Santa Inês breed in tropical conditions. The phenotypic records were collected from 700 animals, belonging to four flocks located south-east and north-east in Brazil.

Genomic regions and enrichment analyses associated with carcass composition indicator traits in Nellore cattle.

The aim of this study was to estimate genetic parameters and identify genomic regions associated with carcass traits obtained by ultrasound and visual scores in Nellore cattle. Data from ~66,000 animals from the National Association of Breeders and Researchers (ANCP) were used. The variance components for backfat thickness, rump fat thickness and Longissimus muscle area (LMA) were estimated considering a linear model whereas a threshold model for body structure (BS), finishing precocity (FP) and musculature (MS) traits.

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.

Association study between copy number variation and beef fatty acid profile of Nellore cattle.

The aim of this study was to analyze the association between the copy number variation regions (CNVRs) and fatty acid profile phenotypes for saturated (SFA), monosaturated (MUFA), polyunsaturated (PUFA), ω6 and ω3 fatty acids, PUFA/SFA and ω6/ω3 ratios, as well as for their sums, in Nellore cattle (Bos primigenius indicus). A total of 963 males were finished in feedlot and slaughtered with approximately 2 years of age. Animals were genotyped with the BovineHD BeadChip (Illumina Inc.

Application of single step genomic BLUP under different uncertain paternity scenarios using simulated data.

The objective of this study was to investigate the application of BLUP and single step genomic BLUP (ssGBLUP) models in different scenarios of paternity uncertainty with different strategies of scaling the G matrix to match the A22 matrix, using simulated data for beef cattle. Genotypes, pedigree, and phenotypes for age at first calving (AFC) and weight at 550 days (W550) were simulated using heritabilities based on real data (0.12 for AFC and 0.

Genomic regions and pathways associated with gastrointestinal parasites resistance in Santa Inês breed adapted to tropical climate.

Background: The aim of this study was to estimate variance components and to identify genomic regions and pathways associated with resistance to gastrointestinal parasites, particularly in a breed of sheep adapted to tropical climate. Phenotypes evaluations were performed to verify resistance to gastrointestinal parasites, and were divided into two categories: i) farm phenotypes, assessing body condition score (BCS), degree of anemia assessed by the famacha chart (FAM), fur score (FS) and feces consistency (FC); and ii) lab phenotypes, comprising blood analyses for hematocrit (HCT), white blood cell count (WBC), red blood cell count (RBC), hemoglobin (HGB), platelets (PLT) and transformed (log) egg per gram of feces (EPG). A total of 576 animals were genotyped with the Ovine SNP12k BeadChip (Illumina, Inc.

Physical and chemical characteristics of the longissimus dorsi from swine reared in climate-controlled and uncontrolled environments.

The aim of this study was to evaluate the effect of ambient temperature on the physical and chemical characteristics of the longissimus dorsi muscle by comparing the quality of meat from pigs reared in a controlled and in an uncontrolled environment, the latter provided with a shallow pool. Twenty castrated male pigs of the Topigs line were randomly allotted to two treatments: a controlled environment, with constant temperature (22 °C) and relative humidity (70%); and an uncontrolled environment in a conventional shed for rearing pigs equipped with a shallow pool, where pigs were subject to climatic variations. Meat from pigs kept in the controlled environment showed a greater capacity to retain intracellular water, higher tenderness, and lower cholesterol levels than meat from pigs reared in the uncontrolled environment, but displayed higher lipid oxidation and a lower concentration of DHA.

Genomic prediction for beef fatty acid profile in Nellore cattle.

The objective of this study was to compare SNP-BLUP, BayesCπ, BayesC and Bayesian Lasso methodologies to predict the direct genomic value for saturated, monounsaturated, and polyunsaturated fatty acid profile, omega 3 and 6 in the Longissimus thoracis muscle of Nellore cattle finished in feedlot. A total of 963 Nellore bulls with phenotype for fatty acid profiles, were genotyped using the Illumina BovineHD BeadChip (Illumina, San Diego, CA) with 777,962 SNP. The predictive ability was evaluated using cross validation.

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.

Genetic correlation estimates between beef fatty acid profile with meat and carcass traits in Nellore cattle finished in feedlot.

The objective of this study was to estimate the genetic-quantitative relationships between the beef fatty acid profile with the carcass and meat traits of Nellore cattle. A total of 1826 bulls finished in feedlot conditions and slaughtered at 24 months of age on average were used. The following carcass and meat traits were analysed: subcutaneous fat thickness (BF), shear force (SF) and total intramuscular fat (IMF).

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.

Genetic analysis on accumulated productivity and calving intervals in Nelore cattle.

The aim of this study was to estimate genetic parameters for accumulated productivity (ACP), first calving interval (CI1), second calving interval (CI2), and mean calving interval (MCI) in Nelore beef cattle. The ACP trait is a reproduction index and comprises the total number of calves born per dam, weight of weaned calves, and age of the dam at calving. Genetic parameters were estimated by the average information restricted maximum likelihood method in two-trait analyses.

Growing-finishing performance and carcass yield of pigs reared in a climate-controlled and uncontrolled environment.

The objective of this study was to evaluate the effect of temperature on the performance and carcass yield of pigs housed in different environments. Twenty castrated male pigs of the Topigs line were assigned to two treatments: T1, controlled environment, and T2, uncontrolled environment containing a shallow pool. A completely randomized design consisting of two treatments and ten repetitions each was used.