EEF1A1 transcription cofactor gene polymorphism is associated with muscle gene expression and residual feed intake in Nelore cattle

Cis-acting effects of noncoding variants on gene expression and regulatory molecules constitute a significant factor for phenotypic variation in complex traits. To provide new insights into the impacts of single-nucleotide polymorphisms (SNPs) on transcription factors (TFs) and transcription cofactors (TcoF) coding genes, we carried out a multi-omic analysis to identify cis-regulatory effects of SNPs on these genes' expression in muscle and describe their association with feed efficiency-related traits in Nelore cattle. As a result, we identified one SNP, the rs137256008C > T, predicted to impact the EEF1A1 gene expression (β = 3.02; P-value = 3.51E-03) and the residual feed intake trait (β = - 3.47; P-value = 0.02). This SNP was predicted to modify transcription factor sites and overlaps with several QTL for feed efficiency traits. In addition, co-expression network analyses showed that animals containing the T allele of the rs137256008 SNP may be triggering changes in the gene network. Therefore, our analyses reinforce and contribute to a better understanding of the biological mechanisms underlying gene expression control of feed efficiency traits in bovines. The cis-regulatory SNP can be used as biomarker for feed efficiency in Nelore cattle.

Genomewide association study for production and meat quality traits in Canchim beef cattle

The commercial value of the bovine carcass is determined by a set of traits, such as weight, yield, back fat thickness, and marbling; therefore, the genetic improvement of growth, meat, and carcass quality traits is an important tool to add value to the supply chain. Genomewide association studies (GWAS) enable the identification of loci that control phenotypic expression of quantitative traits (QTL). Therefore, the objective of this work was to perform a GWAS to identify genomic regions and genes associated with growth, carcass traits, and meat quality in Canchim beef cattle. These traits were yearling weight (YW), rib eye area (REA), back fat thickness (BFT), and marbling (MARB). To increase sample size and marker density, genotype imputation was performed, and only markers imputed with greater than 95% accuracy were used. Genomewide association study was performed using a Bayesian approach, by the Bayes B statistical method, incorporating genotypes and phenotypes from 614 animals from both the Canchim breed and the MA genetic group (offspring of Charolais bulls and one-half Canchim + one-half Zebu cows). This investigation identified 1 and 4 genomic regions explaining 0.23 and 7.35% of the genetic variance for REA and YW, respectively. These regions harbor a total of 19 genes, 7 of which were classified for biological functions by functional analysis. Significant associations were not observed for BFT and MARB. The identification of QTL that had been previously described in the literature reinforces associations found in this study.

Genomewide association mapping and pathway analysis of meat tenderness in Polled Nellore cattle

Brazil is one of the world's largest beef exporters, although the product has a low price due to quality issues. The meat exported by Brazil is considered medium and low quality by international buyers, mainly due to lack of tenderness. The predominant Zebu breeds (80% Nellore) are known for producing tougher beef than taurine breeds. Nonetheless, some studies have shown that there is substantial genetic variability for tenderness within the Nellore breed, although it is a difficult trait to improve by conventional selection methods. Therefore, the aim of this study was to perform a genomewide association study (GWAS) and a gene set enrichment analysis to identify genomic regions and biologically relevant pathways associated with meat tenderness in Polled Nellore cattle. Data consisted of Warner-Bratzler shear force values of LM from 427 Polled Nellore animals divided into 3 experimental slaughters (years 2005, 2008, and 2010). The animals were genotyped with either the Illumina BovineHD BeadChip (777k, on 61 samples) or the GGP Indicus HD chip (77k, on 366 samples). Single nucleotide polymorphisms were excluded when the call rate was <90%, the Hardy-Weinberg proportions -value was <1% (Fisher exact test, Bonferroni adjusted), and the minor allele frequency was <1%. Imputation from the GGP Indicus HD chip to the Illumina BovineHD BeadChip was performed using the FImput program. Genomewide association analysis was performed using the Efficient Mixed Model Association eXpedited (EMMAx) and the population parameters previously determined (P3D) methods. The GWAS was complemented with a gene set enrichment analysis performed using the FatiGO procedure. Significant markers ( < 0.0001) explaining a larger proportion of variation than other significant SNPs were located on chromosomes 3, 13, 17, 20, 21, and 25, indicating QTL associated with meat tenderness throughout the genome. Additionally, gene set analysis identified 22 Gene Ontology functional terms and 2 InterPro entries that showed significant enrichment of genes associated with tenderness. The functional categories included protein tyrosine and serine/threonine kinase activity, calcium ion binding, lipid metabolic process, and growth factors, among others. These results help to elucidate the genetic architecture and metabolic pathways underlying this trait, which is of extreme economic and social importance to Brazil, because Nellore is the dominant beef cattle breed in the country.

Candidate genes for carcass traits in a tropical-adapted Brazilian composite beef breed

Backfat thickness (BFT) and ribeye area (REA) are important production traits but, because they are measured late in the animal's life, they have not been efficiently included in breeding programs. The aim of this study was to evaluate whether single nucleotide polymorphisms (SNPs) mapped to the leptin, PPARGC1A, PSMC1, CRH, and FABP4 genes, which influence BFT and REA in Canchim cattle, a composite beef breed (5/8 Charolais + 3/8 Zebu). BFT and REA phenotypic records were obtained by ultrasound measurements from 18-month-old animals. All SNP markers were genotyped by restriction fragment length polymorphism-polymerase chain reaction. Restricted maximum likelihood analysis revealed that the non-synonymous SNP located in exon 2 of the FABP4 gene has an additive effect on BFT (P ≤ 0.05). Significant allele substitution effects showed that the substitution of G by A may lead to a decrease of 0.1055 mm in mean BFT. This information can be used for inclusion of this trait-associated marker in commercial SNP panels.

Sequenciamento parcial dos genes TOX e NCOA2 em bubalinos

Os bubalinos são animais com uma importância grande para a produção de alimentos, além da ação sócio-econômica na região tropical. A caracterização de genes possibilita o estudo de características próprias da espécie e o desenvolvimento de tecnologia para sua produção. Esse trabalho estudou parcialmente os genes thymus high mobility group box protein (TOX) e o Nuclear Receptor Coactivator 2 (NCOA2) em femêas bubalinas da raça Murrah pela técnica de PCR-sequenciamento. Seis SNPs foram identificados em cada gene. Dois SNPs adjacentes no gene TOX criaram/destruíram um sitio de produção de um miRNA e são bons candidatos para serem estudos no futuro. A homologia das regiões desses genes com as correspondentes em bovinos é muito alta (99 %).

Single nucleotide polymorphisms in candidate genes associated with gastrointestinal nematode infection in goats

Cytokines are small cell-signaling proteins that play an important role in the immune system, participating in intracellular communication. Four candidate genes of the cytokine family (IL2, IL4, IL13, and IFNG) were selected to identify Single Nucleotide Polymorphisms (SNPs) that might be associated with resistance to gastrointestinal endoparasites in goats. A population of 229 goats, F2 offspring from an F1 intercross was produced by crossing pure Saanen goats, considered as susceptible to gastrointestinal endoparasites, with pure Anglo-Nubian goats, considered resistant. Blood was collected for DNA extraction and fecal samples were also collected for parasite egg count. Polymorphisms were prospected by sequencing animals with extreme phenotype for fecal egg count (FEC) distribution. The association between SNPs and phenotype was determined by using the Fisher exact test with correction for multiple tests. Three of the 10 SNPs were identified as significant (P ≤ 0.03). They were found in intron 1 of IL2 (ENSBTA00000020883), intron 3 of IL13 (ENSBTA00000015953) and exon 3 of IFNG (ENSBTA00000012529), suggesting an association between them and gastrointestinal endoparasite resistance. Further studies will help describe the effects of these markers accurately before implementing them in marker assisted selection. This study is the pioneer in describing such associations in goats.

Genome scan for meat quality traits in Nelore beef cattle

Meat quality traits are economically important because they affect consumers' acceptance, which, in turn, influences the demand for beef. However, selection to improve meat quality is limited by the small numbers of animals on which meat tenderness can be evaluated due to the cost of performing shear force analysis and the resultant damage to the carcass. Genome wide-association studies for Warner-Bratzler shear force measured at different times of meat aging, backfat thickness, ribeye muscle area, scanning parameters [lightness, redness (a*), and yellowness] to ascertain color characteristics of meat and fat, water-holding capacity, cooking loss (CL), and muscle pH were conducted using genotype data from the Illumina BovineHD BeadChip array to identify quantitative trait loci (QTL) in all phenotyped Nelore cattle. Phenotype count for these animals ranged from 430 to 536 across traits. Meat quality traits in Nelore are controlled by numerous QTL of small effect, except for a small number of large-effect QTL identified for a*fat, CL, and pH. Genomic regions harboring these QTL and the pathways in which the genes from these regions act appear to differ from those identified in taurine cattle for meat quality traits. These results will guide future QTL mapping studies and the development of models for the prediction of genetic merit to implement genomic selection for meat quality in Nelore cattle.

Characterization of the exonic regions of the JY-1 gene in zebu cattle and buffaloes

Protein JY-1 is an oocyte-specific protein that plays an important regulatory role in the granulosa cell layer and during the early embryo development stages. It is the first specific protein of maternal origin discovered in a single-ovulating species. In this study, the exon regions of the JY-1 gene were characterized by sequencing in 20 unrelated cattle (Bos taurus indicus) and 20 unrelated buffaloes (Bubalus bubalis). Eighteen polymorphisms were detected in cattle and 10 polymorphisms in buffaloes. Some of the polymorphisms were identified in codifying regions and caused amino acid changes. The insertion of a thymine was detected in the codifying region of exon 3 of the buffalo sequence when compared to the cattle one. This insertion causes a change in the codons frameshift from this point onwards, modifying the 19 terminal amino acids of the buffalo protein and creating a premature stop codon. This finding may explain reproductive differences between cattle and buffaloes in terms of follicle recruitment, embryo development and incidence of twin pregnancies.

Candidate genes for production traits in Nelore beef cattle

Meat quality is an important trait for the beef industry. Backfat thickness, ribeye area, and shear force are traits measured late in life, and the investigation of molecular markers associated with these traits can help breeding programs. In cattle, some polymorphisms have been related to production traits. Thus, the purpose of this study was to assess the presence of polymorphisms in the candidate genes insulin-like growth factor 1 (IGF1), fatty acid-binding protein 4 (FABP4), and peroxisome proliferative active receptor gamma coactivator 1 A (PPARGC1A) and associate them with production traits in reference families of Nelore cattle. We used 270 steers descendent from 20 sires that were chosen to represent variability in this breed. The investigation of marker effects on the traits was performed using a mixed model under the restricted maximum likelihood method. A significant allele substitution effect was found for IGF1 and yearling weight (P ≤ 0.017). The mean allele substitution effect was 6.9 kg, with the 229 allele associated with reduced yearling weight in this Nelore population.

Whole-genome analysis for backfat thickness in a tropically adapted, composite cattle breed from Brazil

Backfat thickness affects the preservation of the beef carcass after slaughter and confers organoleptic characteristics assessed by the consumer. One of the breeding goals for Canchim, a tropically adapted breed, is to comprehensively increase fat thickness. Our goals were to identify genomic regions associated with backfat in Canchim populations and validate the association of single nucleotide polymorphisms (SNPs) overlapping previously identified QTL regions known to affect fat deposition. Fifteen animals with lower and 15 animals with higher residues for backfat, according to a linear model using the SAS GLM procedure, were selected from a population of 1171 animals and genotyped using the BovineSNP50 BeadChip. Initial analysis revealed more than 100 SNPs that discriminated the tails of phenotypic distribution. One extended region of association included the centromeric region of chromosome (Chr) 14. Because this region overlapped with QTL from previous reports, we developed SNP assays to interrogate two linkage disequilibrium blocks, one in the centromeric region and another in the middle region of Chr 14 to confirm the association. The analysis validated the presence of specific haplotypes affecting fat thickness.

Candidate gene region for control of rib eye area in Canchim beef cattle

Investigation of molecular marker effects on production traits is essential to define marker assisted selection strategies in beef cattle. We looked for a possible association of molecular markers and backfat thickness (BFT) and rib eye area (REA) in Canchim (5/8 Charolais + 3/8 Zebu) and MA (offspring of Charolais bulls and 1/2 Canchim + 1/2 Zebu cows) animals raised exclusively on pasture. Traits were measured on 987 individuals from seven herds from two Brazilian States (São Paulo and Goiás), in March and April from 2005 to 2007, when animals were, on average, 19 months of age. Five microsatellite markers lying in QTL regions for BFT and REA (BMS490 and ETH10 on chromosome 5, INRA133 and ILSTS090 on chromosome 6, and BMS2142 on chromosome 19) were genotyped and association analyses were performed under an animal model using the restricted maximum likelihood method. After correction for multiple tests, a significant effect of microsatellite BMS490 on REA was observed, suggesting that at least one QTL affecting carcass traits in this region of the BTA5. No significant effect on BFT was observed for these markers.

Prospecting candidate SNPs for backfat in Canchim beef cattle

Canchim is a composite cattle breed developed in Brazil for beef production. One of the breeding objectives is to increase fat deposition. QTLs for fat thickness and/or marbling have been reported on BTA4 and BTA14. The IGFBP3 and DDEF1 genes, mapped to BTA4 and BTA14, respectively, affect adipogenesis. We looked for SNPs in the IGFBP3 and DDEF1 genes that could be associated with backfat thickness in Canchim beef cattle. For SNP identification, sires with the highest accuracy were ranked according to expected breeding value for fat thickness; the 12 extremes (six sires with the highest and six with the lowest expected breeding value for the trait) were chosen. Six regions of the IGFBP3 and 14 regions of the DDEF1 were sequenced using the Sanger method. Nine SNPs were identified in IGFBP3 and 76 in the DDEF1. After an initial analysis, two SNPs were selected to be genotyped for the whole population; these were DDEF1g.279401A>G and IGFBP3c.4394T>C(Trp>Arg). We found a significant effect (P ≤ 0.05) of allele substitution on backfat thickness; however, the IGFBP3 SNP did not significantly affect this trait.

Association of an insulin-like growth factor 1 gene microsatellite with phenotypic variation and estimated breeding values of growth traits in Canchim cattle

A population of 1398 Canchim (CA) cattle was genotyped to assess the association of an insulin-like growth factor 1 (IGF1) gene microsatellite with phenotypic variation and estimated breeding values of pre-weaning, weaning and post-weaning growth traits. After an initial analysis, the IGF1 genotype only had a significant effect (P < 0.05) on birth weight (BW) and weaning weight adjusted to 240 days (WW240). For these two traits, direct and maternal breeding values were estimated using the restricted maximum likelihood (reml). Two analyses were carried out. In the first (Model I), all fixed effects were fitted. In the second (Model II), the fixed effect of the IGF1 genotype was omitted. The estimated genetic and phenotypic components of variance were similar for every trait in both models. For Model I, estimated direct and maternal heritabilities were 0.26 and 0.16 for BW and 0.23 and 0.14 for WW240 respectively. The genetic and phenotypic correlations between BW and WW240 were 0.38 and 0.38 (Model I) and 0.19 and 0.38 (Model II) respectively. Fifty animals were classified according to their direct and maternal breeding values for both traits. Spearman rank-order correlation between animal rankings in the two models was used to assess the effect of including the IGF1 genotype in the model. Non-significant values from this correlation were indicative of a difference in breeding value rankings between the two approaches. The IGF1 gene was found to be associated with phenotypic variation and breeding values in the early phase of growth.

Detection of Babesia bigemina in cattle of different genetic groups and in Rhipicephalus (Boophilus) microplus tick

Babesia bigemina infections were investigated in four genetic groups of beef cattle and in Rhipicephalus (Boophilus) microplus engorged female ticks. Blood samples and engorged female ticks were collected from 15 cows and 15 calves from each of the following genetic groups: Nelore, Angus x Nelore, Canchim x Nelore, and Simmental x Nelore. Microscopic examination of blood smears and tick hemolymph revealed that merozoites of B. bigemina (6/60) as well as kinetes of Babesia spp. (9/549) were only detected in samples (blood and ticks, respectively) originated from calves. PCR-based methods using primers for specific detection of B. bigemina revealed 100% infection in both calves and cows, regardless the genetic group. Tick infection was detected by nested-PCR amplifications showing that the frequency of B. bigemina was higher (P<0.01) in female ticks collected from calves (134/549) than in those collected from cows (52/553). The frequency of B. bigemina was similar in ticks collected from animals, either cows or calves, of the four genetic groups (P>0.05).

Mapping of quantitative trait loci controlling tick [Riphicephalus (Boophilus) microplus] resistance on bovine chromosomes 5, 7 and 14

Differences in domestication and selection processes have contributed to considerable phenotypic and genotypic differences between Bos taurus and Bos indicus cattle breeds. Of particular interest in tropical and subtropical production environments are those genetic differences between subspecies that underlie the phenotypic extremes in tolerance and susceptibility to parasite infection. In general, B. taurus cattle are more susceptible to ectoparasites than B. indicus cattle in tropical environments, and much of this difference is under genetic control. To identify genomic regions involved in tick resistance, we developed a B. taurus x B. indicus F(2) experimental population to map quantitative trait loci (QTL) for resistance to the Riphicephalus (Boophilus) microplus tick. About 300 individuals were measured for parasite load in two seasons (rainy and dry) and genotyped for 23 microsatellite markers covering chromosomes 5, 7 and 14. We mapped a suggestive chromosome-wide QTL for tick load in the rainy season (P < 0.05) on chromosome 5. For the dry season, suggestive (P < 0.10) chromosome-wide QTL were mapped on chromosomes 7 and 14. The additive effect of the QTL on chromosome 14 corresponds to 3.18% of the total observed phenotypic variance. Our QTL-mapping study has identified different genomic regions controlling tick resistance; these QTL were dependent upon the season in which the ticks were counted, suggesting that the QTL in question may depend on environmental factors.