Weighted genomic prediction for growth and carcass-related traits in Nelore cattle.

This study aimed to assess the impact of differential weighting in genomic regions harboring candidate causal loci on the genomic prediction accuracy and dispersion for growth and carcass-related traits in Nelore cattle. The dataset contained 168 793 phenotypic records for adjusted weight at 450 days of age (W450), 83 624 for rib eye area (REA), 24 480 for marbling (MAR) and 82 981 for subcutaneous backfat thickness (BFT) and rump fat thickness (RFT). The pedigree harbored information from 244 254 animals born between 1977 and 2016, including 6283 sires and 50 742 dams. Animals (n = 7769) were genotyped with the low-density panel (Clarifide® Nelore 3.0), and the genotypes were imputed to a panel containing 735 044 markers. A linear animal model was applied to estimate the genetic parameters and to perform the weighted single-step genome-wide association study (WssGWAS). A total of seven models for genomic prediction were evaluated combining the SNP weights obtained in the iterations of the WssGWAS and the candidate QTL. The heritability estimated for W450 (0.35) was moderate, and for carcass-related traits, the estimates were moderate for REA (0.27), MAR (0.28) and RFT (0.28), and low for BFT (0.18). The prediction accuracy for W450 incorporating reported QTL previously described in the literature along with different SNPs weights was like those described for the default ssGBLUP model. The use of the ssGWAS to weight the SNP effects displayed limited advantages for the REA prediction accuracy. Comparing the ssGBLUP with the BLUP model, a meaningful improvement in the prediction accuracy from 0.09 to 0.63 (700%) was observed for MAR. The highest prediction accuracy was obtained for BFT and RFT in all evaluated models. The application of information obtained from the WssGWAS is an alternative to reduce the genomic prediction dispersion for growth and carcass-related traits, except for MAR. Furthermore, the results obtained herein pointed out that is possible to improve the prediction accuracy and reduce the genomic prediction dispersion for growth and carcass-related traits in young animals.

Genomic evaluation of commercial herds with different pedigree structures using the single-step genomic BLUP in Nelore cattle.

The aim of this work was to evaluate the impact of applying genomic information in pedigree uncertainty situations on genetic evaluations for growth- and cow productivity-related traits in Nelore commercial herds. Records for accumulated cow productivity (ACP) and adjusted weight at 450 days of age (W450) were used, as well as genotypes of registered and commercial herd animals, genotyped with the Clarifide Nelore 3.1 panel (~29,000 SNPs). The genetic values for commercial and registered populations were estimated using different approaches that included (ssGBLUP) or did not include genomic information (BLUP), with different pedigree structures. Different scenarios were tested, varying the proportion of young animals with unknown sires (0, 25, 50, 75, and 100%), and unknown maternal grandsires (0, 25, 50, 75, and 100%). The prediction accuracies and abilities were calculated. The estimated breeding value accuracies decreased as the proportion of unknown sires and maternal grandsires increased. The genomic estimated breeding value accuracy using the ssGBLUP was higher in scenarios with a lower proportion of known pedigree when compared to the BLUP methodology. The results obtained with the ssGBLUP showed that it is possible to obtain reliable direct and indirect predictions for young animals from commercial herds without pedigree structure.

Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattle.

This study aimed to integrate analyses of structural variations and differentially expressed genes (DEGs) associated with the beef fatty acid (FA) profile in Nellore cattle. Copy numbers variation (CNV) detection was performed using the penncnv algorithm and CNVRuler software in 3794 genotyped animals through the High-Density Bovine BeadChip. In order to perform the genomic wide association study (GWAS), a total of 963 genotyped animals were selected to obtain the intramuscular lipid concentration and quantify the beef FA profile. A total of 48 animals belonging to the same farm and management lot were extracted from the 963 genotyped and phenotyped animals to carry out the transcriptomic and differentially expressed gene analyses. The GWAS with extreme groups of FA profiles was performed using a logistic model. A total of 43, 42, 66 and 35 significant CNV regions (p < 0.05) for saturated, monounsaturated, polyunsaturated and omega 3 and 6 fatty acids were identified respectively. The paired-end sequencing of 48 samples was performed using the Illumina HiSeq2500 platform. Real-time quantitative PCR was used to validate the DEGs identified by RNA-seq analysis. The results showed several DEGs associated with the FA profile of Longissimus thoracis, such as BSCL2 and SAMD8. Enriched terms as the cellular response to corticosteroid (GO:0071384) and glucocorticoid stimulus (GO:0071385) could be highlighted. The identification of structural variations harboring candidate genes for beef FA must contribute to the elucidation of the genetic basis that determines the beef FA composition of intramuscular fat in Nellore cattle. Our results will contribute to the identification of potential biomarkers for complex phenotypes, such as the FA profile, to improve the reliability of the genomic predictions including pre-selected variants using differentiated weighting in the genomic models.

Effects of Feeding Increasing Levels of Yerba Mate on Lamb Meat Quality and Antioxidant Activity.

The present study investigated the inclusion of yerba mate extract (YME) in the lamb's diet on meat quality traits, antioxidant activity, and shelf-life. Thirty-six lambs were distributed according to a block design with the following groups: control group without YME (0%) and three treatment groups with 1, 2, and 4% YME inclusion in the dry matter. The animals were fed these diets for 53 days. Samples were collected from the Longissimusthoracis (LT) muscle to analyze antioxidant activity and meat quality. Samples were placed on a counter display simulating a retail environment for 0, 3, and 6 days at 4 ± 2 °C. All data were analyzed using a MIXED model with orthogonal contrasts. Inclusion of 1 and 4% YME in the diet changed the yellow (b*) and the chroma (C*) of the meat (p ≤ 0.05). The pH, colour, thiobarbituric acid reactive substances, and carbonyl values were influenced by the retail display time for all the evaluated treatments (p ≤ 0.03). However, neither diet nor the retail display time influenced the oxidation of proteins or the antioxidant enzyme activities of catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPX) and glutathione activity (GSH) in meat. Therefore, the inclusion of 4% YME showed positive results in the yellow and colour stability parameters of the meat without increasing the lipid peroxidation values or altering the normal meat quality parameters in lambs.

Effects of n-3 and n-6 feeding sources on the quality and lipid oxidation of meat from feedlot-finished Bos indicus steers.

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.

Meat quality of lambs supplemented with intramuscular vitamin E / Qualidade da carne de cordeiros suplementados com vitamina E por via intramuscular

This study evaluated the effects of intramuscular alpha-tocopherol (vitamin E) supplementation on meat quality characteristics of Santa Inês and Dorper crossbreed lambs. All animals were feed with a high concentrated diet in feedlot. Eight days before slaughter, the animals were distributed into four blocks according to weight gain. At the seventh and fourth days before slaughter, they were intramuscularly treated with 0, 10 or 20 IU of DL-alpha-tocopherol per kg of metabolic body weight. At slaughter they had 138 days of age and 43.6 kg of live weight, in average. Carcasses were stored for 24 hours under refrigeration at 2°C. Longissimus thoracis muscle pH (pH24h) and color (lightness, yellowness and redness) were analyzed and its samples were collected for evaluation of shear force (SF), cooking loss (WLC), fatty acid composition (FA) and thiobarbituric acid reactive substances after one (TBARS1m) and after five months (TBARS5m) of freezing. Linearity deviation effect was observed for lightness (L*; P=0.0042) and yellowness (b*; P=0.0082). Intramuscular administration of 10 or 20 IU of alpha-tocopherol/kg of metabolic weight did not influence the conservation of fatty acid in the carcasses, but benefit L* and b* values.(AU)

O estudo avaliou os efeitos da suplementação pela via intramuscular de alfa-tocoferol (vitamina E) na qualidade da carne de cordeiros mestiços Santa Inês e Dorper. Os animais foram mantidos em confinamento, sendo alimentados com dieta contendo alto teor de concentrado energético. Oito dias antes do abate os cordeiros foram distribuídos em quatro blocos, de acordo com seu ganho de peso. No sétimo e quarto dias antes do abate eles foram tratados por via intramuscular com 0, 10 ou 20 UI de DL-alfa-tocoferol por kg de peso metabólico. No momento do abate os animais tinham, em média, 138 dias de idade e 43,6 kg de peso vivo. As carcaças foram armazenadas a 2°C por 24 horas. Foram determinados pH (pH24h) e cor (luminosidade, teor de vermelho e teor de amarelo) do músculo Longissimus thoracis, bem como força de cisalhamento, perda por cocção, composição dos ácidos graxos e quantidade de substâncias reativas ao ácido tiobarbitúrico após um e cinco meses de congelamento. Observou-se efeito de desvio da linearidade para luminosidade (L*; P=0.0042) e para o croma amarelo (b*; P=0.0082). A administração intramuscular de 10 e 20 UI de alfa-tocoferol/kg de peso metabólico não influenciou a conservação de ácidos graxos das carcaças, mas melhorou os valores de L* e b*.(AU)

Whole cottonseed, vitamin E and finishing period affect the fatty acid profile and sensory traits of meat products from Nellore cattle.

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.

Gene expression profile of intramuscular muscle in Nellore cattle with extreme values of fatty acid.

BACKGROUND: Fatty acid type in beef can be detrimental to human health and has received considerable attention in recent years. The aim of this study was to identify differentially expressed genes in longissimus thoracis muscle of 48 Nellore young bulls with extreme phenotypes for fatty acid composition of intramuscular fat by RNA-seq technique. RESULTS: Differential expression analyses between animals with extreme phenotype for fatty acid composition showed a total of 13 differentially expressed genes for myristic (C14:0), 35 for palmitic (C16:0), 187 for stearic (C18:0), 371 for oleic (C18:1, cis-9), 24 for conjugated linoleic (C18:2 cis-9, trans11, CLA), 89 for linoleic (C18:2 cis-9,12 n6), and 110 genes for α-linolenic (C18:3 n3) fatty acids. For the respective sums of the individual fatty acids, 51 differentially expressed genes for saturated fatty acids (SFA), 336 for monounsaturated (MUFA), 131 for polyunsaturated (PUFA), 92 for PUFA/SFA ratio, 55 for ω3, 627 for ω6, and 22 for ω6/ω3 ratio were identified. Functional annotation analyses identified several genes associated with fatty acid metabolism, such as those involved in intra and extra-cellular transport of fatty acid synthesis precursors in intramuscular fat of longissimus thoracis muscle. Some of them must be highlighted, such as: ACSM3 and ACSS1 genes, which work as a precursor in fatty acid synthesis; DGAT2 gene that acts in the deposition of saturated fat in the adipose tissue; GPP and LPL genes that support the synthesis of insulin, stimulating both the glucose synthesis and the amino acids entry into the cells; and the BDH1 gene, which is responsible for the synthesis and degradation of ketone bodies used in the synthesis of ATP. CONCLUSION: Several genes related to lipid metabolism and fatty acid composition were identified. These findings must contribute to the elucidation of the genetic basis to improve Nellore meat quality traits, with emphasis on human health. Additionally, it can also contribute to improve the knowledge of fatty acid biosynthesis and the selection of animals with better nutritional quality.

Genome-wide association between single nucleotide polymorphisms with beef fatty acid profile in Nellore cattle using the single step procedure.

BACKGROUND: Saturated fatty acids can be detrimental to human health and have received considerable attention in recent years. Several studies using taurine breeds showed the existence of genetic variability and thus the possibility of genetic improvement of the fatty acid profile in beef. This study identified the regions of the genome associated with saturated, mono- and polyunsaturated fatty acids, and n-6 to n-3 ratios in the Longissimus thoracis of Nellore finished in feedlot, using the single-step method. RESULTS: The results showed that 115 windows explain more than 1 % of the additive genetic variance for the 22 studied fatty acids. Thirty-one genomic regions that explain more than 1 % of the additive genetic variance were observed for total saturated fatty acids, C12:0, C14:0, C16:0 and C18:0. Nineteen genomic regions, distributed in sixteen different chromosomes accounted for more than 1 % of the additive genetic variance for the monounsaturated fatty acids, such as the sum of monounsaturated fatty acids, C14:1 cis-9, C18:1 trans-11, C18:1 cis-9, and C18:1 trans-9. Forty genomic regions explained more than 1 % of the additive variance for the polyunsaturated fatty acids group, which are related to the total polyunsaturated fatty acids, C20:4 n-6, C18:2 cis-9 cis12 n-6, C18:3 n-3, C18:3 n-6, C22:6 n-3 and C20:3 n-6 cis-8 cis-11 cis-14. Twenty-one genomic regions accounted for more than 1 % of the genetic variance for the group of omega-3, omega-6 and the n-6:n-3 ratio. CONCLUSIONS: The identification of such regions and the respective candidate genes, such as ELOVL5, ESSRG, PCYT1A and genes of the ABC group (ABC5, ABC6 and ABC10), should contribute to form a genetic basis of the fatty acid profile of Nellore (Bos indicus) beef, contributing to better selection of the traits associated with improving human health.