Genome-Wide Association Study for Fatty Acid Composition in American Angus Cattle

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.

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.

Leveraging Functional Genomics for Understanding Beef Quality Complexities and Breeding Beef Cattle for Improved Meat Quality

Consumer perception of beef is heavily influenced by overall meat quality, a critical factor in the cattle industry. Genomics has the potential to improve important beef quality traits and identify genetic markers and causal variants associated with these traits through genomic selection (GS) and genome-wide association studies (GWAS) approaches. Transcriptomics, proteomics, and metabolomics provide insights into underlying genetic mechanisms by identifying differentially expressed genes, proteins, and metabolic pathways linked to quality traits, complementing GWAS data. Leveraging these functional genomics techniques can optimize beef cattle breeding for enhanced quality traits to meet high-quality beef demand. This paper provides a comprehensive overview of the current state of applications of omics technologies in uncovering functional variants underlying beef quality complexities. By highlighting the latest findings from GWAS, GS, transcriptomics, proteomics, and metabolomics studies, this work seeks to serve as a valuable resource for fostering a deeper understanding of the complex relationships between genetics, gene expression, protein dynamics, and metabolic pathways in shaping beef quality.

A genome-wide association study for the fatty acid composition of breast meat in an F2 crossbred chicken population

The composition of fatty acids determines the flavor and quality of meat. Flavor compounds are generated during the cooking process by the decomposition of volatile fatty acids via lipid oxidation. A number of research on candidate genes related to fatty acid content in livestock species have been published. The majority of these studies focused on pigs and cattle; the association between fatty acid composition and meat quality in chickens has rarely been reported. Therefore, this study investigated candidate genes associated with fatty acid composition in chickens. A genome-wide association study (GWAS) was performed on 767 individuals from an F2 crossbred population of Yeonsan Ogye and White Leghorn chickens. The Illumina chicken 60K significant single-nucleotide polymorphism (SNP) genotype data and 30 fatty acids (%) in the breast meat of animals slaughtered at 10 weeks of age were analyzed. SNPs were shown to be significant in 15 traits: C10:0, C14:0, C18:0, C18:1n-7, C18:1n-9, C18:2n-6, C20:0, C20:2, C20:3n-6, C20:4n-6, C20:5n-3, C24:0, C24:1n-9, monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids (PUFA). These SNPs were mostly located on chromosome 10 and around the following genes: ACSS3, BTG1, MCEE, PPARGC1A, ACSL4, ELOVL4, CYB5R4, ME1, and TRPM1. Both oleic acid and arachidonic acid contained the candidate genes: MCEE and TRPM1. These two fatty acids are antagonistic to each other and have been identified as traits that contribute to the production of volatile fatty acids. The results of this study improve our understanding of the genetic mechanisms through which fatty acids in chicken affect the meat flavor.

Comprehensive Analysis of the Longissimus Dorsi Transcriptome and Metabolome Reveals the Regulatory Mechanism of Different Varieties of Meat Quality

The beef quality significantly varies between breeds. Pingliang Red Cattle resembles Wagyu in fat deposition and flavor. To screen key factors affecting beef quality, we performed meat quality trait testing, RNA-seq, and metabolomics on the longissimus dorsi of Pingliang Red Cattle, Wagyu cross F1 generation, and Simmental cattle. The gene and metabolite expression profiles were similar between Pingliang Red Cattle and Wagyu cross F1 generation. Genes such as FASN, ACACA, PLIN1, and FABP4 were significantly upregulated in the Pingliang Red Cattle and Wagyu cross F1 generation (P < 0.05). Similarly, numerous metabolites, such as 3-iodo-l-tyrosine, arachidonic acid, and cis-aconitate, which may improve the beef quality such as fat deposition and tenderness, were found in higher levels in the Pingliang Red Cattle and Wagyu cross F1 generation. This study revealed differences in the transcriptional and metabolic levels between Pingliang Red Cattle and premium beef breeds, suggesting that Pingliang Red Cattle harbors the genetic potential for breeding high-grade beef cattle.

Genome-Wide Associative Study of Phenotypic Parameters of the 3D Body Model of Aberdeen Angus Cattle with Multiple Depth Cameras

Simple Summary

This article aims to develop a new approach to the lifetime evaluation of cattle by 3-D visualization of economic-biological and genetic features. The following indicators were selected as phenotypic features: chest width and chest girth retrieved by 3-D model and meat output on the bones. Correlation analysis showed a reliable positive relationship between chest width and meat output on the bones, which can potentially be used for lifetime evaluation of meat productivity of animals. Genome-wide associations analysis revealed the following potential loci of quantitative traits on cattle chromosomes for chest width, chest girth, and meat output on bones.

Abstract

In beef cattle breeding, genome-wide association studies (GWAS) using single nucleotide polymorphisms (SNPs) arrays can reveal many loci of various production traits, such as growth, productivity, and meat quality. With the development of genome sequencing technologies, new opportunities are opening up for more accurate identification of areas associated with these traits. This article aims to develop a novel approach to the lifetime evaluation of cattle by 3-D visualization of economic-biological and genetic features. The purpose of this study was to identify significant variants underlying differences in the qualitative characteristics of meat, using imputed data on the sequence of the entire genome. Samples of biomaterial of young Aberdeen-Angus breed cattle (n = 96) were the material for carrying out genome-wide SNP genotyping. Genotyping was performed using a high-density DNA chip Bovine GPU HD BeadChip (Illumina Inc., San Diego, CA, USA), containing ~150 thousand SNPs. The following indicators were selected as phenotypic features: chest width and chest girth retrieved by 3-D model and meat output on the bones. Correlation analysis showed a reliable positive relationship between chest width and meat output on the bones, which can potentially be used for lifetime evaluation of meat productivity of animals.

Towards Sustainable Sources of Omega-3 Long-Chain Polyunsaturated Fatty Acids in Northern Australian Tropical Crossbred Beef Steers through Single Nucleotide Polymorphisms in Lipogenic Genes for Meat Eating Quality

This study aimed to identify single nucleotide polymorphisms (SNP) in lipogenic genes of northern Australian tropically adapted crossbred beef cattle and to evaluate associations with healthy lipid traits of the Longissimus dorsi (loin eye) muscle. The hypothesis tested was that there are significant associations between SNP loci encoding for the fatty acid binding protein 4 (FABP4), stearoyl-CoA desaturase (SCD) and fatty acid synthase (FASN) genes and human health beneficial omega-3 long-chain polyunsaturated fatty acids (ω3 LC-PUFA) within the loin eye muscle of northern Australian crossbred beef cattle. Brahman, Charbray, and Droughtmaster crossbred steers were fed on Rhodes grass hay augmented with desmanthus, lucerne, or both, for 140 days and the loin eye muscle sampled for intramuscular fat (IMF), fat melting point (FMP), and fatty acid composition. Polymorphisms in FABP4, SCD, and FASN genes with significant effects on lipid traits were identified with next-generation sequencing. The GG genotype at the FABP4 g.44677239C>G locus was associated with higher proportion of linoleic acid than the CC and CG genotypes (p < 0.05). Multiple comparisons of genotypes at the SCD g.21266629G>T locus indicated that the TT genotype had significantly higher eicosapentaenoic, docosapentaenoic, and docosahexaenoic acids than GG genotype (p < 0.05). Significant correlations (p < 0.05) between FASN SNP and IMF, saturated and monounsaturated fatty acids were observed. These results provide insights into the contribution of lipogenic genes to intramuscular fat deposition and SNP marker-assisted selection for improvement of meat-eating quality, with emphasis on alternate and sustainable sources of ω3 LC-PUFA, in northern Australian tropical crossbred beef cattle, hence an acceptance of the tested hypothesis.