Comparison between haplotype-based and individual snp-based genomic predictions for beef fatty acid profile in Nelore cattle Fabieli Loise Braga Feitosa, Angélica Simone Cravo Pereira, Sabrina Thaise Amorim, Elisa Peripolli, Rafael Medeiros de Oliveira Silva, et al. Journal of Animal Breeding and Genetics, 2020 The aim of this study was to evaluate the genomic predictions using the single-step genomic best linear unbiased predictor (ssGBLUP) method based on SNPs and haplotype markers associated with beef fatty acids (FAs) profile in Nelore cattle. The data set contained records from 963 Nelore bulls finished in feedlot (±90 days) and slaughtered with approximately 24 months of age. Meat samples from the Longissimus dorsi muscle were taken for FAs profile measurement. FAs were quantified by gas chromatography using a SP-2560 capillary column. Animals were genotyped with the high-density SNP panel (BovineHD BeadChip assay) containing 777,962 markers. SNPs with a minor allele frequency and a call rate lower than 0.05 and 0.90, respectively, monomorphic, located on sex chromosomes, and with unknown position were removed from the data set. After genomic quality control, a total of 469,981 SNPs and 892 samples were available for subsequent analyses. Missing genotypes were imputed and phased using the FImpute software. Haplotype blocks were defined based on linkage disequilibrium using the Haploview software. The model to estimate variance components and genetic parameters and to predict the genomic values included the random genetic additive effects, fixed effects of the contemporary group and the age at slaughter as a linear covariate. Accuracies using the haplotype-based approach ranged from 0.07 to 0.31, and those SNP-based ranged from 0.06 to 0.33. Regression coefficients ranged from 0.07 to 0.74 and from 0.08 to 1.45 using the haplotype- and SNP-based approaches, respectively. Despite the low to moderate accuracies for the genomic values, it is possible to obtain genetic progress trough selection using genomic information based either on SNPs or haplotype markers. The SNP-based approach allows less biased genomic evaluations, and it is more feasible when taking into account the computational and operational cost underlying the haplotypes inference.
Performance, carcass traits, meat quality and composition of non-castrated Nellore and crossbred male cattle fed soybean oil D.S. Antonelo, J.F.M. Gómez, R.S. Goulart, M. Beline, N.R.B. Cônsolo, et al. Livestock Science, 2020 The effects of soybean oil inclusion in a high concentrate diet on performance, carcass traits, meat quality and fatty acid (FA) composition of 30 Nellore (NEL) and 30 non-castrated crossbred Angus x Nellore (AxN) animals were evaluated in an 133-d feeding study. Animals were assigned in a randomized complete block (initial body weight) design using a 2×2 factorial arrangement. Treatments consisted of two genetic groups (NEL and AxN) and two diets: 1) a basal diet containing no soybean oil (CON) and 2) a basal diet containing 3.5% of soybean oil (SBO). Performance data were obtained during the feeding period. After slaughter, carcass traits were recorded and longissimus muscle samples were collected for FA composition and meat quality. No diet x genetic group interaction was detected for any trait. Diet did not affect meat colour or tenderness; however, C14:0, conjugated linolenic acid and the n-6:n-3 polyunsaturated FA (PUFA) ratio increased (P
Effects of n-3 and n-6 feeding sources on the quality and lipid oxidation of meat from feedlot-finished Bos indicus steers Fabiane S. Costa, Anderson R. Cabral, Saulo L. Silva, Marilia A.I. Silva, Wignez Henrique, et al. Meat Science, 2020 This study was conducted to evaluate the fatty acid profile, sensory properties and lipid oxidation of meat on retail display (RD) from Nellore steers (n = 96) fed diets containing soybean (SOY), sunflower (SUN), or linseed (LIN) oil or a control diet (CON). After slaughtering, samples of the Longissimus muscle were collected for sensory properties (1 day), fatty acid composition (1 day) and oxidation stability (3 days under RDC) evaluations. No differences in total lipids, cholesterol, TBARS, and total SFAs, MUFAs, PUFAs, and PUFA/SFA were observed. However, meat from animals fed vegetable oil had more CLA than that of the CON samples. The flavour, juiciness and overall acceptability were affected by the treatments (P < 0.05), but no consistent effect of a specific oil source was observed. Meat colour was not affected by diets or days under RD, and 7-ketocholesterol was not detected in any sample. The oil sources used in this work were not effective in consistently changing meat properties.
Gender status effect on carcass and meat quality traits of feedlot Angus × Nellore cattle Lenise Freitas Mueller, Júlio César Carvalho Balieiro, Adrielle Matias Ferrinho, Taiane da Silva Martins, Rosana Ruegger Pereira Silva Corte, et al. Animal Science Journal, 2019 The study evaluated the effect of gender status on carcass and meat quality of feedlot Angus × Nellore cattle. A total of 176 cattle, 20 months old, were confined for 190-days and assigned to four treatments: bulls, immunocastrated, steers, and heifers. Bulls had greater rib eye area and HCW (p = 0.0001). Heifers had increased fat thickness (p = 0.0001). Steers and heifers had higher marbling scores (p = 0.0001). There was interaction between gender and aging time for Warner-Bratzler Shear Force (p = 0.0002), L* (p = 0.0118), and b* (p = 0.0113) values of beef. The sensory panel results showed that beef from bulls had the lowest consumer overall acceptance (p = 0.0278). Especially, regardless tenderness, steers and immunocastrated beef were considered tender, independent of aging time. Beef produced by heifers, steers, and immunocastrated is considered to be of higher quality than bulls. Thus, it is may be an interesting alternative to produce high-quality beef than bulls, to attend the consumer demand for high-quality products. Additionally, the low fatty acids n6 levels and low n6:n3 ratio, high levels of CLA, MUFAs, and oleic acid suggests that the heifer meat is favorable for human health.
Effect of growth path on carcass and meat-quality traits of Hereford steers finished on pasture or in feedlot Adrielle Matias Ferrinho, Elisa Peripolli, Georgget Banchero, Angélica Simone Cravo Pereira, Gustavo Brito, et al. Animal Production Science, 2019 The objective of this study was to evaluate the effect of nutritional management during rearing and finishing phases on beef fatty acid composition, and carcass and beef quality traits of Hereford cattle. The study used 240 castrated male calves weaned at 8 months of age, and with an average weight of 170 ± 17 kg. After weaning, the experiment was divided in to three phases in a 4 × 2 factorial design: a 93-day winter period with four treatment groups (on pasture or in feedlot and at high or low feeding levels); a 196-day compensatory-growth phase on pasture; and a finishing phase either on pasture or in feedlot. Animals were slaughtered when each group attained a mean liveweight of 500 kg. The winter growth × finishing management interaction significantly affected hot carcass weight (P = 0.0029). There was no differences observed for feedlot-finished steers, but for pasture-finished steers, those pasture-reared had higher hot carcass weight (kg) than those feedlot-reared (low pasture 256.30 ± 1.60, high pasture 253.72 ± 1.60, low feedlot 249.85 ± 1.66, high feedlot 247.60 ± 1.62). Feedlot-finished steers showed higher (P &lt; 0.05) mean values than pasture-finished steers for ribeye area (55.61 ± 0.69 cm2 vs 53.18 cm2), backfat thickness (8.62 ± 0.32 mm vs 6.21 mm), marbling score (237.97 ± 13.06 vs 171.70) and final pH (5.53 ± 0.02 vs 5.48). Additionally, feedlot-finished steers raised in feedlot during the winter-growth period displayed the heaviest hindquarter cuts. Meat from pasture-finished steers had lower (P &lt; 0.05) shear-force values than from feedlot-finished cattle (2.95 ± 0.18 vs 3.66 ± 0.17 kg), and when reared on either high or low pasture during winter-growth, they showed the highest (P &lt; 0.05) conjugated linoleic acid (cis-9, trans-11) and n-3 polyunsaturated fatty acid concentrations. In conclusion, growing and finishing cattle on pasture improved the carcass yield of retail cuts because of low fat concentration, and improved the nutritional and health value of the beef fatty acid profile.
Genomic prediction ability for beef fatty acid profile in Nelore cattle using different pseudo-phenotypes Hermenegildo Lucas Justino Chiaia, Elisa Peripolli, Rafael Medeiros de Oliveira Silva, Fabiele Loise Braga Feitosa, Marcos Vinícius Antunes de Lemos, et al. Journal of Applied Genetics, 2018 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 (0.58), another with low heritability (0.13). Ten replicates were performed for each trait and results were averaged among replicates. A historical population was created from generation zero to 2020, with a constant size of 2000 animals (from generation zero to 1000) to produce different levels of linkage disequilibrium (LD). Therefore, there was a gradual reduction in the number of animals (from 2000 to 600), producing a “bottleneck effect” and consequently, genetic drift and LD starting in the generation 1001 to 2020. A total of 335,000 markers (with MAF greater or equal to 0.02) and 1000 QTL were randomly selected from the last generation of the historical population to generate genotypic data for the test population. The phenotypes were computed as the sum of the QTL effects and an error term sampled from a normal distribution with zero mean and variance equal to 0.88. For simulated data, 4000 animals of the generations 7, 8, and 9 (with genotype and phenotype) were used as training population, and 1000 animals of the last generation (10) were used as validation population. A total of 937 Nelore bulls with phenotype for fatty acid profiles (Sum of saturated, monounsaturated, omega 3, omega 6, ratio of polyunsaturated and saturated and polyunsaturated fatty acid profile) were genotyped using the Illumina BovineHD BeadChip (Illumina, San Diego, CA) with 777,962 SNP. To compare the accuracy and bias of direct genomic value (DGV) for different pseudo-phenotypes, the correlation between true breeding value (TBV) or DGV with pseudo-phenotypes and linear regression coefficient of the pseudo-phenotypes on TBV for simulated data or DGV for real data, respectively. For simulated data, the correlations between DGV and TBV for high heritability traits were higher than obtained with low heritability traits. For simulated and real data, the prediction ability was higher for GEBV than for Yc and EBV. For simulated data, the regression coefficient estimates (b(Yc,DGV)), were on average lower than 1 for high and low heritability traits, being inflated. The results were more biased for Yc and EBV than for GEBV. For real data, the GEBV displayed less biased results compared to Yc and EBV for SFA, MUFA, n-3, n-6, and PUFA/SFA. Despite the less biased results for PUFA using the EBV as pseudo-phenotype, the b(Yi,DGV estimates obtained for the different pseudo-phenotypes (Yc, EBV and GEBV) were very close. Genomic information can assist in improving beef fatty acid profile in Zebu cattle, since the use of genomic information yielded genomic values for fatty acid profile with accuracies ranging from low to moderate. Considering both simulated and real data, the ssGBLUP model is an appropriate alternative to obtain more reliable and less biased GEBVs as pseudo-phenotype in situations of missing pedigree, due to high proportion of multiple sires, being more adequate than EBV and Yc to predict direct genomic value for beef fatty acid profile.
Association study between copy number variation and beef fatty acid profile of Nellore cattle Marcos Vinicius Antunes de Lemos, Elisa Peripolli, Mariana Piatto Berton, Fabiele Loise Braga Feitosa, Bianca Ferreira Olivieri, et al. Journal of Applied Genetics, 2018 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., San Diego, CA, USA). The copy number variation (CNV) detection was performed using the PennCNV algorithm. Log R ratio (LRR) and allele B frequency (BAF) were used to estimate the CNVs. The association analyses were done using the CNVRuler software and applying a logistic regression model. The phenotype was adjusted using a linear model considering the fixed effects of contemporary group and the animal age at slaughter. The fatty acid profile was analyzed on samples of longissimus thoracis muscle using gas chromatography with a 100-m capillary column. For the association analysis, the adjusted phenotypic values were considered for the traits, while the data was adjusted for the effects of the farm and year of birth, management groups at birth, weaning, and superannuation. A total of 186 CNVRs were significant for SFA (43), MUFA (42), PUFA (66), and omega fatty acid (35) groups, totaling 278 known genes. On the basis of the results, several genes were associated with several fatty acids of different saturations. Olfactory receptor genes were associated with C12:0, C14:0, and C18:0 fatty acids. The SAMD8 and BSCL2 genes, both related to lipid metabolic process, were associated with C12:0. The RAPGEF6 gene was found to be associated with C18:2 cis-9 cis-12 n-6, and its function is related to regulation of GTPase activity. Among the results, we highlighted the olfactory receptor activity (GO:0004984), G-protein-coupled receptor activity (GO:0004930), potassium:proton antiporter activity (GO:0015386), sodium:proton antiporter activity (GO:0015385), and odorant-binding (GO:0005549) molecular functions. A large number of genes associated with fatty acid profile within the CNVRs were identified in this study. These findings must contribute to better elucidate the genetic mechanism underlying the fatty acid profile of intramuscular fat in Nellore cattle.
Whole cottonseed, vitamin E and finishing period affect the fatty acid profile and sensory traits of meat products from Nellore cattle Adrielle M. Ferrinho, Renata T. Nassu, Noelia Aldai, Leire Bravo-Lamas, Maísa L.N. Furlan, et al. Meat Science, 2018 This study investigated how different finishing periods and the inclusion of whole cottonseed and vitamin E in diets fed to feedlot cattle affect meat lipid composition and sensory traits of fresh beef and hamburgers. Fifty-four Nellore bulls were fed 3 different diets (C: control; WCS: 30% whole cottonseed; WCSE: 30% whole cottonseed plus vitamin E) during finishing periods of 83, 104, and 111days. The inclusion of cottonseed did not affect saturated fatty acid levels (SFA), but increased the levels of certain polyunsaturated fatty acids (PUFA) in meat. The SFA levels and n-6/n-3 ratio increased over the length of finishing period. In general, meat products from animals fed the WCS and WCSE diets were more tender and juicier (P<0.05); however, an off-flavor was detected by the panelists (P<0.05). The sensory difference test results showed that the WCS hamburger flavor was not significantly different for the studied lengths of finishing period. Addition of 30% DM cottonseed in diets for cattle did not promote changes likely to affect human health, and it provided a more tender and juiciness meat, however differences in the off flavor were perceived only by panelist.
Genetic parameters for fatty acids in intramuscular fat from feedlot-finished Nelore carcasses Carolyn Aboujaoude, Angélica Simone Cravo Pereira, Fabieli Louise Braga Feitosa, Marcos Vinicius Antunes de Lemos, Hermenegildo Lucas Justino Chiaia, et al. Animal Production Science, 2018 The aim of the present study was to estimate covariance components and genetic parameters for beef fatty acid (FA) composition of intramuscular fat in the longissimus thoracis muscle in Nelore bulls finished in feedlot. Twenty-two FAs were selected. The heritability estimates for individual FAs ranged from 0.01 to 0.35. The heritability estimates for myristic (0.25 ± 0.09), palmitic (0.18 ± 0.07), oleic (0.28 ± 0.09), linoleic (0.16 ± 0.06) and α-linolenic (0.35 ± 0.10) FAs were moderate. Stearic, elaidic, palmitoleic, vaccenic, conjugated linoleic acid, docosahexanoic, eicosatrienoic and arachidonic FAs had heritability estimates below 0.15. The genetic-correlation estimates between the individual saturated FAs (SFAs) were low and negative between myristic and stearic FAs (–0.22 ± 0.84), moderate between palmitic and myristic FAs (0.58 ± 0.56) and negative between palmitic and stearic FAs (–0.69 ± 0.45). The genetic correlations between the individual long-chain polyunsaturated FAs (PUFAs) were positive and moderate (>0.30). However, the genetic-correlation estimates between long-chain PUFAs and α-linolenic acid were low (<0.30), except for the correlation between arachidonic and α-linolenic acids. The genetic correlation estimates of the sums of SFAs with monounsaturated fatty acids and omega 6 FAs were low (0.25 ± 0.59 and –0.02 ± 0.51 respectively), high with PUFAs and omega 9 FAs (–0.85 ± 0.15 and 0.86 ± 0.17 respectively) and moderate with omega 3FAs (–0.67 ± 0.26). The present study demonstrated the existence of genetic variation and, hence, the possibility to increase the proportion of healthy and favourable beef FAs through selection. The results obtained in the study have provided knowledge to elucidate the additive genetic influence on FA composition of intramuscular fat. In addition, genetic-relationship estimates of intramuscular FA profile help seek strategies for genetic selection or genetic-based diet management to enhance the FA profile in Zebu cattle.
