BackgroundSaturated 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.ResultsThe 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2511-y) contains supplementary material, which is available to authorized users.

BackgroundFatty 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.ResultsDifferential 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.ConclusionSeveral 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3232-y) contains supplementary material, which is available to authorized users.

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ABSTRACT:The aim of this study was to verify the importance of genotype-environment interaction (GEI) for age at first calving (AFC), scrotal circumference (SC) and yearling weight (YW) in Nellore cattle, using reaction norms in multi-trait random regression models and analyze the efficiency of selection for AFC based on SC and YW in different environments. The research was conducted using 28,871, 41,386 and 89,152 records for AFC, SC and YW, respectively. Environmental groups (EGs) were defined based on farm and year of birth and management group (at birth, weaning and yearling) for all traits. For YW sex of animal was added to EGs. Average post-weaning weight gain was used to assess environmental conditions. Models for SC and YW included contemporary group and the covariate, age of animal at evaluation, as fixed effects, and the residual and direct additive genetic effects as random effects. The same model was used for AFC, excluding age of animal effects. The (co)variance components were estimated using Wombat software. The additive genetic and phenotypic variances estimates for AFC, SC and YW increased as the environmental conditions improved, with a greater intensity for AFC. The heritability estimates for all traits increased as the environment became more favorable and ranged from low to medium for AFC (0.04 to 0.48), high for SC (0.51 to 0.67) and medium to high for YW (0.23 to 0.76). The genetic correlation estimates between AFC and SC, AFC and YW, YW and SC in different environments, ranged from -0.15 to -0.68, -0.18 to -0.35, -0.1 to +0.68, respectively. The efficiency of indirect selection for AFC using YW and SC ranged from 4 to 395 and from 12 to 333, respectively. There is an important GEI effect for AFC, SC and YW traits, so the expected genetic gain for these traits depend on the environment in which the animals are exploited. The SC and YW traits can be used as a selection criterion for sexual precocity in unfavorable environments.

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.

The objective of this study was to estimate the genetic-quantitative relationships between the beef fatty acid profile with the carcass and meat traits of Nellore cattle. A total of 1826 bulls finished in feedlot conditions and slaughtered at 24 months of age on average were used. The following carcass and meat traits were analysed: subcutaneous fat thickness (BF), shear force (SF) and total intramuscular fat (IMF). The fatty acid (FA) profile of the Longissimus thoracis samples was determined. Twenty-five FAs (18 individuals and seven groups of FAs) were selected due to their importance for human health. The animals were genotyped with the BovineHD BeadChip and, after quality control for single nucleotide polymorphisms (SNPs), only 470,007 SNPs from 1556 samples remained. The model included the random genetic additive direct effect, the fixed effect of the contemporary group and the animal's slaughter age as a covariable. The (co)variances and genetic parameters were estimated using the REML method, considering an animal model (single-step GBLUP). A total of 25 multi-trait analyses, with four traits, were performed considering SF, BF and IMF plus each individual FA. The heritability estimates for individual saturated fatty acids (SFA) varied from 0.06 to 0.65, for monounsaturated fatty acids (MUFA) it varied from 0.02 to 0.14 and for polyunsaturated fatty acids (PUFA) it ranged from 0.05 to 0.68. The heritability estimates for Omega 3, Omega 6, SFA, MUFA and PUFA sum were low to moderate, varying from 0.09 to 0.20. The carcass and meat traits, SF (0.06) and IMF (0.07), had low heritability estimates, while BF (0.17) was moderate. The genetic correlation estimates between SFA sum, MUFA sum and PUFA sum with BF were 0.04, 0.64 and -0.41, respectively. The genetic correlation estimates between SFA sum, MUFA sum and PUFA sum with SF were 0.29, -0.06 and -0.04, respectively. The genetic correlation estimates between SFA sum, MUFA sum and PUFA sum with IMF were 0.24, 0.90 and -0.67, respectively. The selection to improve meat tenderness in Nellore cattle should not change the fatty acid composition in beef, so it is possible to improve this attribute without affecting the nutritional beef quality in zebu breeds. However, selection for increased deposition of subcutaneous fat thickness and especially the percentage of intramuscular fat should lead to changes in the fat composition, highlighting a genetic antagonism between meat nutritional value and acceptability by the consumer.

The objective of this study was to compare SNP-BLUP, BayesCπ, BayesC and Bayesian Lasso methodologies to predict the direct genomic value for saturated, monounsaturated, and polyunsaturated fatty acid profile, omega 3 and 6 in the Longissimus thoracis muscle of Nellore cattle finished in feedlot. A total of 963 Nellore bulls with phenotype for fatty acid profiles, were genotyped using the Illumina BovineHD BeadChip (Illumina, San Diego, CA) with 777,962 SNP. The predictive ability was evaluated using cross validation. To compare the methodologies, the correlation between DGV and pseudo-phenotypes was calculated. The accuracy varied from -0.40 to 0.62. Our results indicate that none of the methods excelled in terms of accuracy, however, the SNP-BLUP method allows obtaining less biased genomic evaluations, thereby; this method is more feasible when taking into account the analyses' operating cost. Despite the lowest bias observed for EBV, the adjusted phenotype is the preferred pseudophenotype considering the genomic prediction accuracies regarding the context of the present study.

This study aimed to characterise progeny of sires representing major families in the Poll Nellore breed. Fourteen Poll Nellore sires, two Angus sires and one Brahman sire were mated by AI to~400 multiparous Poll Nellore dams. Calves were raised and stocked on pasture in central Brazil until reaching~18 months of age, then fed a sugarcane bagasse-based diet on an ad libitum basis until reaching market weight and finish (average 23 months). There were 236 Poll Nellore (N), 38 Angus · Poll Nellore (AN) and 31 Brahman · Poll Nellore (BN) calves born in total. The weaning and 423-day weight weights, and growth rates and pre-and post-weaning were greater (P < 0.05) in males than in female calves, and were influenced by breed and by sire within the N animals. The weaning weights were higher (P < 0.05) in AN and BN than in N calves. The 423-day weight weights were greater (P < 0.05) in AN calves, followed by BN, with straightbred N being lightest. Feedlot average daily gain was unaffected (P > 0.05) by sex or by sire within N, but was lowest (P < 0.05) in N cattle, and highest in AN and BN animals, which did not differ (P > 0.05). Heifers reached the end of the study with lower bodyweight (BW) and dressing percentage than steers, resulting in lower carcass weights, smaller longissimus muscle areas (LMA), but greater 12th to 13th rib backfat (BF) and similar marbling score and mean shear force. However, the proportion of carcasses grading Choice or Prime was numerically greater in heifers than in steers (23.6% vs 9.8%). AN cattle reached greater harvest weights than BN, and those were heavier than N cattle (P < 0.001). However, dressing percentages were lowest in AN animals, so that there was no significant difference in carcass weight between AN and BN cattle. AN carcasses also had greater LMA, BF and marbling scores than the N carcasses. The proportion of carcasses grading Choice or Prime was numerically greater in AN cattle than in the BN and N groups (25.9%, 11.8% and 15.9%, respectively). Steaks from AN calves were more tender than N steaks, with the BN steaks being intermediate. There was significant variation among N sires for final BW, dressing percentage, carcass weight, LMA and marbling score, but not for BF or mean shear force. The percentages of carcasses of N cattle grading Choice or Prime ranged from 0% to 61.5%. Three N sires produced progeny with greater than 40% of carcasses grading Choice or above (Berílio OB, Furador OB, and Litoral OB). Likewise, three N sires (Blitz OB, Furador OB and Sossego OB) had progeny with 67%, 62% and 75%, respectively, of steaks classified as tender. This study confirmed that Zebu cattle have inferior carcass and meat quality relative to AN crossbreds under tropical conditions, however there is substantial variation within the N breed for these traits, and several sires have a proportion of their progeny comparable in terms of meat tenderness to those of Angus sires.