Association of leptin genotypes with beef cattle characteristics

A single nucleotide polymorphism (C/T) in bovine leptin, resulting in an arginine to cysteine amino acid substitution (p.Arg25Cys), has previously been shown to have an impact on carcass characteristics. Given the significant energetic relationship between fat and animal efficiency, further evaluation of this SNP across larger animal populations is warranted. Of the total number of 136 286 genotyped cattle in this study, 92 112 and 53 189 were analysed for backfat and body weight measurements, respectively. Results showed a significant positive relationship (P < 0.0001) between the T allele frequency and animal backfat, with TT, CT and CC animals having estimates of 6.79 ± 0.02, 6.49 ± 0.01 and 6.28 ± 0.01 mm, respectively. Calculations using rate of backfat accretion showed that animals with CC genotypes would require more days to reach 12 mm of backfat (45 days) than animals with CT (42 days) and TT (38 days) genotypes. Animal weight was also shown to be positively associated (P < 0.0001) with genotype, as animals of the TT, CT and CC genotypes weighed 484.2 ± 0.7, 488.0 ± 0.5 and 487.3 ± 0.6 kg, respectively, further underscoring the effects of this SNP on key market cattle characteristics.     

A potential association between the BM 1500 microsatellite and fat deposition in beef cattle

The obese gene was hypothesized as a candidate gene for fat characteristics in beef cattle. The BM 1500 microsatellite, near the obese gene, was characterized in 158 purebred beef bulls for which carcass trait information was available. Four breeds were included in the analyses—Angus, Charolais, Hereford, and Simmental. Four alleles were found. Lengths were approximately 138, 147, 149, and 140 bp with genotypic frequencies of 0.47, 0.44, 0.09, and 0.003 respectively. The carcass traits %rib fat, %rib lean, average fat, and grade fat were found to be significantly associated with the different alleles. The presence of the 138-bp allele in the genotype of an animal is correlated with higher levels of fat, whereas the 147-bp allele has the opposite effect. The 149-bp allele was found in low numbers, and a homozygote was never identified. Hereford and Angus bulls had the greatest frequencies of 138-bp alleles (Hereford = 0.57, Angus = 0.59), while Charolais and Simmental had a greater proportion of 147-bp alleles (Charolais = 0.54, Simmental = 0.58). This information may aid cattle producers in selecting cattle for markets that differ in the amount of fat required. Received: 27 October 1997 / Accepted: 23 January 1998     

Identification of genetic polymorphisms in FABP3 and FABP4 and putative association with back fat thickness in Korean native cattle

The aim of this study was to determine whether single nucleotide polymorphisms (SNP) in the beef cattle adipocyte fatty-acid binding protein 3 and 4 (FABP3 and FABP4) genes are associated with carcass weight (CW) and back fat thickness (BF) of beef cattle. By direct DNA sequencing in 24 unrelated Korean native cattle, we identified 20 SNPs in FABP3 and FABP4. Among them, 10 polymorphic sites were selected for genotyping in our beef cattle. We performed SNP, haplotype and linkage disequilibrium studies on 419 Korean native cattle with the 10 SNPs in the FABP genes. Statistical analysis revealed that 220AG (I74V) and 348+303TC polymorphisms in FABP4 showed putative associations with BF traits (P=0.02 and 0.01, respectively). Our findings suggest that the polymorphisms in FABP4 may play a role in determining one of the important genetic factors that influence BF in beef cattle.     

Identification of polymorphisms in the malic enzyme 1, NADP(+)-dependent, cytosolic and nuclear receptor subfamily 0, group B, member 2 genes and their associations with meat and carcass quality traits in commercial Angus cattle

Genes involved in the physiological control of energy and triglyceride synthesis, such as malic enzyme 1, NADP(+)-dependent, cytosolic (ME1) and nuclear receptor subfamily 0, group B, member 2 (NR0B2), are key candidates that may have effects on meat and carcass quality traits. These genes were sequenced in Aberdeen Angus beef cattle, and the possibility of associations between SNPs and economically important carcass and meat quality traits was tested. Six novel SNPs, five in ME1 and one in NR0B2, were identified. A SNP in exon eight of ME1 resulted in a non-synonymous amino acid change from valine to isoleucine. Phenotypic data were recorded on 536 commercial Aberdeen Angus-cross beef cattle, which comprised 28 carcass quality, tenderness and sensory traits. The majority of the SNPs were associated with at least one of these traits, including an association between the NR0B2 SNP and fat class, and associations between at least one of the ME1 SNPs and eye muscle area, sirloin weight before maturation, sirloin steak tail length, and juiciness.     

Genome-wide association study reveals five nucleotide sequence variants for carcass traits in beef cattle

Genetic associations of nucleotide sequence variants with carcass traits in beef cattle were investigated using a genome-wide single nucleotide polymorphism (SNP) assay. Three hundred and thirteen Korean cattle were genotyped with the Illumina BovineSNP50 BeadChip, and 39,129 SNPs from 311 animals were analysed for each carcass phenotype after filtering by quality assurance. Five sequence markers were associated with one of the meat quantity or quality traits; rs109593638 on chromosome 3 with marbling score, rs109821175 on chromosome 11 and rs110862496 on chromosome 13 with backfat thickness (BFT), and rs110228023 on chromosome 6 and rs110201414 on chromosome 16 with eye muscle area (EMA) (P < 1.27 × 10(-6) , Bonferonni P < 0.05). The ss96319521 SNP, located within a gene with functions of muscle development, dishevelled homolog 1 (DVL1), would be a desirable candidate marker. Individuals with genotype CC at this gene appeared to have increased both EMA and carcass weight. Fine-mapping would be required to refine each of the five association signals shown in the current study for future application in marker-assisted selection for genetic improvement of beef quality and quantity.     

Effects of leptin Arg25Cys on peripheral mononuclear cell counts and antibody response to vaccination in beef cattle

A single nucleotide polymorphism (SNP) in the leptin gene that results in Arg25Cys has been associated with beef carcass quality and milk composition in dairy cattle. However, leptin (LEP) also plays a role in immune performance and hence it was important to determine whether selection based on this SNP would negatively affect immune cell numbers or antibody production. LEP c.73C>T was assessed for effects on immune cell counts and antibody titres in 27 beef cattle herds ( n  = 556). A commercial rabies vaccine had been administered to these animals. Prior to being vaccinated, counts of several important mononuclear cells (total and activated B lymphocytes, total and activated T helper and T cytotoxic, WC1 T lymphocytes and monocytes) as well as baseline serum antibody titres were determined for each animal. On day 21, antibody titres were measured and a booster vaccine was administered. Finally on day 42, antibody titres and mononuclear cell types were again counted. Counts of six different cell types were significantly associated with the LEP genotype; however, no consistent patterns were observed between LEP genotype (TT, CT or CC) and peripheral blood mononuclear cell populations. Significant differences in the production of rabies antibodies in response to vaccination were observed relative to LEP genotype. Our results suggest that selection for either the C or T allele would not detrimentally impact on the measured indicators of immune function in beef cattle.     

Genetic association of <Emphasis Type="Italic">Phosphodiesterase 1B</Emphasis> (PDE1B) with carcass traits in Korean cattle

Quantitative trait loci for fat deposition and carcass traits have been identified in the vicinity of the gene encoding phosphodiesterase 1B (PDE1B) on bovine chromosome 5. Therefore, the PDE1B gene can be considered as a positional and functional candidate gene for carcass traits in beef cattle. This study aimed to identify single nucleotide polymorphisms (SNPs) in the PDE1B gene and to evaluate their associations with carcass traits in Korean cattle. Eight SNPs, g.440T>G, g.17122A>G, g.17507A>C, g.17575A>G, g.17607T>C, g.17609C>A, g.17692C>T, and g.17707C>G, were identified in the region ranged from exon 1 to intron 6. Five of them were used for association analysis because of their availability of restriction fragment length polymorphisms. As a result, g.17122A>G in intron 3 was significantly associated with backfat thickness (BFT), and g.17507A>C in exon 5 was associated with longissimus dorsi muscle area (LMA, P < 0.05). Animals with the AG genotype of g.17122 had thicker BFT than those with the AA genotype. Animals with the AA or AC genotype of g.17507A>C had larger LMA than those with the CC genotype. We suggested the PDE1B gene as a candidate gene for carcass traits of beef cattle. Fine mapping would be required for application to marker-assisted selection.     

Association between a single nucleotide polymorphism in the bovine chemerin gene and carcass traits in Qinchuan cattle

Qinchuan is a red or yellow draft and beef breed in China. In order to identify a predictor of carcass traits on the basis of associations between carcass traits and gene polymorphism, variation in the bovine chemerin gene was investigated using PCR-single-strand conformational polymorphism and DNA sequencing. An SNP of A868G located in exon 2 of the Bos taurus chemerin gene was detected in 716 samples of six breeds (Jiaxian red, Luxi, Nan yang, Qinchuan, Simmental and Luxi crossbred steers, and Xia'nan), all in China, and three genotypes (AA, AG and GG) were found. Based on the χ(2) test, the AA/AG/GG genotype frequencies of all six breeds were found to be in Hardy-Weinberg equilibrium. A possible association of A868G with some carcass traits was investigated in 106 Qinchuan cattle. Animals with the AG genotype were found to have significantly lower mean loin eye area and meat tenderness compared to those with the AA and GG genotypes. However, there was no significant association between any individual haplotype and backfat thickness, water holding capacity or marbling score. We suggest that A868G could be used as a molecular marker in marker-assisted selection for carcass traits.     

A splice site single nucleotide polymorphism of the fatty acid binding protein 4 gene appears to be associated with intramuscular fat deposition in longissimus muscle in Australian cattle

Fatty acid binding protein 4 ( FABP4 ) is a candidate gene affecting fatness traits of mammals. However, its association with fatness traits in cattle and other livestock species is not consistent from one study to another. Here, we sequenced the coding sequence of FABP4 looking for non-synonymous variants. We identified a splice site mutation between the third exon and the third intron of bovine FABP4 . We genotyped this SNP, FABP4 :g.2502C>G, in 1409 cattle with intramuscular fat measurements from seven breeds. The average allele frequency of the C allele was 0.66 with a range of 0.45 to 0.85. A regression on the number of G alleles shows a statistically significant effect of α = 0.11, P  =   0.044. This appears to confirm an association between IMF and variation at FABP4 , with an effect of 0.3% of the variation in our sample when using this SNP.     

Molecular characterization, polymorphism of the ACOX1 gene and association with ultrasound traits in Bos taurus

Acyl-coenzyme A oxidase 1 (ACOX1) is the first enzyme in peroxisomal fatty acid β-oxidation; it is rate-limiting and plays a key role in fatty acid metabolism and fat deposition. ACOX1 is an important candidate gene for meat quality selection through marker-assisted selection. Genomic structural analysis showed that bovine ACOX1 shares 86% identity with human ACOX1. Using PCR-SSCP technology, we discovered a single nucleotide polymorphism (SNP) (A1865C) in exon 13 of the ACOX1 gene. Allele frequencies of this SNP were investigated and evaluated with the χ(2) test in 641 cattle populations; only the Jiaxian red population was not in Hardy-Weinberg equilibrium. Gene heterozygosity, effective allele numbers and polymorphism information content of the bovine ACOX1 locus in seven populations varied from 0.2778 to 0.4954, 1.3846 to 1.9817 and 0.2392 to 0.3727, respectively. We also looked for a potential association of this SNP with ultrasound traits in 327 individuals and found a significant effect on ultrasound backfat thickness and ultrasound marbling score (P < 0.05). Meat quality traits were analyzed in another 71 Qinchuan individuals to determine associations with genotype. Animals with genotype AA had higher mean values of backfat thickness than those with genotypes AC and CC. A represents the base before mutation and C represents the base after mutation. We conclude that this SNP of the ACOX1 gene has potential as a genetic marker for meat quality traits in cattle reproduction and breeding.     

Accuracy of predicting genomic breeding values for carcass merit traits in Angus and Charolais beef cattle

Accuracy of predicting genomic breeding values for carcass merit traits including hot carcass weight, longissimus muscle area (REA), carcass average backfat thickness (AFAT), lean meat yield (LMY) and carcass marbling score (CMAR) was evaluated based on 543 Angus and 400 Charolais steers genotyped on the Illumina BovineSNP50 Beadchip. For the genomic prediction within Angus, the average accuracy was 0.35 with a range from 0.32 (LMY) to 0.37 (CMAR) across different training/validation data‐splitting strategies and statistical methods. The within‐breed genomic prediction for Charolais yielded an average accuracy of 0.36 with a range from 0.24 (REA) to 0.46 (AFAT). The across‐breed prediction had the lowest accuracy, which was on average near zero. When the data from the two breeds were combined to predict the breeding values of either breed, the prediction accuracy averaged 0.35 for Angus with a range from 0.33 (REA) to 0.39 (CMAR) and averaged 0.33 for Charolais with a range from 0.18 (REA) to 0.46 (AFAT). The prediction accuracy was slightly higher on average when the data were split by animal's birth year than when the data were split by sire family. These results demonstrate that the genetic relationship or relatedness of selection candidates with the training population has a great impact on the accuracy of predicting genomic breeding values under the density of the marker panel used in this study.     

A polymorphism in XKR4 is significantly associated with serum prolactin concentrations in beef cows grazing tall fescue

Fescue toxicosis is a common syndrome of poor growth and reproductive performance of beef cattle grazing endophyte‐infected tall fescue infected with Lolium arundinaceum Schreb. Together with decreased feed intake, decreased growth rates and tissue necrosis due to vasoconstriction, depressed circulating serum prolactin concentrations are typically observed in cattle afflicted with fescue toxicosis. Polymorphisms within the XK, Kell blood group complex subunit‐related family, member 4 (XKR4) gene located on BTA14 have been previously reported to be associated with rump fat thickness, residual feed intake, average daily feed intake and average daily gain in cattle. Associations also have been reported between XKR4 genotype and effectiveness of the dopamine antagonist iloperidone as a treatment of schizophrenia in humans. Domperidone, a related dopamine antagonist, mediates effects of fescue toxicosis on livestock, including restoring depressed concentrations of prolactin. A mixed‐breed population of 592 beef cattle grazing endophyte‐infected tall fescue was used to examine the association between XKR4 genotype and circulating prolactin concentrations. The SNP rs42646708 was significantly (P = 0.0002) associated with serum prolactin concentrations and explained 2.45% of the phenotypic variation. Effect of genotype at the SNP was tested across five breeds, with significant associations within both Angus (P = 0.0275) and Simmental (P = 0.0224) breeds. These results suggest XKR4 may play a role in mediating the negative effects of fescue toxicosis, and polymorphisms within this gene may be useful markers for selection for genetic resistance to the debilitating effects of endophyte‐infected tall fescue.     

Genetic parameters for carcass weight,conformation and fat in five beef cattle breeds

Profitability of beef production can be increased by genetically improving carcass traits. To construct breeding value evaluations for carcass traits, breed-specific genetic parameters were estimated for carcass weight, carcass conformation and carcass fat in five beef cattle breeds in Finland (Hereford, Aberdeen Angus, Simmental, Charolais and Limousin). Conformation and fat were visually scored using the EUROP carcass classification. Each breed was separately analyzed using a multitrait animal model. A total of 6879–19 539 animals per breed had phenotypes. For the five breeds, heritabilities were moderate for carcass weight (h²=0.39 to 0.48, s.e.=0.02 to 0.04) and slightly lower for conformation (h²=0.30 to 0.44, s.e.=0.02 to 0.04) and carcass fat (h²=0.29 to 0.44, s.e.=0.02 to 0.04). The genetic correlation between carcass weight and conformation was favorable in all breeds (r_G=0.37 to 0.53, s.e.=0.04 to 0.05), heavy carcasses being genetically more conformed. The phenotypic correlation between carcass weight and carcass fat was moderately positive in all breeds (r_P=0.21 to 0.32), implying that increasing carcass weight was related to increasing fat levels. The respective genetic correlation was the strongest in Hereford (r_G=0.28, s.e.=0.05) and Angus (r_G=0.15, s.e.=0.05), the two small body-sized British breeds with the lowest conformation and the highest fat level. The correlation was weaker in the other breeds (r_G=0.08 to 0.14). For Hereford, Angus and Simmental, more conformed carcasses were phenotypically fatter (r_P=0.11 to 0.15), but the respective genetic correlations were close to zero (r_G=−0.05 to 0.04). In contrast, in the two large body-sized and muscular French breeds, the genetic correlation between conformation and fat was negative and the phenotypic correlation was close to zero or negative (Charolais: r_G=−0.18, s.e.=0.06, r_P=0.02; Limousin: r_G=−0.56, s.e.=0.04, r_P=−0.13). The results indicate genetic variation for the genetic improvement of the carcass traits, favorable correlations for the simultaneous improvement of carcass weight and conformation in all breeds, and breed differences in the correlations of carcass fat.     

Association of selected SNP with carcass and taste panel assessed meat quality traits in a commercial population of Aberdeen Angus-sired beef cattle

Background

The purpose of this study was to evaluate the effects of eight single nucleotide polymorphisms (SNP), previously associated with meat and milk quality traits in cattle, in a population of 443 commercial Aberdeen Angus-cross beef cattle. The eight SNP, which were located within five genes: μ-calpain (CAPN1), calpastatin (CAST), leptin (LEP), growth hormone receptor (GHR) and acylCoA:diacylglycerol acyltransferase 1 (DGAT1), are included in various commercial tests for tenderness, fatness, carcass composition and milk yield/quality.

Methods

A total of 27 traits were examined, 19 relating to carcass quality, such as carcass weight and fatness, one mechanical measure of tenderness, and the remaining seven were sensory traits, such as flavour and tenderness, assessed by a taste panel.

Results

An SNP in the CAPN1 gene, CAPN316, was significantly associated with tenderness measured by both the tenderometer and the taste panel as well as the weight of the hindquarter, where animals inheriting the CC genotype had more tender meat and heavier hindquarters. An SNP in the leptin gene, UASMS2, significantly affected overall liking, where animals with the TT genotype were assigned higher scores by the panellists. The SNP in the GHR gene was significantly associated with odour, where animals inheriting the AA genotype produced steaks with an intense odour when compared with the other genotypes. Finally, the SNP in the DGAT1 gene was associated with sirloin weight after maturation and fat depth surrounding the sirloin, with animals inheriting the AA genotype having heavier sirloins and more fat.

Conclusion

The results of this study confirm some previously documented associations. Furthermore, novel associations have been identified which, following validation in other populations, could be incorporated into breeding programmes to improve meat quality.     

Prospecting candidate SNPs for backfat in Canchim beef cattle

Canchim is a composite cattle breed developed in Brazil for beef production. One of the breeding objectives is to increase fat deposition. QTLs for fat thickness and/or marbling have been reported on BTA4 and BTA14. The IGFBP3 and DDEF1 genes, mapped to BTA4 and BTA14, respectively, affect adipogenesis. We looked for SNPs in the IGFBP3 and DDEF1 genes that could be associated with backfat thickness in Canchim beef cattle. For SNP identification, sires with the highest accuracy were ranked according to expected breeding value for fat thickness; the 12 extremes (six sires with the highest and six with the lowest expected breeding value for the trait) were chosen. Six regions of the IGFBP3 and 14 regions of the DDEF1 were sequenced using the Sanger method. Nine SNPs were identified in IGFBP3 and 76 in the DDEF1. After an initial analysis, two SNPs were selected to be genotyped for the whole population; these were DDEF1g.279401A>G and IGFBP3c.4394T>C(Trp>Arg). We found a significant effect (P ≤ 0.05) of allele substitution on backfat thickness; however, the IGFBP3 SNP did not significantly affect this trait.     

Proteome differences associated with fat accumulation in bovine subcutaneous adipose tissues

Background  

The fat components of red meat products have been of interest to researchers due to the health aspects of excess fat consumption by humans. We hypothesized that differences in protein expression have an impact on adipose tissue formation during beef cattle development and growth. Therefore, in this study we evaluated the differences in the discernable proteome of subcutaneous adipose tissues of 35 beef crossbred steers [Charolais × Red Angus (CHAR) (n = 13) and Hereford × Angus (HEAN) (n = 22)] with different back fat (BF) thicknesses. The goal was to identify specific protein markers that could be associated with adipose tissue formation in beef cows.     

Live animal measurements, carcass composition and plasma hormone and metabolite concentrations in male progeny of sires differing in genetic merit for beef production

In genetic improvement programmes for beef cattle, the effect of selecting for a given trait or index on other economically important traits, or their predictors, must be quantified to ensure no deleterious consequential effects go unnoticed. The objective was to compare live animal measurements, carcass composition and plasma hormone and metabolite concentrations of male progeny of sires selected on an economic index in Ireland. This beef carcass index (BCI) is expressed in euros and based on weaning weight, feed intake, carcass weight and carcass conformation and fat scores. The index is used to aid in the genetic comparison of animals for the expected profitability of their progeny at slaughter. A total of 107 progeny from beef sires of high (n = 11) or low (n = 11) genetic merit for the BCI were compared in either a bull (slaughtered at 16 months of age) or steer (slaughtered at 24 months of age) production system, following purchase after weaning (8 months of age) from commercial beef herds. Data were analysed as a 2 × 2 factorial design (two levels of genetic merit by two production systems). Progeny of high BCI sires had heavier carcasses, greater (P < 0.01) muscularity scores after weaning, greater (P < 0.05) skeletal scores and scanned muscle depth pre-slaughter, higher (P < 0.05) plasma insulin concentrations and greater (P < 0.01) animal value (obtained by multiplying carcass weight by carcass value, which was based on the weight of meat in each cut by its commercial value) than progeny of low BCI sires. Regression of progeny performance on sire genetic merit was also undertaken across the entire data set. In steers, the effect of BCI on carcass meat proportion, calculated carcass value (c/kg) and animal value was positive (P < 0.01), while a negative association was observed for scanned fat depth pre-slaughter and carcass fat proportion (P < 0.01), but there was no effect in bulls. The effect of sire expected progeny difference (EPD) for carcass weight followed the same trends as BCI. Muscularity scores, carcass meat proportion and calculated carcass value increased, whereas scanned fat depth, carcass fat and bone proportions decreased with increasing sire EPD for conformation score. The opposite association was observed for sire EPD for fat score. Results from this study show that selection using the BCI had positive effects on live animal muscularity, carcass meat proportion, proportions of high-value cuts and carcass value in steer progeny, which are desirable traits in beef production.