Heat stress is an important issue in the global dairy industry. In tropical areas, an alternative to overcome heat stress is the use of crossbred animals or synthetic breeds, such as the Girolando. In this study, we performed a genome-wide association study (GWAS) and post-GWAS analyses for heat stress in an experimental Gir × Holstein F 2 population. Rectal temperature (RT) was measured in heat-stressed F 2 animals, and the variation between 2 consecutive RT measurements (ΔRT) was used as the dependent variable. Illumina BovineSNP50v1 BeadChip (Illumina Inc., San Diego, CA) and single-SNP approach were used for GWAS. Post-GWAS analyses were performed by gene ontology terms enrichment and gene-transcription factor (TF) networks, generated from enriched TF. The breed origin of marker alleles in the F 2 population was assigned using the breed of origin of alleles (BOA) approach. Heritability and repeatability estimates (± standard error) for ΔRT were 0.13 ± 0.08 and 0.29 ± 0.06, respectively. Association analysis revealed 6 SNP significantly associated with ΔRT. Genes involved with biological processes in response to heat stress effects (LIF, OSM, TXNRD2, and DGCR8) were identified as putative candidate genes. After performing the BOA approach, the 10% of F 2 animals with the lowest breeding values for ΔRT were classified as low-ΔRT, and the 10% with the highest breeding values for ΔRT were classified as high-ΔRT. On average, 49.4% of low-ΔRT animals had 2 alleles from the Holstein breed (HH), and 39% had both alleles from the Gir breed (GG). In high-ΔRT animals, the average proportion of animals for HH and GG were 1.4 and 50.2%, respectively. This study allowed the identification of candidate genes for ΔRT in Gir × Holstein crossbred animals. According to the BOA approach, Holstein breed alleles could be associated with better response to heat stress effects, which could be explained by the fact that Holstein animals are more affected by heat stress than Gir animals and thus require a genetic architecture to defend the body from the deleterious effects of heat stress. Future studies can provide further knowledge to uncover the genetic architecture underlying heat stress in crossbred cattle.

Rhipicephalus (Boophilus) microplus is the main cattle ectoparasite in tropical areas. Gir × Holstein crossbred cows are well adapted to different production systems in Brazil. In this context, we performed genome-wide association study (GWAS) and post-GWAS analyses for R. microplus resistance in an experimental Gir × Holstein F population. Single nucleotide polymorphisms (SNP) identified in GWAS were used to build gene networks and to investigate the breed of origin for its alleles. Tick artificial infestations were performed during the dry and rainy seasons. Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA) and single-step BLUP procedure was used for GWAS. Post-GWAS analyses were performed by gene ontology terms enrichment and gene transcription factors networks, generated from enriched transcription factors, identified from the promoter sequences of selected gene sets. The genetic origin of marker alleles in the F population was assigned using the breed of origin of alleles approach. Heritability estimates for tick counts were 0.40 ± 0.11 in the rainy season and 0.54 ± 0.11 in the dry season. The top ten 0.5-Mbp windows with the highest percentage of genetic variance explained by SNP markers were found in chromosomes 10 and 23 for both the dry and rainy seasons. Gene network analyses allowed the identification of genes involved with biological processes relevant to immune system functions (TREM1, TREM2, and CD83). Gene-transcription factors network allowed the identification of genes involved with immune functions (MYO5A, TREML1, and PRSS16). In resistant animals, the average proportion of animals showing significant SNPs with paternal and maternal alleles originated from Gir breed was 44.8% whereas the proportion of animals with both paternal and maternal alleles originated from Holstein breed was 11.3%. Susceptible animals showing both paternal and maternal alleles originated from Holstein breed represented 44.6% on average, whereas both paternal and maternal alleles originated from Gir breed animals represented 9.3%. This study allowed us to identify candidate genes for tick resistance in Gir × Holstein crossbreds in both rainy and dry seasons. According to the origin of alleles analysis, we found that most animals classified as resistant showed 2 alleles from Gir breed, while the susceptible ones showed alleles from Holstein. Based on these results, the identified genes may be thoroughly investigated in additional experiments aiming to validate their effects on tick resistance phenotype in cattle.

Backfat is an important trait in pork production, and it has been included in the breeding objectives of genetic companies for decades. Although adipose tissue is a good energy storage, excessive fat results in reduced efficiency and economical losses. A large QTL for backfat thickness on chromosome 5 is still segregating in different commercial pig breeds. We fine mapped this QTL region using a genome-wide association analysis (GWAS) with 133,358 genotyped animals from five commercial populations (Landrace, Pietrain, Large White, Synthetic, and Duroc) imputed to the porcine 660K SNP chip. The lead SNP was located at 5:66103958 (G/A) within the third intron of the CCND2 gene, with the G allele associated with more backfat, while the A allele is associated with less backfat. We further phased the QTL region to discover a core haplotype of five SNPs associated with low backfat across three breeds. Linkage disequilibrium analysis using whole-genome sequence data revealed three candidate causal variants within intronic regions and downstream of the CCND2 gene, including the lead SNP. We evaluated the association of the lead SNP with the expression of the genes in the QTL region (including CCND2) in a large cohort of 100 crossbred samples, sequenced in four different tissues (lung, spleen, liver, muscle). Results show that the A allele increases the expression of CCND2 in an additive way in three out of four tissues. Our findings indicate that the causal variant for this QTL region is a regulatory variant within the third intron of the CCND2 gene affecting the expression of CCND2.

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We aimed to evaluate the effects of sex and the linear and quadratic components of age of dam at calving, as well as apply a mixed model including maternal effect for the genetic evaluation of weaning (WW) and yearling (YW) weights. The phenotypic database was composed by Charolais, Caracu, Aberdeen Angus, and Canchim purebred and crossbred animals. Single-trait analyses were performed using models that included the maternal effect for WW and YW traits, and a model ignoring this effect on YW (YWNM). The Deviance Information Criterion (DIC), model posterior probabilities (MPP), accuracy of breeding values (ACC), and Spearman's rank correlation were applied to compare the models including and ignoring the maternal effect on YW. Sex and age of dam at calving had significant effects on WW and YW. The direct heritability estimates were 0.21±0.03 and 0.05±0.02, and the maternal heritabilities were 0.11±0.02 and 0.02±0.01 for WW and YW, respectively. The heritabilities estimated for YW may have been influenced by the several genetic groups in the population and by used conventional animal model, which may not have been the better fit model to evaluate YW in this population. The DIC, MPP, and ACC values indicated that YW outperformed the YWNM model, but the rank correlation and percentages of individuals selected in common suggested that the best animals would be selected independently of the model chosen.

Context Greater production of oocytes and embryos from Gir donors contributes to greater fertility and genetic progress. Aims This study aimed to obtain genetic parameters for oocyte and embryo production in the Gir breed. Methods Repeatability and random regression models were applied to data consisting of 17 526 Ovum Pick Up observations from 1641 Gir donors from five different herds. Single and multi-trait analyses were carried out with the application of both models for the traits: number of viable oocytes, number of total oocytes and number of embryos, using the BLUPF90 family programs. Legendre polynomials of second order were used in the random regression model. Key results Considering the repeatability model, additive genetic variance ranged from 0.06 to 0.13 and permanent environment variance ranged from 0.05 to 0.08 for all evaluated traits. Residual variance ranged from 0.30 to 0.45. Heritability estimates were 0.10 for number of embryos, 0.24 for total oocytes, and 0.25 for viable oocytes. Repeatability estimates were moderate, ranging from 0.20 to 0.40, and genetic correlation estimates were always above 0.80. Phenotypic correlation was high only between viable and total oocytes (0.95), and moderate in the other cases. Random regression model results were consistent with those from the repeatability model. The heritability values remained similar throughout the donors’ ages, with moderate values for viable and total oocytes, and low values for number of embryos. Genetic correlations among ages for each trait were moderate to high. Also, the genetic correlations between traits within each age were high, with values always above 0.7. Conclusions Selection of Gir donors for total oocyte production at any time, between 1 and 16 years of age, might lead to an increase in the number of viable oocytes and embryos obtained, but it’s preferable at younger ages to hasten genetic progress. Repeatability models could be the best method, as they require less computational effort when compared to the random regression models and the parameter estimates do not vary substantially throughout different ages of the donor. Implications The use of repeatability models to estimate genetic parameters of oocytes and embryos resulted in similar results compared to random regression models.

Cattle population history, breeding systems, and geographic subdivision may be reflected in runs of homozygosity (ROH), effective population size (Ne), 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, Ne, 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 Ne 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.

Dietary l‐arginine (ARG) supplementation has been studied as a nutritional strategy to improve reproductive performance of pregnant sows, since arginine is a conditionally essential amino acid. However, reports addressing the molecular mechanisms that mediate supplementation effects on embryos and fetuses development are still scarce. Therefore, we aimed to evaluate the effects of 1.0% ARG supplementation of commercial pregnant gilts on genes and proteins from energy metabolism and antioxidant defense pathways in embryos and fetuses. We also analyzed the global transcriptome profile of 25‐ and 35‐day‐old conceptuses. At Day 25, we observed a lower abundance of phospho‐AMP‐activated protein kinase (phospho‐AMPK) protein and downregulation of oxidative phosphorylation system genes in ARG embryos. On the other hand, ARG fetuses showed greater expression of MLST8 and lower expression of MTOR genes, in addition to lower abundance of phospho‐AMPK and phospho‐mammalian target of rapamycin (phospho‐mTOR) proteins. Transcriptome analysis at Day 35 did not present differentially expressed genes. For the antioxidant defense pathway, no differences were found between CON and ARG conceptuses, only trends. In general, supplementation of gilts with 1.0% ARG during early gestation affects energy sensitive pathways in 25‐ and 35‐day conceptuses; however, no effects of supplementation were found on the antioxidative defense pathway in 25‐day embryos.