Genomic prediction of breeding values for carcass traits in Nellore cattle.

BACKGROUND: The objective of this study was to evaluate the accuracy of genomic predictions for rib eye area (REA), backfat thickness (BFT), and hot carcass weight (HCW) in Nellore beef cattle from Brazilian commercial herds using different prediction models. METHODS: Phenotypic data from 1756 Nellore steers from ten commercial herds in Brazil were used. Animals were offspring of 294 sires and 1546 dams, reared on pasture, feedlot finished, and slaughtered at approximately 2 years of age. All animals were genotyped using a 777k Illumina Bovine HD SNP chip. Accuracy of genomic predictions of breeding values was evaluated by using a 5-fold cross-validation scheme and considering three models: Bayesian ridge regression (BRR), Bayes C (BC) and Bayesian Lasso (BL), and two types of response variables: traditional estimated breeding value (EBV), and phenotype adjusted for fixed effects (Y*). RESULTS: The prediction accuracies achieved with the BRR model were equal to 0.25 (BFT), 0.33 (HCW) and 0.36 (REA) when EBV was used as response variable, and 0.21 (BFT), 0.37 (HCW) and 0.46 (REA) when using Y*. Results obtained with the BC and BL models were similar. Accuracies increased for traits with a higher heritability, and using Y* instead of EBV as response variable resulted in higher accuracy when heritability was higher. CONCLUSIONS: Our results indicate that the accuracy of genomic prediction of carcass traits in Nellore cattle is moderate to high. Prediction of genomic breeding values from adjusted phenotypes Y* was more accurate than from EBV, especially for highly heritable traits. The three models considered (BRR, BC and BL) led to similar predictive abilities and, thus, either one could be used to implement genomic prediction for carcass traits in Nellore cattle.

Identification and Functional Annotation of Genes Related to Horses' Performance: From GWAS to Post-GWAS.

Integration of genomic data with gene network analysis can be a relevant strategy for unraveling genetic mechanisms. It can be used to explore shared biological processes between genes, as well as highlighting transcription factors (TFs) related to phenotypes of interest. Unlike other species, gene-TF network analyses have not yet been well applied to horse traits. We aimed to (1) identify candidate genes associated with horse performance via systematic review, and (2) build biological processes and gene-TF networks from the identified genes aiming to highlight the most candidate genes for horse performance. Our systematic review considered peer-reviewed articles using 20 combinations of keywords. Nine articles were selected and placed into groups for functional analysis via gene networks. A total of 669 candidate genes were identified. From that, gene networks of biological processes from each group were constructed, highlighting processes associated with horse performance (e.g., regulation of systemic arterial blood pressure by vasopressin and regulation of actin polymerization and depolymerization). Transcription factors associated with candidate genes were also identified. Based on their biological processes and evidence from the literature, we identified the main TFs related to horse performance traits, which allowed us to construct a gene-TF network highlighting TFs and the most candidate genes for horse performance.

Genome-wide scan highlights the role of candidate genes on phenotypic plasticity for age at first calving in Nellore heifers.

Age at first calving (AFC) plays an important role in the economic efficiency of beef cattle production. This trait can be affected by a combination of genetic and environmental factors, leading to physiological changes in response to heifers' adaptation to a wide range of environments. Genome-wide association studies through the reaction norm model were carried out to identify genomic regions associated with AFC in Nellore heifers, raised under different environmental conditions (EC). The SNP effects for AFC were estimated in three EC levels (Low, Medium, and High, corresponding to average contemporary group effects on yearling body weight equal to 159.40, 228.6 and 297.6 kg, respectively), which unraveled shared and unique genomic regions for AFC in Low, Medium, and High EC levels, that varied according to the genetic correlation between AFC in different EC levels. The significant genomic regions harbored key genes that might play an important biological role in controlling hormone signaling and metabolism. Shared genomic regions among EC levels were identified on BTA 2 and 14, harboring candidate genes associated with energy metabolism (IGFBP2, IGFBP5, SHOX, SMARCAL1, LYN, RPS20, MOS, PLAG1, CHCD7, and SDR16C6). Gene set enrichment analyses identified important biological functions related to growth, hormone levels affecting female fertility, physiological processes involved in female pregnancy, gamete generation, ovulation cycle, and age at puberty. The genomic regions highlighted differences in the physiological processes linked to AFC in different EC levels and metabolic processes that support complex interactions between the gonadotropic axes and sexual precocity in Nellore heifers.

Spliced genes in muscle from Nelore Cattle and their association with carcass and meat quality.

Transcript data obtained by RNA-Seq were used to identify differentially expressed alternatively spliced genes in ribeye muscle tissue between Nelore cattle that differed in their ribeye area (REA) or intramuscular fat content (IF). A total of 166 alternatively spliced transcripts from 125 genes were significantly differentially expressed in ribeye muscle between the highest and lowest REA groups (p ≤ 0.05). For animals selected on their IF content, 269 alternatively spliced transcripts from 219 genes were differentially expressed in ribeye muscle between the highest and lowest IF animals. Cassette exons and alternative 3' splice sites were the most frequently found alternatively spliced transcripts for REA and IF content. For both traits, some differentially expressed alternatively spliced transcripts belonged to myosin and myotilin gene families. The hub transcripts were identified for REA (LRRFIP1, RCAN1 and RHOBTB1) and IF (TRIP12, HSPE1 and MAP2K6) have an important role to play in muscle cell degradation, development and motility. In general, transcripts were found for both traits with biological process GO terms that were involved in pathways related to protein ubiquitination, muscle differentiation, lipids and hormonal systems. Our results reinforce the biological importance of these known processes but also reveal new insights into the complexity of the whole cell muscle mRNA of Nelore cattle.

Genetic analysis of carcass and meat quality traits in Nelore cattle1.

The objective of this study was to estimate genetic parameters for carcass and meat quality traits, as well as their genetic correlations using pedigree and genomic information. A total of 3,716; 3,702; 3,439; 3,705; and 3,714 records of 12th-13th rib LM area (LMA), backfat thickness (BF), HCW, marbling score (MARB), and Warner-Bratzler peak shear force (WBSF), respectively, were used. Animals were genotyped with BovineHD BeadChip and GeneSeek Genomic Profiler Indicus HD - GGP75Ki panel. The (co)variance components were estimated by Bayesian inference using a multitrait ssGBLUP analysis. The animal model included fixed effects of contemporary group (defined by the combination of farm and year of birth, and management group at yearling) and age of animal at slaughtering as a covariate (linear). Direct additive genetic and residual effects were fitted as random. The posterior means and SD of heritabilities for LMA, BF, HCW, MARB, and WBSF were 0.28 (0.03), 0.21 (0.04), 0.21 (0.04), 0.12 (0.04), and 0.11 (0.03), respectively. The posterior means for genetic correlations between LMA and meat quality were positive and moderate with MARB (0.38 ± 0.12) and negative with WBSF (-0.47 ± 0.12). Low genetic correlations were estimated between BF and WBSF (-0.03 ± 0.16) and between HCW and MARB (-0.04 ± 0.14), indicating that these traits are not controlled by the same set or linked genes. Carcass traits (LMA, BF, and HCW) presented moderate heritability providing quick response to the selection purpose. The estimates of heritability for meat quality traits (MARB and WBSF) were low and indicate that the rate of genetic improvement for these traits would be slow. Genetic correlations indicated that selection for carcass traits would not be strongly antagonistic for improving meat quality.

Genomic association for sexual precocity in beef heifers using pre-selection of genes and haplotype reconstruction.

Reproductive traits are of the utmost importance for any livestock farming, but are difficult to measure and to interpret since they are influenced by various factors. The objective of this study was to detect associations between known polymorphisms in candidate genes related to sexual precocity in Nellore heifers, which could be used in breeding programs. Records of 1,689 precocious and non-precocious heifers from farms participating in the Conexão Delta G breeding program were analyzed. A subset of single nucleotide polymorphisms (SNP) located in the region of the candidate genes at a distance of up to 5 kb from the boundaries of each gene, were selected from the panel of 777,000 SNPs of the High-Density Bovine SNP BeadChip. Linear mixed models were used for statistical analysis of early heifer pregnancy, relating the trait with isolated SNPs or with haplotype groups. The model included the contemporary group (year and month of birth) as fixed effect and parent of the animal (sire effect) as random effect. The fastPHASE® and GenomeStudio® were used for reconstruction of the haplotypes and for analysis of linkage disequilibrium based on r2 statistics. A total of 125 candidate genes and 2,024 SNPs forming haplotypes were analyzed. Statistical analysis after Bonferroni correction showed that nine haplotypes exerted a significant effect (p<0.05) on sexual precocity. Four of these haplotypes were located in the Pregnancy-associated plasma protein-A2 gene (PAPP-A2), two in the Estrogen-related receptor gamma gene (ESRRG), and one each in the Pregnancy-associated plasma protein-A gene (PAPP-A), Kell blood group complex subunit-related family (XKR4) and mannose-binding lectin genes (MBL-1) genes. Although the present results indicate that the PAPP-A2, PAPP-A, XKR4, MBL-1 and ESRRG genes influence sexual precocity in Nellore heifers, further studies are needed to evaluate their possible use in breeding programs.

Genome-Wide Association Study of Meat Quality Traits in Nellore Cattle.

The objective of this study was to identify genomic regions that are associated with meat quality traits in the Nellore breed. Nellore steers were finished in feedlots and slaughtered at a commercial slaughterhouse. This analysis included 1,822 phenotypic records of tenderness and 1,873 marbling records. After quality control, 1,630 animals genotyped for tenderness, 1,633 animals genotyped for marbling, and 369,722 SNPs remained. The results are reported as the proportion of variance explained by windows of 150 adjacent SNPs. Only windows with largest effects were considered. The genomic regions were located on chromosomes 5, 15, 16 and 25 for marbling and on chromosomes 5, 7, 10, 14 and 21 for tenderness. These windows explained 3,89% and 3,80% of the additive genetic variance for marbling and tenderness, respectively. The genes associated with the traits are related to growth, muscle development and lipid metabolism. The study of these genes in Nellore cattle is the first step in the identification of causal mutations that will contribute to the genetic evaluation of the breed.