Genetic effects of heat stress on milk fatty acids in Brazilian Holstein cattle.

The present study aimed to estimate covariance components of milk fatty acids (FA) and to compare the genomic estimated breeding values under general and heat-stress effects. Data consisted of 38,762 test-day records from 6,344 Holstein cows obtained from May 2012 through January 2018 on 4 dairy herds from Brazil. Single-trait repeatability test-day models with random regressions as a function of temperature-humidity index values were used for genetic analyses. The models included contemporary groups, parity order (1-6), and days in milk classes as fixed effects, and general and thermotolerance additive genetic and permanent environmental as random effects. Notably, differences in heritability estimates between environments (general and heat stress) increased (0.03 to 0.06) for unsaturated FA traits, such as unsaturated, monounsaturated, and polyunsaturated, at higher heat-stress levels. In contrast, heritability estimated between environments for saturated FA traits, including saturated FA, palmitic acid (C16:0), and stearic acid (C18:0) did not observe significant differences between environments. In addition, our study revealed negative genetic correlations between general and heat-stress additive genetic effects (antagonistic effect) for the saturated FA, C16:0, C18:0, and C18:1, which ranged from -0.007 to -0.32. Spearman's ranking correlation between genomic estimated breeding values ranged from -0.27 to 0.99. Results indicated a moderate to strong interaction of genotype by the environment for most FA traits comparing a heat-stress environment with thermoneutral conditions. Our findings point out novel opportunities to explore the use of FA milk profile and heat-stress models.

Genetic dissection of bull fertility in US Jersey dairy cattle.

The service sire has been recognized as an important factor affecting herd fertility in dairy cattle. Recent studies suggest that genetic factors explain part of the difference in fertility among Holstein sires. The main objective of this study was to dissect the genetic architecture of sire fertility in US Jersey cattle. The dataset included 1.5 K Jersey bulls with sire conception rate (SCR) records and 96 K single nucleotide polymorphism (SNP) markers spanning the whole genome. The analysis included whole-genome scans for both additive and non-additive effects and subsequent functional enrichment analyses using KEGG Pathway, Gene Ontology (GO) and Medical Subject Headings (MeSH) databases. Ten genomic regions located on eight different chromosomes explained more than 0.5% of the additive genetic variance for SCR. These regions harbor genes, such as PKDREJ, EPB41L2, PDGFD, STX2, SLC25A20 and IP6K1, that are directly implicated in testis development and spermatogenesis, sperm motility and the acrosome reaction. In addition, the genomic scan for non-additive effects identified two regions on BTA11 and BTA25 with marked recessive effects. These regions harbor three genes-FER1L5, CNNM4 and DNAH3-with known roles in sperm biology. Moreover, the gene-set analysis revealed terms associated with calcium regulation and signaling, membrane fusion, sperm cell energy metabolism, GTPase activity and MAPK signaling. These gene sets are directly implicated in sperm physiology and male fertility. Overall, this integrative genomic study unravels genetic variants and pathways affecting Jersey bull fertility. These findings may contribute to the development of novel genomic strategies for improving sire fertility in Jersey cattle.

Genotypic and allelic frequencies of gene polymorphisms associated with meat tenderness in Nellore beef cattle.

The objectives of this study were to characterize the allelic and genotypic frequencies of polymorphisms in the µ-calpain and calpastatin genes, and to assess their association with meat tenderness and animal growth in Nellore cattle. We evaluated 605 Nellore animals at 24 months of age, on average, at slaughter. The polymorphisms were determined for the molecular markers CAPN316, CAPN530, CAPN4751, CAPN4753, and UOGACAST1. Analyses of meat tenderness at 7, 14, and 21 days of maturation were performed in samples of longissimus thoracis obtained between the 12th and 13th rib and sheared using a Warner Bratzler Shear Force. Significant effects were observed for meat tenderness at days 7, 14, and 21 of maturation for the marker CAPN4751, at day 21 for the marker CAPN4753, and at days 14 and 21 for the marker UOGCAST1. For genotypic combinations of markers, the results were significant for the combination CAPN4751/UOGCAST1 in the three maturation periods and CAPN4753/UOGCAST1 at days 14 and 21 of maturation.

Quantitative genetic study of age at subsequent rebreeding in Nellore cattle by using survival analysis.

The continuous trait age at subsequent rebreeding (ASR) was evaluated using survival analysis in Nellore breed cows that conceived for the first time at approximately 14 months of age. This methodology was chosen because the restricted breeding season produces censored data. The dataset contained 2885 records of ASR (in days). Records of females that did not produce calves in the following year after being exposed to a sire were considered censored (48.3% of the total). The statistical model used was a Weibull mixed survival model, which included fixed effects of contemporary groups (CG) and period and a random effect of individual animal. The effect of contemporary groups on ASR was significant (P < 0.01). Heritabilities obtained for ASR were 0.03 and 0.04 in logarithmic and original scales, respectively. These results indicate that the genetic selection response for subsequent reproduction of 2-year-old Nellore breed females is not expected to be effective based on survival analysis. Furthermore, these results suggest that environmental improvement is fundamental to this important trait. It should be highlighted that an increase in the average date of birth can produce an adverse effect in the future, since this cannot be compensated by genetic improvement.

Sire effects on carcass and meat quality traits of young Nellore bulls.

Meat quality is being increasingly demanded by consumers in recent years. Several factors can affect meat quality, ranging from animal traits such as breed and genetic heritage to pre- and post-slaughter processes. This study investigated the influence of Nellore bulls on carcass and meat quality traits. We used 475 young uncastrated males, the progeny of 54 bulls, to evaluate characteristics of the following carcass traits: hot carcass weight, rib-eye area, and fat thickness. We also evaluated the following beef quality traits: marbling, color, drip loss, cooking loss, and shear force at 0, 7, and 14 days of aging. Bulls had a significant influence (P≤0.05) on rib-eye area, fat thickness, marbling, drip loss at 14 days of aging and color at all aging periods. Based on these results, the use of bulls with high breeding values for these traits can provide important advances in carcass traits and meat quality in breeding programs of Nellore cattle that are raised in tropical conditions.

Protein synthesis and degradation gene SNPs related to feed intake, feed efficiency, growth, and ultrasound carcass traits in Nellore cattle.

We looked for possible associations of SNPs in genes related to protein turnover, with growth, feed efficiency and carcass traits in feedlot Nellore cattle. Purebred Nellore bulls and steers (N = 290; 378 ± 42 kg body weight, 23 months ± 42 days old) were evaluated for daily feed intake, body weight gain (BWG), gross feed efficiency, feed conversion ratio, partial efficiency of growth, residual feed intake (RFI), ultrasound backfat, rump fat, and ribeye area. Genotypes were obtained for SNPs in the growth hormone receptor (GHR-1 and GHR-2); calpain (CAPN4751); calpastatin (UoGCAST); ubiquitin-conjugating enzyme 2I (UBE2I-1 and UBE2I-2); R3H domain containing 1 (R3HDM1-1, -2, -3, and -4), ring finger protein 19 (RNF19); proteasome 26S subunit, non-ATPase, 13 (PSMD13); ribosomal protein, large, P2 (RPLP2); and isoleucine-tRNA synthetase 2, mitochondrial (IARS2) genes. Allelic substitution, additive and dominant effects were tested and molecular breeding values were computed. CAPN4751, GHR-1 and -2, IARS2, R3HDM1-4, and UoGCAST were found to be normally segregating polymorphisms. Additive and dominance effects were observed on BWG, feed efficiency and carcass traits, although dominant effects predominated. Significant allelic substitution effects were observed for CAPN4751, GHR-1 and -2, and UoGCAST on BWG, gross feed efficiency, RFI, and carcass traits, under single- or multiple-marker analyses. Correlations between molecular breeding values and phenotypes were low, excepted for RFI, based on allelic substitution estimates obtained by stepwise linear regression. We conclude that SNPs in genes related to protein turnover are related to economically important traits in Nellore cattle.

Association of single nucleotide polymorphisms in the bovine leptin and leptin receptor genes with growth and ultrasound carcass traits in Nellore cattle.

Given the important role of leptin in metabolism, we looked for a possible association of leptin and leptin receptor polymorphisms with carcass and growth traits in Nellore cattle. We examined associations of leptin and leptin receptor SNPs with ultrasound carcass (longissimus dorsi muscle area (ribeye area), backfat thickness and rump fat thickness and growth traits (weaning weight adjusted to 210 days of age, yearling weight adjusted to 550 days of age, weight gain of weaning to yearling and scrotal circumference adjusted to 550 days of age) of 2162 Bos primigenius indicus (Nellore) animals. Allele and genotypic frequencies were calculated for each marker. Allele substitution, additive and dominance effects of the polymorphisms were also evaluated. Some alleles of the molecular markers had low frequencies, lower than 1%, in the sample analyzed, although the same polymorphisms described for B. p. taurus cattle were found. Due to very low allelic frequencies, the E2JW, A59V and UASMS2 markers were not included in the analysis, because they were almost fixed. E2FB was found to be significantly associated with weight gain, ribeye area and backfat thickness. The promoter region markers, C963T and UASMS1, were also found to be significantly associated with ribeye area. T945M was significantly associated with weight gain. We conclude that the leptin and receptor gene markers would be useful for marker-assisted selection.

Single nucleotide polymorphisms in CAPN and leptin genes associated with meat color and tenderness in Nellore cattle.

We analyzed single nucleotide polymorphisms in calpain, leptin, leptin receptor, and growth hormone receptor genes and their association with color, drip and cooking losses of longissimus muscle at 7, 14 and 21 days postmortem in 638 purebred Nellore bulls slaughtered between 22 and 26 months of age. Meat samples were vacuum-packed and aged at 4°C. The single nucleotide polymorphisms T945M, GHR2, E2FB, and CAPN4751 were evaluated. All genotypic classes were observed; however, the T/T genotype of T945M and E2FB was found at a low frequency. A significant association of E2FB with drip loss (a measure of water-holding capacity) was detected at seven days of meat aging. CAPN4751 had an additive effect on red and yellow color intensities. The T allele of CAPN4751 was found to be positively associated with improved meat color, but not with meat tenderness, differing from a previous report indicating that it is associated with meat tenderness. We conclude that the potential for use of CAPN4751 as a marker for these meat quality traits requires further research.

Association of SNPs on CAPN1 and CAST genes with tenderness in Nellore cattle.

We examined whether single-nucleotide polymorphisms (SNPs) in the calpain (CAPN) and calpastatin (CAST) genes, described from Bos primigenius taurus, are polymorphic in Nellore cattle. We also looked for a possible association of linkage disequilibrium of this polymorphism with tenderness of the longissimus dorsi muscle after 7, 14 and 21 days of postmortem aging in 638 purebred Nellore bulls. Meat tenderness was measured as Warner-Bratzler shear force. Additive and dominance effects were tested for SNPs of the three genotypic classes; the substitution effect was tested for SNPs with missing genotypic classes. Genotypic and gene frequencies were also calculated for the different SNPs. An increase in tenderness was observed from 7 to 21 days; the average values for shear force at 7, 14 and 21 days of aging were 5.92 +/- 0.06, 4.92 +/- 0.05, and 4.38 +/- 0.04 kg, respectively. All markers showed polymorphism, but there was no CC genotype for CAPN316, and few animals showed the AA genotype for CAPN530. The alleles CAPN4751, UOGCAST1, and WSUCAST were found to have additive and dominance effects for shear force at 7, 14 and 21 days, while CAPN316 showed a substitution effect for shear force at 7 and 21 days. An additive-by-additive epistatic interaction was observed between CAPN4751 and markers on the CAST gene. In conclusion, these markers should be considered for use in breeding programs.

Association of single nucleotide polymorphisms with carcass traits in Nellore cattle.

The association between two single nucleotide polymorphisms (SNPs), T945M and UCP1SNP1, with hot carcass weight (HCW, kg, N = 618), longissimus dorsi muscle area (REA, cm(2), N = 633), and backfat thickness (BF, mm, N = 625), measured in Nellore cattle in Brazil, was evaluated. Likelihood ratio tests were used to evaluate reduced (fixed effects of general mean, contemporary group, yearling weight, age at slaughter, and random effect of infinitesimal genetic value) and full model (reduced model effects plus quantitative trait locus effects). Additive and dominance effects were tested for each SNP. Genotypic and gene frequencies were also obtained for the SNPs and a descriptive phenotype analysis was made. Mean values for HCW, REA and BF were equal to 288.13 +/- 0.55 kg, 73.14 +/- 0.27 cm(2), and 4.28 +/- 0.07 mm, respectively; the coefficients of variation were 4.74, 9.24, and 42.43%, respectively. Gene frequencies for T945M and UCP1SNP1 were f(C) = 0.89, f(T) = 0.11, f(C) = 0.81, and f(G) = 0.19. The SNP T945M had a genotypic frequency of only three animals for TT genotype. Additive effects were observed for T945M on REA and BF, while UCP1SNP1 affected HCW and BF. Based on the significant additive effects of the SNPs and the gene frequencies that we found, we can expect genetic gains with marker assisted selection.

Estimates of genetic trend for carcass traits in a commercial broiler line.

Data from the slaughter of 24,001 chickens that were part of a selection program for the production of commercial broilers were used to estimate genetic trend for absolute carcass (CW), breast meat (BRW), and leg (LW) weights, and relative carcass (CY), breast meat (BRY), and leg (LY) weights. The components of (co)variance and breeding values of individuals were obtained by the restricted maximum likelihood method applied to animal models. The relationship matrix was composed of 132,442 birds. The models included as random effects, maternal additive genetic and permanent environmental for CW, BRW, LW, CY, and BRY, and only maternal permanent environmental for LY, besides the direct additive genetic and residual effects, and as fixed effects, hatch week, parents' mating group and sex. The estimates of genetic trend were obtained by average regression of breeding value on generation, and the average genetic trend was estimated by regression coefficients. The genetic trends for CW (+6.0336 g/generation), BRW (+3.6723 g/generation), LW (+1.5846 g/generation), CY (+0.1195%/generation), and BRY (+0.1388%/generation) were positive, and they were in accordance with the objectives of the selection program for these traits. The genetic trend for LY (-0.0019%/generation) was negative, possibly due to the strong emphasis on selection for BRY and the negative correlations between these two traits.

Genetic trends of absolute and relative heart weight in a male broiler line.

Data of chickens from a broiler-breeding program have been collected and used for determination of genetic trends of absolute and relative heart weight. The genetic trends have been estimated by regression of the genetic values of the traits over hatch-year. Genetic values of 42,912 individuals, obtained by restricted maximum likelihood, were used for regression analysis. The estimates of the genetic trends for absolute and relative heart weight were found to be -0.08 g and -0.004% per hatch-year, respectively. These trends show that heart weight in the line analyzed, in absolute and relative terms, has tended to decrease, which can make the metabolic disorders due to the reduction in heart weight in broilers even worse.

Genetic trends of absolute and relative heart weight in a male broiler line

Data of chickens from a broiler-breeding program have been collected and used for determination of genetic trends of absolute and relative heart weight. The genetic trends have been estimated by regression of the genetic values of the traits over hatch-year. Genetic values of 42,912 individuals, obtained by restricted maximum likelihood, were used for regression analysis. The estimates of the genetic trends for absolute and relative heart weight were found to be -0.08 g and -0.004% per hatch-year, respectively. These trends show that heart weight in the line analyzed, in absolute and relative terms, has tended to decrease, which can make the metabolic disorders due to the reduction in heart weight in broilers even worse.

Heritability and genetic correlation estimates for performance and carcass and body composition traits in a male broiler line.

The current research was conducted to estimate the heritability coefficients and the genetic correlations for performance and carcass and body composition traits in a single sire broiler line. The performance traits analyzed were BW at 38 d, ultrasound records of pectoral muscle depth, feed intake, feed conversion ratio, and BW at 42 d. The carcass traits analyzed were eviscerated BW, breast weight, and leg weight, and the body composition traits analyzed were abdominal fat content, heart weight, gizzard weight, liver weight, and intestine weight. The number of observations varied between 4,120 and 29,040 for each trait. The (co)variance components, heritability, and genetic correlation estimates were obtained by restricted maximum likelihood. The numerator relationship matrix had 42,912 animals. Based on the heritability estimates obtained, the analyzed traits seemed to be able to respond to selection, at variable intensities. The genetic correlation estimates between a great number of performance traits, as well as between a great number of carcass traits, were suggestive of a close genetic relationship between these traits. The genetic correlation estimates between body composition traits were variable. A large genetic association between a great number of performance and carcass traits seemed to exist. The genetic correlation estimates between performance and body composition traits were variable, and important associations between carcass and body composition traits did not seem to exist.

Genetic trends of abdominal fat content in a male broiler chicken line

Data of chickens from a broiler-breeding program were collected and used to determine the genetic trends of absolute and relative abdominal fat content. The genetic trends were estimated by the regression of trait genetic value averages on hatch-years. Genetic values from 32,485 individuals were used for regression analysis. The genetic trend estimate for absolute abdominal fat content was +0.39 g per year, indicating that abdominal fat deposition in the analyzed line, in absolute terms, tended to increase, making the existing excess fat deposition in the broilers even worse. However, the genetic trend of relative abdominal fat content was not significant, indicating that there is no increase on abdominal fat content when it is corrected for body weight.