Estimates of genetic parameters for fatty acids in brisket adipose tissue of Canadian commercial crossbred beef steers

Differentially expressed messenger RNA isoforms in beef cattle skeletal muscle with different fatty acid profiles

This study aimed to identify mRNA isoforms that were expressed differently in the muscle tissue of Nellore cattle based on their intramuscular fatty acid profile. Forty-eight young bulls were used to quantify beef fatty acids (FA) and perform RNA sequencing analysis. The young bulls were divided into three different groups based on quantifying FA using k-means analysis. The Grp1 clustered animals with significantly elevated levels of PUFA, ω6, ω3, linoleic acid, α-linolenic acid, and PUFA/SFA ratios, indicating a more favorable fatty acid profile. Animals in Group 3 demonstrated significantly higher levels of palmitic acid, stearic acid, myristic acid, and SFA, which are less favorable fatty acid profiles. Grp2 included bulls with intermediate levels of fatty acids, positioned between the profiles of Grp1 and Grp3. Differential expression (DE) analyses were performed to compare these three distinct groups through the contrasts: Grp1 vs. Grp2, Grp1 vs. Grp3, and Grp2 vs. Grp3. The DE analyses identified a total of 62, 26, and 30 transcripts for the contrasts Grp1 vs. Grp2, Grp1 vs. Grp3, and Grp2 vs. Grp3, respectively. In the comparison between the Grp1 and Grp2 groups, we identified three mRNA isoforms, C7-203, ADD1-204, and OXT-201, which are involved in glycogen and lipid metabolism. These mRNA isoforms regulate the key genes responsible for fatty acid synthesis, leading to a higher PUFA content profile. On the other hand, in the comparison between the Grp1 and Grp3 groups, the mRNA isoforms RBM3-202 and TRAG1-202 were identified and play a crucial role in muscle development, adipogenesis, and concentration of PUFA and MUFA, respectively. The downregulation of THRSP-201 and FABP4-201, isoforms identified in both, Grp1 vs. Grp2 and Grp2 vs. Grp3, contrasts may contribute to lower levels of MUFA and SFA and higher levels of PUFA. In addition, these mRNA isoforms were associated with lipogenesis, fatty acid transport, and inhibition of lipolysis. Our findings suggest that the identified mRNA isoforms could serve as promising candidates to help develop strategies to select animals of higher nutritional meat quality.

Multiple strategies association revealed functional candidate FASN gene for fatty acid composition in cattle

Fatty acid composition (FA) is an important indicator of meat quality in beef cattle. We investigated potential functional candidate genes for FA in beef cattle by integrating genomic and transcriptomic dataset through multiple strategies. In this study, we observed 65 SNPs overlapping with five candidate genes (CCDC57, FASN, HDAC11, ALG14, and ZMAT4) using two steps association based on the imputed sequencing variants. Using multiple traits GWAS, we further identified three significant SNPs located in the upstream of FASN and one SNP (chr19:50779529) was embedded in FASN. Of those, two SNPs were further identified as the cis-eQTL based on transcriptomic analysis of muscle tissues. Moreover, the knockdown of FASN yielded a significant reduction in intracellular triglyceride content in preadipocytes and impeded lipid droplet accumulation in adipocytes. RNA-seq analysis of preadipocytes with FASN interference revealed that the differentially expressed genes were enriched in cell differentiation and lipid metabolic pathway. Our study underscored the indispensable role of FASN in orchestrating adipocyte differentiation, and fatty acid metabolism. The integrative analysis with multiple strategies may contribute to the understanding of the genetic architecture of FA in farm animals.

Candidate genes associated with fatty acid compositions in north American Atlantic salmon (Salmo salar)

Fatty acids are a requirement for normal development, however, since humans are unable to de novo produce essential fatty acids, they must be obtained from diet. Atlantic salmon is a major dietary source of nutritious and digestible fatty acids. Here, we set out to uncover the genomic basis of individual fatty acids and indices (saturated fatty acids, monounsaturated fatty acids, polyunsaturated fatty acids, n-3, and n-6) in 208 North American Atlantic salmon, to understand selection potential toward increasing relative quantities of essential fatty acids and to identify candidate genes for future research. Total n-6 (pro-inflammatory) was higher than total n-3 (anti-inflammatory) fatty acids with a ratio of 1 : 1.31 (n-3 : n-6). Heritability of fatty acids ranged from 0 to 0.99, however, most fatty acids and indices had moderate to high heritabilities (ranged from 0.20 to 0.88), implying that selection for improvement of traits could be possible. We found the same significant markers on chromosome 23 (based on false discovery rate thresholds of 2.0e-6 and suggestive significant thresholds of 2.0e-5 in Manhattan plots) in four fatty acids (γ-linoleic acid, stearidonic acid, dihimo-γ-linolenic acid, and eicosatrienoic acid), where three genes (sin3b, acbd6, and fads2) are known to be involved in lipid metabolism. These genes, fads2 in particular, would all make ideal candidates for future functional studies. In addition, there were four fatty acids with loci over the suggestive significant threshold with a variety of markers on different chromosomes (lauric acid, stearic acid, eicosatetraenoic acid (ETA), and docosadienoic acid), with associated genes that had relevant functions to fatty acids or adipose cells in general.

Exploring the impact of fatty acid composition on carcass and meat quality in Bos taurus indicus influenced cattle

The study of fatty acid (FA) and mineral content in beef is crucial for bridging health and taste. Understanding these components is essential for catering to consumer preferences for nutritious and tasty food, in line with current dietary trends and health recommendations. This holistic view of beef quality is key to helping both producers and consumers make more knowledgeable and health-oriented decisions in meat consumption. The objectives of this study were to 1) characterize the FA composition and mineral concentration of beef from Brangus cattle; 2) estimate their heritability; and 3) calculate the genetic and phenotypic correlations of carcass and meat quality traits to FA composition and mineral concentrations. Brangus steers were evaluated for meat quality and sampled for nutritional content measurements. Brangus cattle had palmitic acid levels as low as 21%, and stearic acid levels as high as 26%, which is notable since stearic acid is considered to have a neutral or potentially beneficial impact on cholesterol levels, unlike other saturated fats. Additionally, Brangus cattle had oleic acid levels as high as 53%, a beneficial monounsaturated fat, and linoleic acid concentrations as high as 12%, an essential omega-6 FA. Saturated FA showed weak negative correlations (-0.06 to -0.15) with hot carcass weight, marbling, and fat over ribeye, similar to polyunsaturated FA which had moderate negative correlations (-0.19 to -0.37) with these traits. Conversely, monounsaturated FA was positively correlated (0.16 to 0.34) with these traits, suggesting that higher levels of monounsaturated FA, particularly oleic acid, are associated with improved meat quality and consumer-desirable traits such as increased marbling. This relationship where higher marbling is linked with increased monounsaturated FA and decreased saturated FA is unique in Brangus cattle, differing from other breeds where increased intramuscular fat typically raises FA saturation levels. The variation in FA observed in Brangus cattle highlights the breed's potential to provide nutritionally enriched beef. With selective breeding, it may be possible to improve both the nutritional value and marbling of the meat, meeting consumer demand for healthier, tastier options. Overall, the study underscores the intricate relationships between FA composition, mineral content, and meat quality, with implications for breeding and nutrition strategies aimed at improving meat quality and healthfulness.

Nair M, Hernandez-Sintharakao MJ, Geornaras I, Engle T, Belk KE, Woerner DR. Changes in the flavor profile of ground beef resulting from the application of antimicrobial interventions

The objective of this study was to characterize flavor, fatty acid composition, and volatile compounds of beef treated with common antimicrobial interventions in beef processing facilities. The effect of three pre-chilling antimicrobial interventions (4.5% lactic acid, LA; 400ppm peroxyacetic acid acidified to pH 1.2 with a sulfuric acid and sodium sulfate blend, aPAA; or untreated, CON) and four post-chilling treatments (CON; LA; aPAA; or a 2.5% solution of a commercial blend of lactic and citric acid, LAC) were analyzed. Briskets (n=30/treatment) were treated in a 3x4 factorial arrangement of pre- and post-chilling interventions using a custom-built pilot-sized spray cabinet, ground twice, and formed into patties. Cooked patties were analyzed by a trained sensory panel, and a subset of raw samples (N=72, n=6) were analyzed for fatty acid composition and volatile compounds. Trained taste panelist ratings for sour and chemical were rated highest (P < 0.01) for the LA pre-chilling treatment compared to CON and aPAA. Ratings for browned attributes were greater (P < 0.05) for samples subjected to aPAA than CON or LA samples. No differences (P > 0.05) were found for beef flavor ID, roasted, metallic, fat-like, rancid, warmed over, or liver-like ratings due to the pre-chilling treatments. Post-chilling treatments did not create any significant (P > 0.05) flavor attribute differences. Fatty acid analysis showed minimal differences due to the use of chemical interventions, and only C10:0 was affected by LAC treatment post-chilling, with greater (P < 0.05) concentrations of C10:0 compared to LA-treated samples.  Among the volatile compounds, the relative abundance of pentanal was greater (P < 0.05) in LA-treated post-chilling intervention samples than in the other treatments. Overall, these results demonstrated that the pre-chilling antimicrobial interventions impacted ground beef flavor, whereas the pre- and post-chilling antimicrobial treatments had minimal impact on fatty acid and volatile compounds.

Hepatic transcriptome analysis identifies genes, polymorphisms and pathways involved in the fatty acids metabolism in sheep

Fatty acids (FA) in ruminants, especially unsaturated FA (USFA) have important impact in meat quality, nutritional value, and flavour quality of meat, and on consumer’s health. Identification of the genetic factors controlling the FA composition and metabolism is pivotal to select sheep that produce higher USFA and lower saturated (SFA) for the benefit of sheep industry and consumers. Therefore, this study was aimed to investigate the transcriptome profiling in the liver tissues collected from sheep with divergent USFA content in longissimus muscle using RNA deep-sequencing. From sheep (n = 100) population, liver tissues with higher (n = 3) and lower (n = 3) USFA content were analysed using Illumina HiSeq 2500. The total number of reads produced for each liver sample were ranged from 21.28 to 28.51 million with a median of 23.90 million. Approximately, 198 genes were differentially regulated with significance level of p-adjusted value <0.05. Among them, 100 genes were up-regulated, and 98 were down-regulated (p<0.01, FC>1.5) in the higher USFA group. A large proportion of key genes involved in FA biosynthesis, adipogenesis, fat deposition, and lipid metabolism were identified, such as APOA5, SLC25A30, GFPT1, LEPR, TGFBR2, FABP7, GSTCD, and CYP17A. Pathway analysis revealed that glycosaminoglycan biosynthesis- keratan sulfate, adipokine signaling, galactose metabolism, endocrine and other factors-regulating calcium metabolism, mineral metabolism, and PPAR signaling pathway were playing important regulatory roles in FA metabolism. Importantly, polymorphism and association analyses showed that mutation in APOA5, CFHR5, TGFBR2 and LEPR genes could be potential markers for the FA composition in sheep. These polymorphisms and transcriptome networks controlling the FA variation could be used as genetic markers for FA composition-related traits improvement. However, functional validation is required to confirm the effect of these SNPs in other sheep population in order to incorporate them in the sheep breeding program.

Influence of beef genotypes on animal performance, carcass traits, meat quality, and sensory characteristics in grazing or feedlot-finished steers

A 2-yr study was conducted to evaluate the effects of beef genotypes and feeding systems on performance, carcass traits, meat quality, and sensory attributes. A 2×2 factorial experiment was used to randomly allocate 60 steers in year 1 (YR1) and 44 steers in year 2 (YR2). The two beef genotypes evaluated were Red Angus (RA), and RA x Akaushi (AK) crossbreed. The steers were allotted to two finishing feeding systems: grazing, a multi-species forage mixture (GRASS) and feedlot finishing, conventional total mixed ration (GRAIN). All steers were slaughtered on the same day, at 26 and 18 mo of age (GRASS and GRAIN, respectively), and carcass data were collected 48 h postmortem. Growth and slaughter characteristics were significantly impacted by the finishing system (P < 0.01), with the best results presented by GRAIN. Beef genotype affected dressing percent (P < 0.01), ribeye area (P = 0.04), and marbling score (P = 0.01). The AK steers had a tendency (P = 0.09) for lower total gain; however, carcass quality scores were greater compared to RA. There was a genotype by system interaction for USDA yield grade (P < 0.01), where it was lower in GRASS compared to GRAIN in both genotypes, and no difference was observed between the two genotypes for any GRASS or GRAIN systems. There was no difference in meat quality or sensory attributes (P > 0.10) between the two genotypes, except that steaks from AK tended to be juicier than RA (P = 0.06). Thawing loss and color variables were impacted by the finishing system (P < 0.01). L* (lightness) and hue angle presented greater values while a* (redness), b* (yellowness), and chroma presented lower values in GRAIN compared to GRASS. Sensory attributes were scored better in GRAIN than GRASS beef (P < 0.01). There was a genotype by system interaction for flavor (P = 0.02), where beef from RA had a lower flavor rating in GRASS than in GRAIN, and no difference was observed for AK. Within each system, no difference was observed for flavor between RA and AK. Beef from steers in GRASS had greater (P < 0.01) WBSF than those from GRAIN. These results indicate that steers from GRAIN had superior performance and carcass merit and that AK enhanced these traits to a greater degree compared to RA. Furthermore, the beef finishing system had a marked impact on the steaks’ sensory attributes and consumer acceptability. The favorable results for texture and juiciness in GRAIN, which likely impacted overall acceptability, may be related to high marbling.

Application of Fat-Tailed Sheep Tail and Backfat to Develop Novel Warthog Cabanossi with Distinct Sensory Attributes

This study compared the use of pork backfat (PF) and fat-tailed sheep tail and backfat (SF) on the physicochemical, fatty acids and sensory attributes of warthog cabanossi. There were no differences between weight loss during drying, moisture content, pH, water activity, salt content and lipid oxidation between the cabanossi types. However, protein and ash contents were higher in PF cabanossi whilst fat content was higher in SF cabanossi. The PF cabanossi had higher polyunsaturated fatty acids (especially n-6), lower monounsaturated fatty acids whilst the saturated fatty acid content was similar between the two cabanossi products. The n-3:n-6 ratio was more beneficial in the SF cabanossi. The descriptive sensory analysis showed two distinct products where PF cabanossi scored higher for most attributes. Although SF cabanossi scored less for these attributes, this cabanossi had unique and acceptable sensory attributes. This study concluded that fat-tailed sheep tail and backfat could be used to produce a unique cabanossi product of acceptable quality.

Differentially expressed genes identified through RNA-seq with extreme values of principal components for beef fatty acid in Nelore cattle

The aim of this study was to identify differentially expressed genes (DEG) in the Longissimus thoracis muscle of Nelore cattle related to fatty acid (FA) profile through RNA sequencing and principal component analysis (PCA). Two groups of 10 animals each were selected containing PC1 and PC2 extreme DEG values (HIGH × LOW) for each FA group. The intramuscular fat (IMF) was compared between cluster groups by ANOVA, and only the sum of monounsaturated FA (MUFA) and ω3 showed significant differences (p < .05). Interestingly, the highest percentage (95%) of phenotypic variation explained by the sum of the first two PC was observed for ω3, which also displayed the lowest number of DEG (n = 1). The lowest percentage (59%) was observed for MUFA, which also revealed the largest number of DEG (n = 66). Since only MUFA and ω3 exhibited significant differences between cluster groups, we can conclude that the differences observed for the remaining groups are not due to the percentage of IMF. Several genes that have been previously associated with meat quality and FA traits were identified as DEG in this study. The functional analysis revealed one KEGG pathway and eight GO terms as significant (p < .05), in which we highlighted the purine metabolism, glycolytic process, adenosine triphosphate binding and bone development. These results strongly contribute to the knowledge of the biological mechanisms involved in meat FA profile of Nelore cattle.

Genome wide association study identifies SNPs associated with fatty acid composition in Chinese Wagyu cattle

Background

Fatty acids are important traits that affect meat quality and nutritive values in beef cattle. Detection of genetic variants for fatty acid composition can help to elucidate the genetic mechanism underpinning these traits and promote the improvement of fatty acid profiles. In this study, we performed a genome-wide association study (GWAS) on fatty acid composition using high-density single nucleotide polymorphism (SNP) arrays in Chinese Wagyu cattle.

Results

In total, we detected 15 and 8 significant genome-wide SNPs for individual fatty acids and fatty acid groups in Chinese Wagyu cattle, respectively. Also, we identified nine candidate genes based on 100 kb regions around associated SNPs. Four SNPs significantly associated with C14:1 cis-9 were embedded with stearoyl-CoA desaturase (SCD), while three SNPs in total were identified for C22:6 n-3 within Phospholipid scramblase family member 5 (PLSCR5), Cytoplasmic linker associated protein 1 (CLASP1), and Chymosin (CYM). Notably, we found the top candidate SNP within SCD can explain ~ 7.37% of phenotypic variance for C14:1 cis-9. Moreover, we detected several blocks with high LD in the 100 kb region around SCD. In addition, we found three significant SNPs within a 100 kb region showing pleiotropic effects related to multiple FA groups (PUFA, n-6, and PUFA/SFA), which contains BAI1 associated protein 2 like 2 (BAIAP2L2), MAF bZIP transcription factor F (MAFF), and transmembrane protein 184B (TMEM184B).

Conclusions

Our study identified several significant SNPs and candidate genes for individual fatty acids and fatty acid groups in Chinese Wagyu cattle, and these findings will further assist the design of breeding programs for meat quality in cattle.

Genetic parameters for fatty acids in intramuscular fat from feedlot-finished Nelore carcasses

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.

Phenotypic and genetic relationships of residual feed intake measures and their component traits with fatty acid composition in subcutaneous adipose of beef cattle

Feed efficiency is of particular interest to the beef industry because feed is the largest variable cost in production and fatty acid composition is emerging as an important trait, both economically and socially, due to the potential implications of dietary fatty acids on human health. Quantifying correlations between feed efficiency and fatty acid composition will contribute to construction of optimal multiple-trait selection indexes to maximize beef production profitability. In the present study, we estimated phenotypic and genetic correlations of feed efficiency measures including residual feed intake (RFI), RFI adjusted for final ultrasound backfat thickness (RFIf); their component traits ADG, DMI, and metabolic BW; and final ultrasound backfat thickness measured at the end of feedlot test with 25 major fatty acids in the subcutaneous adipose tissues of 1,366 finishing steers and heifers using bivariate animal models. The phenotypic correlations of RFI and RFIf with the 25 individual and grouped fatty acid traits were generally low (<0.25 in magnitude). However, relatively stronger genetic correlation coefficients of RFI and RFIf with PUFA traits including the -6:-3 ratio (0.52 ± 0.29 and 0.45 ± 0.31, respectively), 18:2-6 (0.45 ± 0.18 and 0.40 ± 0.19, respectively), -6 (0.43 ± 0.18 and 0.38 ± 0.19, respectively), PUFA (0.42 ± 0.18 and 0.36 ± 0.20, respectively), and 9-16:1 (-0.43 ± 0.20 and -0.33 ± 0.22, respectively) were observed. Hence, selection for low-RFI or more efficient beef cattle will improve fatty acid profiles by lowering the content of -6 PUFA, thus reducing the ratio of -6 to -3 along with increasing the amount of 9-16:1. Moderate to moderately high genetic correlations were also observed for DMI with 9-14:1 (-0.32 ± 0.17) and the sum of CLA analyzed (SumCLA; -0.45 ± 0.21), suggesting that selection of beef cattle with lower DMI will lead to an increase amount of 9-14:1 and SumCLA in the subcutaneous adipose tissue. However, unfavorable genetic correlations were detected for ADG with 11-18:1 (-0.38 ± 0.23) and SumCLA (-0.73 ± 0.26), implying that selection of beef cattle with a better growth rate will decrease the contents of healthy fatty acids 11-18:1 and SumCLA. Therefore, it is recommended that a multiple-trait selection index be used when genetic improvements of fatty acid composition, feed efficiency, feed intake, and growth are important in the breeding objective.

Phenotypic and genetic correlations of fatty acid composition in subcutaneous adipose tissue with carcass merit and meat tenderness traits in Canadian beef cattle

Bivariate animal models were used to estimate phenotypic and genetic correlations between 9 carcass merit and meat tenderness traits with 25 individual and grouped fatty acids in the subcutaneous adipose tissue of a population of 1,366 Canadian beef cattle finishing heifers and steers. In general, phenotypic correlations were low (<0.25 in magnitude) except for moderate phenotypic correlations of 9-17:1 (-0.29 ± 0.16), 18:0 (0.26 ± 0.14), 11-18:1 (-0.33 ± 0.15), 11-18:1 (0.35 ± 0.14) with Warner-Bratzler shear force measured 3 d postmortem and between 14:0 (-0.36 ± 0.1), 9-14:1 (-0.34 ± 0.08), 9-16:1 (-0.36 ± 0.08), 9-18:1 (0.26 ± 0.07), and sum of branched-chain fatty acids (BCFA; -0.27 ± 0.06) and back fat thickness (BFAT). Genetic correlations were also low for most of the traits. However, moderate to moderately high genetic correlations (0.25 to 0.50 in magnitude) were detected for some traits, including 17:0 (0.4 ± 0.11), 18:0 (0.44 ± 0.12), 9-14:1 (-0.47 ± 0.11), 9-16:1 (-0.43 ± 0.11), and the -6:-3 PUFA ratio (-0.5 ± 0.15) with HCW; 9-14:1 (-0.41 ± 0.13) and 9-16:1 (-0.42 ± 0.13) with BFAT; 17:0 (0.43 ± 0.19) and BCFA (0.45 ± 0.19) with lean meat yield; 13-18:1 (0.40 ± 0.15) with carcass marbling score; sum of CLA (0.45 ± 0.22), 18:2-6 (0.47 ± 0.17), and sum of PUFA (0.48 ± 0.17) with overall tenderness measured 3 d postmortem; the -6:-3 PUFA ratio (0.41 ± 0.22) and sum of CLA (0.42 ± 0.25) with overall tenderness measured 29 d postmortem; and BCFA (0.41 ± 0.27) with Warner-Bratzler shear force measured 29 d postmortem. The genetic correlations observed in this study suggest that contents of some fatty acids in beef tissue and carcass merit and meat tenderness traits are likely influenced by a subset of the same genes in beef cattle. Due to some antagonistic genetic correlations, multiple-trait economic indexes are recommended when fatty acid composition, carcass merit, and meat tenderness traits are included in the breeding objective.

Genome wide association study and genomic prediction for fatty acid composition in Chinese Simmental beef cattle using high density SNP array

BACKGROUND

Fatty acid composition of muscle is an important trait contributing to meat quality. Recently, genome-wide association study (GWAS) has been extensively used to explore the molecular mechanism underlying important traits in cattle. In this study, we performed GWAS using high density SNP array to analyze the association between SNPs and fatty acids and evaluated the accuracy of genomic prediction for fatty acids in Chinese Simmental cattle.

RESULTS

Using the BayesB method, we identified 35 and 7 regions in Chinese Simmental cattle that displayed significant associations with individual fatty acids and fatty acid groups, respectively. We further obtained several candidate genes which may be involved in fatty acid biosynthesis including elongation of very long chain fatty acids protein 5 (ELOVL5), fatty acid synthase (FASN), caspase 2 (CASP2) and thyroglobulin (TG). Specifically, we obtained strong evidence of association signals for one SNP located at 51.3 Mb for FASN using Genome-wide Rapid Association Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approaches. Also, region-based association test identified multiple SNPs within FASN and ELOVL5 for C14:0. In addition, our result revealed that the effectiveness of genomic prediction for fatty acid composition using BayesB was slightly superior over GBLUP in Chinese Simmental cattle.

CONCLUSIONS

We identified several significantly associated regions and loci which can be considered as potential candidate markers for genomics-assisted breeding programs. Using multiple methods, our results revealed that FASN and ELOVL5 are associated with fatty acids with strong evidence. Our finding also suggested that it is feasible to perform genomic selection for fatty acids in Chinese Simmental cattle.

Genomic prediction for beef fatty acid profile in Nellore cattle

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.

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.

Electronic supplementary material

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

Genetic correlation estimates between beef fatty acid profile with meat and carcass traits in Nellore cattle finished in feedlot

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.

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.

Electronic supplementary material

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

Genetic parameters and genetic correlations among triacylglycerol and phospholipid fractions in Angus cattle

The objective of this study was to estimate genetic parameters for intramuscular fatty acids from triacylglycerol (TAG) and phospholipid (PL) fractions in beef LM tissue. Longissimus muscle samples were obtained from 1,833 Angus cattle to determine the intramuscular fatty acid composition for 31 lipids and lipid classes from TAG and PL fractions and were classified by structure into saturated (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), omega-3 (n-3), and omega-6 (n-6) fatty acids. An atherogenic index (AI) was also determined as a measure of the unsaturated fatty acid to SFA ratio. Restricted maximum likelihood methods combined with pedigree data were used to estimate variance components with the WOMBAT software package. Heritability estimates ranged from 0.00 to 0.63 for the major classes of fatty acids. Heritability estimates differed between the TAG and PL fractions, with higher estimates for TAG up to 0.64 and lower estimates for PL that ranged from 0.00 to 0.14. Phenotypic and genetic correlations among individual fatty acids were determined for the TAG fraction as well as among carcass traits, including rib eye area, numerical marbling score, yield grade, ether fat, and Warner-Bratzler shear force value. Strong negative or positive genetic correlations were observed among individual fatty acids in the TAG fraction, which ranged from -0.99 to 0.97 ( < 0.05). Moderate correlations between carcass traits and fatty acids from the TAG fraction ranged from -0.43 to 0.32 ( < 0.05). These results indicate that fatty acids prominent in beef tissues show significant genetic variation as well as genetic relationships with carcass traits.

Genome-wide association and genomic prediction of breeding values for fatty acid composition in subcutaneous adipose and longissimus lumborum muscle of beef cattle

BACKGROUND

Identification of genetic variants that are associated with fatty acid composition in beef will enhance our understanding of host genetic influence on the trait and also allow for more effective improvement of beef fatty acid profiles through genomic selection and marker-assisted diet management. In this study, 81 and 83 fatty acid traits were measured in subcutaneous adipose (SQ) and longissimus lumborum muscle (LL), respectively, from 1366 purebred and crossbred beef steers and heifers that were genotyped on the Illumina BovineSNP50 Beadchip. The objective was to conduct genome-wide association studies (GWAS) for the fatty acid traits and to evaluate the accuracy of genomic prediction for fatty acid composition using genomic best linear unbiased prediction (GBLUP) and Bayesian methods.

RESULTS

In total, 302 and 360 significant SNPs spanning all autosomal chromosomes were identified to be associated with fatty acid composition in SQ and LL tissues, respectively. Proportions of total genetic variance explained by individual significant SNPs ranged from 0.03 to 11.06% in SQ, and from 0.005 to 24.28% in the LL muscle. Markers with relatively large effects were located near fatty acid synthase (FASN), stearoyl-CoA desaturase (SCD), and thyroid hormone responsive (THRSP) genes. For the majority of the fatty acid traits studied, the accuracy of genomic prediction was relatively low (<0.40). Relatively high accuracies (> = 0.50) were achieved for 10:0, 12:0, 14:0, 15:0, 16:0, 9c-14:1, 12c-16:1, 13c-18:1, and health index (HI) in LL, and for 12:0, 14:0, 15:0, 10 t,12c-18:2, and 11 t,13c + 11c,13 t-18:2 in SQ. The Bayesian method performed similarly as GBLUP for most of the traits but substantially better for traits that were affected by SNPs of large effects as identified by GWAS.

CONCLUSIONS

Fatty acid composition in beef is influenced by a few host genes with major effects and many genes of smaller effects. With the current training population size and marker density, genomic prediction has the potential to predict the breeding values of fatty acid composition in beef cattle at a moderate to relatively high accuracy for fatty acids that have moderate to high heritability.