Effect of TG5 and LEP polymorphisms on the productivity, chemical composition, and fatty acid profile of meat from Simmental bulls

Background and Aim

Enhancing the nutritional and biological value of meat obtained from young surplus replacement animals of dual-purpose breeds is a critical objective in the livestock industry. This study aimed to investigate the impact of thyroglobulin (TG5, c. -422C > T) and leptin (LEP, c. 239C > T) polymorphisms on the productivity, chemical composition, and fatty acid (FA) profile of meat from Simmental bulls.

Materials and Methods

A total of 26 Simmental bulls were genotyped for TG5 (c. -422C > T) and LEP (c. 239C > T) polymorphisms and reared under the same fattening conditions. Controlled slaughter was conducted at 18 months of age. Subsequently, the experimental animals were evaluated to determine their slaughter traits and the chemical and FA composition of ground beef and the longissimus dorsi muscle.

Results

The results showed that the TG5 (c. -422C > T) polymorphism significantly (p < 0.05) affected the differentiation of bulls in terms of the synthesis of stearic acid, linolenic acid, and total polyunsaturated FAs, as well as the fat and dry matter content in the longissimus dorsi muscle. Conversely, the presence of the T allele in the LEP (c. 239C > T) polymorphism was associated with increased dry matter and fat in ground beef, carcass weight, and internal fat weight.

Conclusion

The analysis of slaughter traits and the chemical and FA composition of meat from the Simmental bulls genotyped for the TG5 and LEP genes revealed a genetic basis for the quantitative and qualitative characteristics of meat productivity. Thus, the genetic variability of bulls regarding the LEP and TG5 genes can be used to improve the quantitative and qualitative indicators of meat productivity in Simmental cattle through marker-assisted selection.

Exploring and Identifying Candidate Genes and Genomic Regions Related to Economically Important Traits in Hanwoo Cattle

The purpose of the current review was to explore and summarize different studies concerning the detection and characterization of candidate genes and genomic regions associated with economically important traits in Hanwoo beef cattle. Hanwoo cattle, the indigenous premium beef cattle of Korea, were introduced for their marbled fat, tenderness, characteristic flavor, and juiciness. To date, there has been a strong emphasis on the genetic improvement of meat quality and yields, such as backfat thickness (BFT), marbling score (MS), carcass weight (CW), eye muscle area (EMA), and yearling weight (YW), as major selection criteria in Hanwoo breeding programs. Hence, an understanding of the genetics controlling these traits along with precise knowledge of the biological mechanisms underlying the traits would increase the ability of the industry to improve cattle to better meet consumer demands. With the development of high-throughput genotyping, genomewide association studies (GWAS) have allowed the detection of chromosomal regions and candidate genes linked to phenotypes of interest. This is an effective and useful tool for accelerating the efficiency of animal breeding and selection. The GWAS results obtained from the literature review showed that most positional genes associated with carcass and growth traits in Hanwoo are located on chromosomes 6 and 14, among which LCORL, NCAPG, PPARGC1A, ABCG2, FAM110B, FABP4, DGAT1, PLAG1, and TOX are well known. In conclusion, this review study attempted to provide comprehensive information on the identified candidate genes associated with the studied traits and genes enriched in the functional terms and pathways that could serve as a valuable resource for future research in Hanwoo breeding programs.

Effects of polymorphism of myostatin and fatty acid-binding protein 4 genes on the chemical composition of meat in cull female Aceh cattle

Aim:

This study aimed to investigate the association of single nucleotide polymorphism of the myostatin (MSTN) and fatty acid-binding protein 4 (FABP4) genes on the total water, ash, fat, protein, and cholesterol contents of sirloin (gluteus medius muscle) and silverside (biceps femoris muscle) meats of cull female Aceh cattle.

Materials and Methods:

This analysis covered a total of 27 cull female Aceh cattle slaughtered at the Animal Slaughterhouse of Banda Aceh that was purposively selected based on hair color referred to the criteria described in the Decree of Ministry of Agriculture of the Republic of Indonesia. Genomic DNA was extracted from 25 mg of fresh meat using the spin column method before subjected to a polymerase chain reaction amplification using primer sets specific for 1346-bp and 275-bp fragments of MSTN and FABP4, respectively. A 4-h digestion reaction was done separately for the MSTN/HaeIII and FABP4/NlaIII loci genotyping. The total protein, ash, and fat of the meat were measured using the Indonesian National Standard (SNI) methods whereas its cholesterol content was determined using the AOAC method. The association between each polymorphism and the variation in meat chemical parameters was analyzed using the Pearson correlation test.

Results:

The results showed that the MSTN/HaeIII locus was polymorphic in Aceh cattle, but the FABP4/NlaIII locus was monomorphic. Meat chemical parameters were not influenced by different commercial cuts and MSTNgenotypes, showing that there was no association between different commercial cuts, cattle hair colors, and MSTN/HaeIII and FABP4/NlaIII markers with the meat chemical parameters in Aceh cattle.

Conclusion:

These results suggest that focusing on the novel effects of MSTN and FABP4 gene polymorphisms on meat production traits might not be useful for marker-assisted selection in Aceh cattle.

Association between polymorphisms of Myf5, MSTN and CAST genes and fattening performance in Brown Swiss and Holstein cattle breeds

This study determined the association between Myf5, CAST and MSTN genes and fattening performance traits in 228 (Holstein = 103 and Brown = 125) cattle breeds. Classification and regression tree (CART) was used to determine association between genes and fattening performance. The allele frequencies of Holstein cattle in terms of Myf5, CAST and MSTN genes were A:0.30, B:0.70; A:0.43, G:0.56; A:0.97, B:0.03, respectively, whereas in the Brown Swiss cattle were A:0.36, B:0.64; A:0.65, G:0.34; A:0.88, B:0.12 respectively. The Myf5, CAST, and MSTN genes were found to be in the Hardy-Weinberg equilibrium (p > 0.05) in both of the cattle breeds. As a result, the association between Myf5, CAST and MSTN genes and fattening performance traits were found to be significant according to CART analysis.

Genome-Wide Association Study Using Fix-Length Haplotypes and Network Analysis Revealed New Candidate Genes for Nematode Resistance and Body Weight in Blackface Lambs

The objectives of this study were to identify genomic regions by Bayesian methods (BayesA, BayesB, or BayesN) that fit fixed-length haplotypes or SNPs using GenSel. Covariates for haplo-type alleles of five lengths (125, 250, 500 kb, 1 or 2 Mb) were generated, and rare haplotypes were removed at three thresholds (1, 5, or 10%). Subsequently, we performed gene network analyses to investigate the biological processes shared by genes that were identified for the same across traits. Genotypes at 41,034 SNPs that were common on OvineSNP50 panel were phased for 751 Scottish Blackface (SBF) lambs. This is the first study to quantify the proportion of genetic variance using haplotypes across the whole genome in an SBF population. The genetic variance explained of haplotype-based GWAS was higher than that of SNP-based GWAS in across traits studied. In this population, fitting 500kb haplotypes with a 1% frequency threshold resulted in the highest proportion of genetic variance explained for nematode resistance and fitting 2Mb haplotypes with a 10% frequency threshold improved genetic variance explained for body weight comparable to fitting SNPs by BayesB. Candidate genes, including CXCR4, STAT4, CCL1, CCL2, CCL3, CCL5, CCL8, CCL16, CCL18, CARMIL2, and HSPA14 were identified for nematode resistance and ADH5, PPP3CA, and FABP4 for body weight traits. Network analysis provided annotation results linking to all identified candidate genes. This study supported previous results from GWAS of nematode resistance and body weight and revealed additional regions in the ovine genome associated with these economically important traits. These results suggest that network analysis can provide new information regarding biological mechanisms and genes leading to complex phenotypes, like nematode resistance and body weight of lamb.

Genome-wide association study for body weight in cattle populations from Siberia

Body weight is a complex trait in cattle associated with commonly used commercial breeding measurements related to growth. Although many quantitative trait loci (QTL) for body weight have been identified in cattle so far, searching for genetic determinants in different breeds or environments is promising. Therefore, we carried out a genome-wide association study (GWAS) in two cattle populations from the Russian Federation (Siberian region) using the GGP HD150K array containing 139 376 single nucleotide polymorphism (SNP) markers. Association tests for 107 550 SNPs left after filtering revealed five statistically significant SNPs on BTA5, considering a false discovery rate of less than 0.05. The chromosomal region containing these five SNPs contains the CCND2 gene, which was previously associated with average daily weight gain and body mass index in US beef cattle populations and in humans respectively. Our study is the first GWAS for body weight in beef cattle populations from the Russian Federation. The results provided here suggest that, despite the existence of breed- and species-specific QTL, the genetic architecture of body weight could be evolutionarily conserved in mammals.

Comprehensive assessment of candidate genes associated with fattening performance in Holstein-Friesian bulls

The objective of this study was to determine the association of single nucleotide polymorphisms (SNPs) in selected candidate genes with fattening performance traits in a commercial cattle herd. Fifteen SNPs in 12 candidate genes (LEP, FABP4, DGAT1, TG, IGF1, IGF1R, MYF5, LGB, CAPN1, CAST, GHR, and OLR1) were evaluated in 296 purebred Holstein-Friesian bulls using PCR-RFLP (polymerase chain reaction - restriction fragment length polymorphism). Associations between each segregating SNP and genetic merit for fattening performance were quantified using linear mixed models. Traits included in the study were fattening period, final weight, dry matter intake, feed conversion rate, and average daily weight gain. Apart from the general determination of the above-mentioned traits, each trait was evaluated based on the fattening periods between five selected target body weights (W1  =  100 kg, W2  =  200 kg, W3  =  300 kg, W4  =  400 kg, W5  =  450 kg). All markers with the exception of CAPN1 530, IGF1R, TG, and DGAT1 were associated with at least one of the traits. Furthermore, novel associations were observed for LEP  ×  GHR, IGF1  ×  LEP, FABP4 3691  ×  FABP4 2834, and FAP4 3533  ×  LEP interactions. The results of this study confirm some previously reported associations. Moreover, novel associations have been identified, which may be incorporated into breeding programs to improve fattening performance.

Individual and combined effects of <i>CAPN1</i>, <i>CAST</i>, <i>LEP</i> and <i>GHR</i> gene polymorphisms on carcass characteristics and meat quality in Holstein bulls

Abstract. The objective of this study was to determine the association of single nucleotide polymorphisms (SNPs) with carcass characteristics and meat quality traits in selected candidate genes in Holstein bulls. Five SNPs in four genes, i.e. calpain 1 (CAPN1), calpastatin (CAST), leptin (LEP) and growth hormone receptor (GHR), were genotyped in 400 purebred bulls using PCR-RFLP. Statistically significant associations were as follows: CAPN1 G316A with live weight, carcass weight, back fat thickness, m. longissimus thoracis et lumborum area and carcass measurements; CAPN1 V530I with pH and L∗; CAST S20T with live weight, inner chest depth and b∗ value; and GHR with ph, a∗ and h∗. In addition, significant genotypic interactions were observed for dressing percentage (LEP A80V  ×  CAST S20T), pH (CAPN1 V530I  ×  GHR S555G and LEP A80V  ×  GHR S555G) and rump width (CAPN1 V530I  ×  CAST S20T). There was no association between the LEP A80V marker and any of the traits evaluated, nor was there any association of the tested SNPs with chest width, C∗ and marbling score. The present results could therefore be indicative for future studies on meat yield and quality.