Genome-wide association study identifies loci and candidate genes for meat quality traits in Simmental beef cattle

Improving meat quality is the best way to enhance profitability and strengthen competitiveness in beef industry. Identification of genetic variants that control beef quality traits can help breeders design optimal breeding programs to achieve this goal. We carried out a genome-wide association study for meat quality traits in 1141 Simmental cattle using the Illumina Bovine HD 770K SNP array to identify the candidate genes and genomic regions associated with meat quality traits for beef cattle, including fat color, meat color, marbling score, longissimus muscle area, and shear force. In our study, we identified twenty significant single-nucleotide polymorphisms (SNPs) (p < 1.47 × 10^?6) associated with these five meat quality traits. Notably, we observed several SNPs were in or near eleven genes which have been reported previously, including TMEM236, SORL1, TRDN, S100A10, AP2S1, KCTD16, LOC506594, DHX15, LAMA4, PREX1, and BRINP3. We identified a haplotype block on BTA13 containing five significant SNPs associated with fat color trait. We also found one of 19 SNPs was associated with multiple traits (shear force and longissimus muscle area) on BTA7. Our results offer valuable insights to further explore the potential mechanism of meat quality traits in Simmental beef cattle.     

Genetic Polymorphisms of the CACNA2D1 Gene and Their Association with Carcass and Meat Quality Traits in Cattle

The objective of this study was to identify genetic polymorphisms of the CACNA2D1 gene and to analyze associations between SNPs and carcass and meat quality traits in cattle. Through PCR-RFLP and DNA sequencing methods, a new allelic variant corresponding to the A → G mutation (aspartic to glycine amino acid replacement) of the bovine CACNA2D1 gene was detected. Two alleles and three genotypes (AA, AG, and GG) were defined. Genetic character indicated that the A526745G locus showed moderate polymorphism and was in Hardy–Weinberg equilibrium. Gene-specific SNP marker association analysis showed that the A526745G mutant was significantly associated with carcass weight, dressing percentage, meat percentage, and backfat thickness. The results add new evidence that CACNA2D1 is an important candidate gene for the selection of carcass and meat quality traits in the cattle industry.     

Association of HSL gene E1-c.276C>T and E8-c.51C>T mutation with economical traits of Chinese Simmental cattle

Hormone-sensitive lipase (HSL) is responsible for the decomposition of triglycerides in adipose tissue to release free fatty acids, and it is a key rate-limiting enzyme in the regulation of adipose tissue deposition and decomposition. The objective of this study was to evaluate the association between novel SNPs in the coding region of bovine HSL gene and carcass and meat quality traits of Chinese Simmental-cross steers. Two novel SNPs were genotyped and the 47 traits of carcass and meat quality traits were measured in the population studied. Statistical analysis revealed that the SNPs of HSL gene were associated with the carcass and meat quality traits. The individuals with TT genotypes of E1-276C>T showed significant higher dressing percentage, net meat rate, hind legs circumference, fat coverage rate, mesenteric fat and kidney fat (p < 0.05). E8-51C>T (P17S) also showed a significant association with the pH of beef and fatty acids content in Chinese Simmental cattle (p < 0.01). Our findings indicated that polymorphisms in HSL might be one of important genetic factors that influence carcass yield and meat quality in beef cattle, and it may be a useful marker for meat quality traits in future marker-assisted selection programs in beef cattle breeding and production.     

Genome-wide methylation changes are associated with muscle fiber density and drip loss in male three-yellow chickens

In eukaryotes, DNA methylation is an important epigenetic modification involved in gene expression regulation. Meat quality traits are complicated traits that are controlled by many genes. Changes in the methylation levels of certain genes controlling meat quality traits will inevitably affect their expression levels, thereby affecting meat quality. The objectives of this study were to investigate the differences in the DNA methylation level in pectoral muscle tissues using fluorescent-labeled methylation sensitive amplified polymorphism and their relationships with meat quality traits in three-yellow chickens. The results showed that the differences in the DNA methylation level had a highly significant effect on muscle fiber density and drip loss (P < 0.01). However, no significant correlations were found between the DNA methylation levels and the other investigated traits (P > 0.05).     

The polymorphisms of LYRM1 gene and their association with body measurement and ultrasound traits of Qinchuan cattle

Body measurement and meat quality traits which play important roles in the assessment of productivity and economy in cattle were influenced by genes and environmental factors. Latest studies showed that LYR motif containing 1 (LYRM1) may be involved in influencing fatness deposition in animals. The objective of this study was to detect bovine LYRM1 gene polymorphism and analyze its association with body measurement and meat quality traits of cattle. Blood samples were taken from a total of 404 Qinchuan cattle aged from 18–24 months. Created restriction site-polymerase chain reaction-restriction fragment length polymorphism (CRS-PCR–RFLP) and DNA sequencing were used to find out LYRM1 single polymorphism nucleotide (SNPs). Sequence analysis of LYRM1 gene revealed two SNPs (g.165 C > A, g.193 A > G) in 3′ untranslated region (3′UTR) of exon 3. And g.165 C > A showed two genotypes namely AC and CC while g.193 A > G showed three genotypes: AA, AG and GG. Analysis results showed that there were significant associations between polymorphism of these two and body measurement and meat quality traits in Qinchuan cattle population. Based on the results obtained from this study, it is inferred that LYRM1 gene may have potential effects on body measurement and meat quality traits in Qinchuan cattle population and could be used for marker-assisted selection.     

Changes in muscle cell cation regulation and meat quality traits are associated with genetic selection for high body weight and meat yield in broiler chickens

Between-breed genetic variation for muscle and meat quality traits was determined at eight weeks of age in 34 lines of purebred commercial broiler and layer lines and traditional breeds (categories) of chickens. Between-breed genetic variation for plasma ion concentrations and element concentration in muscle dry matter and ash were determined. Plasma from broilers had higher concentrations of Na⁺, K⁺, Mg⁺⁺, total and free Ca⁺⁺ and lower free:total Ca⁺⁺ than plasma from layer and traditional lines. Muscle from broilers contained more Na and higher concentrations of K, Mg and Ca per mg of ash but not of dry matter compared with layer and traditional lines. In comparison with layer and traditional lines, broiler genotypes were over three times heavier, their plasma creatine kinase activity (CK), a marker of muscle tissue damage, was higher, their breast muscle colour was lighter (L*) and less red (a*) and yellow (b*) in appearance, the initial and final pH of their muscles were lower, the pH change was higher and their breast muscle was more tender. Thus, genetic selection for broiler traits has markedly altered cation regulation in muscle cells and may be associated with changes in muscle cell function and the development of pathology and meat quality problems.     

Flash dietary methionine supply over growth requirements in pigs: Multi-facetted effects on skeletal muscle metabolism

Dietary methionine affects protein metabolism, lean gain and growth performance and acts in the control of oxidative stress. When supplied in large excess relative to growth requirements in diets for pigs, positive effects on pork quality traits have been recently reported. This study aimed to decipher the molecular and biochemical mechanisms affected by a dietary methionine supply above growth requirements in the loin muscle of finishing pigs. During the last 14 days before slaughter, crossbred female pigs (n = 15 pigs/diet) were fed a diet supplemented with hydroxy-methionine (Met5; 1.1% of methionine) or not (CONT, 0.22% of methionine). Blood was sampled at slaughter to assess key metabolites. At the same time, free amino acid concentrations and expression or activity levels of genes involved in protein or energy metabolism were measured in the longissimus lumborum muscle (LM). The Met5 pigs exhibited a greater activity of creatine kinase in plasma when compared with CONT pigs. The concentrations of free methionine, alpha-aminobutyric acid, anserine, 3-methyl-histidine, lysine, and proline were greater in the LM of Met5 pigs than in CONT pigs. Expression levels of genes involved in protein synthesis, protein breakdown or autophagy were only scarcely affected by the diet. Among ubiquitin ligases, MURF1, a gene known to target creatine kinase and muscle contractile proteins, and OTUD1 coding for a deubiquitinase protease, were up-regulated in the LM of Met5 pigs. A lower activity of citrate synthase, a reduced expression level of ME1 acting in lipogenesis but a higher expression of PPARD regulating energy metabolism, were also observed in the LM of Met5 pigs compared with CONT pigs. Principal component analysis revealed that expression levels of many studied genes involved in protein and energy metabolism were correlated with meat quality traits across dietary treatments, suggesting that subtle modifications in expression of those genes had cumulative effects on the regulation of processes leading to the muscle transformation into meat. In conclusion, dietary methionine supplementation beyond nutritional requirements in pigs during the last days before slaughter modified the free amino acid profile in muscle and its redox capacities, and slightly affected molecular pathways related to protein breakdown and energy metabolism. These modifications were associated with benefits on pork quality traits.     

Meat eating and nutritional quality of lambs sired by high and low muscle density rams

Intramuscular fat (IMF) content affects eating and nutritional quality of lamb meat. Muscle density measured by computer tomography is an in vivo proxy measure of IMF content that affects eating and nutritional quality of lamb meat. Lambs sired by high muscle density (HMD) or low muscle density (LMD) rams, selected for slaughter on commercial criteria were measured for meat quality and nutritional traits. A restricted maximum likelihood model was used to compare lamb traits. Additionally, regression analysis of sire estimated breeding value (EBV) for muscle density was performed for each meat quality trait. Muscle density EBV had a negative regression with IMF content (P < 0.001). For each unit increase in muscle density EBV, there was a significant decrease in loin (− 1.69 mg/100 g fresh weight) and topside IMF (− 0.03 mg/100 g fresh weight). Muscle density EBV had a negative regression with grouped saturated and monounsaturated fatty acids concentration (and monounsaturated proportion P < 0.001). Muscle density EBV had a negative regression with loin sensory traits tenderness, juiciness and overall liking and many novel tenderness sensory traits measured (P < 0.05). Selecting for LMD EBV increased IMF content and favourable meat eating quality traits. In contrast, sire muscle density EBV had a positive regression with loin polyunsaturated:saturated fat ratio and grouped polyunsaturated proportion traits (including total polyunsaturated proportion, total omega-6 (n-6) and total omega-3 (n-3) fatty acids (P < 0.001). This is explained by the fact that as sire muscle density EBV increases, polyunsaturated fatty acid proportion increases and the proportion of saturated and monounsaturated fatty acid content decreases. Muscle density EBV had a positive regression with shear force and the novel toughness sensory traits (P < 0.05). Selection for HMD EBV's increased shear force and toughness traits, which is unfavourable for the consumer. Low muscle density sired meat had higher meat colour traits chroma/saturation (+ 0.64, SD 2.30, P = 0.012), redness (+ 0.52, SD 1.91, P = 0.012) and yellowness (+ 0.31, SD 1.49, P = 0.08) compared to HMD sired meat. Selection for LMD could be used within a breeding programme to increase IMF content and enhance both meat colour and improve eating quality parameters.     

Use of a bovine genome chip to identify new biological pathways for beef quality in cattle

The accumulation of muscle is largely influenced by the genetic background of cattle. Muscle tissue was collected from the longissimus muscle of Lilu beef cattle at 12, 18, 24 and 30?months old. Using meat quality analysis, we found that the Lilu beef cattle have good production and slaughter performance, the performance meets the criterion of beef cattle. Microarray analysis was able to identify a total of 4,219 genes that are differentially expressed (P?≤?0.01) between the two groups of cattle (12 vs 18; 18 vs 24; 24 vs 30). Bioinformatics analysis results suggested that most of the differentially expressed genes are involved in the metabolic pathways and neuroactive ligand–receptor interaction pathways. In the future study that aims to look for genes relating to growth and meat quality, we will focus on the genes that have been shown to have a significant variation between groups and are involved in the two pathways.     

Proopiomelanocortin gene polymorphisms and its association with meat quality traits by ultrasound measurement in Chinese cattle

Ultrasound technology was used to measure live animal meat traits instead of true carcass meat traits for beef production and cattle breeding by an increasing number of institutions. In this study, we analyzed the association between genetic polymorphisms of proopiomelanocortin (POMC) and ultrasound measurement traits in Chinese cattle. Using direct DNA sequencing in 322 individuals of 7 different cattle subpopulation, 7 SNPs were identified for genotyping within 790 bp region of intron 2 and exon 3 of POMC. 6586 T>G in intron 2 and 6769 C>T and 7216 C>T in exon 3 were significantly associated with ultrasound backfat thickness (UBF) (P < 0.05) and ultrasound loin muscle area (ULMA) (P < 0.01) in the total population; 6694 C>T, 6706 T>C, 6796 C>T and 6810 C>T in exon 3 were significantly associated with ULMA (P < 0.0001) in the total population. These results clearly suggest that these SNPs of POMC be benefit for selection of individuals with good quality meat in Chinese cattle breeding program. Following validation in other populations and breeds, these markers could be incorporated into breeding programs to increase the rate of improvement in carcass and meat quality traits.     

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.     

Genes involved in muscle lipid composition in 15 European Bos taurus breeds

Consumers demand healthy and palatable meat, both factors being affected by fat composition. However, red meat has relatively high concentration of saturated fatty acids and low concentration of the beneficial polyunsaturated fatty acids. To select animals prone to produce particular fat types, it is necessary to identify the genes influencing muscle lipid composition. This paper describes an association study in which a large panel of candidate genes involved in adipogenesis, lipid metabolism and energy homoeostasis was tested for effects on fat composition in 15 European cattle breeds. Sixteen genes were found to have significant effects on different lipid traits, and among these, CFL1 and MYOZ1 were found to have large effects on the ratio of 18:2/18:3, CRI1 on the amount of neutral adrenic acid (22:4 n‐6), MMP1 on docosahexaenoic acid (22:6 n‐3) and conjugated linoleic acid, PLTP on the ratio of n‐6:n‐3 and IGF2R on flavour. Several genes – ALDH2, CHRNE, CRHR2, DGAT1, IGFBP3, NEB, SOCS2, SUSP1, TCF12 and FOXO1 – also were found to be associated with both lipid and organoleptic traits although with smaller effect. The results presented here help in understanding the genetic and biochemical background underlying variations in fatty acid composition and flavour in beef.     

Genome-Wide Association Study Identifies Loci and Candidate Genes for Body Composition and Meat Quality Traits in Beijing-You Chickens

Body composition and meat quality traits are important economic traits of chickens. The development of high-throughput genotyping platforms and relevant statistical methods have enabled genome-wide association studies in chickens. In order to identify molecular markers and candidate genes associated with body composition and meat quality traits, genome-wide association studies were conducted using the Illumina 60 K SNP Beadchip to genotype 724 Beijing-You chickens. For each bird, a total of 16 traits were measured, including carcass weight (CW), eviscerated weight (EW), dressing percentage, breast muscle weight (BrW) and percentage (BrP), thigh muscle weight and percentage, abdominal fat weight and percentage, dry matter and intramuscular fat contents of breast and thigh muscle, ultimate pH, and shear force of the pectoralis major muscle at 100 d of age. The SNPs that were significantly associated with the phenotypic traits were identified using both simple (GLM) and compressed mixed linear (MLM) models. For nine of ten body composition traits studied, SNPs showing genome wide significance (P<2.59E−6) have been identified. A consistent region on chicken (Gallus gallus) chromosome 4 (GGA4), including seven significant SNPs and four candidate genes (LCORL, LAP3, LDB2, TAPT1), were found to be associated with CW and EW. Another 0.65 Mb region on GGA3 for BrW and BrP was identified. After measuring the mRNA content in beast muscle for five genes located in this region, the changes in GJA1 expression were found to be consistent with that of breast muscle weight across development. It is highly possible that GJA1 is a functional gene for breast muscle development in chickens. For meat quality traits, several SNPs reaching suggestive association were identified and possible candidate genes with their functions were discussed.     

AGHR polymorphism and its associations with carcass traits in Harrwoo cattle

The growth hormone receptor (GHR) is a membrane transmitter for the growth hormone signal transduction pathway that regulates various metabolic activities, including cell growth and expressions of cytokine genes. The presence or absence of a genetic polymorphism for the LINE-1 retroposon in the PI promoter, which specifically regulates theGHR gene expression in the liver, was screened by a novel detection method and examined for its relationships with carcass traits in Hanwoo cattle. Han woo cattle had taurine type LINE-1 present (alleleI) as well as incidine type LINE-1 absent (alleleA) promoter sequences. Three genotypes,I/I, I/A andA/A, showed frequencies of 49.1, 36.7 and 14.2%, respectively. The effects of allele A were significant on mean differences for final weight, eye muscle area, marbling score and fat color (p<0.05), but not for carcass weight, backfat thickness, final meat quality grade or meat color (p>0.05). Most 30-month old Hanwoo steers bearing the LINE-1 absent promoter had whiter fat color, heavier live weight and higher marbling score, reflecting intramuscular fat deposition inM. longissimus dorsi, compared to animals bearing a LINE-1 present promoter. This suggests that aGHR polymorphism could be a potential genetic marker for improving beef production of Hanwoo cattle.     

Relationships Between Single Nucleotide Polymorphisms of the H-FABP Gene and Slaughter and Meat Quality Traits in Chicken

Using PCR-SSCP with five primer pairs, we detected six single nucleotide polymorphisms of the H-FABP gene: 332G → A, 534G → A, 783C → T, 835C → T, 1198T → C, and 2329C → T. Chi-square results showed significant differences (P < 0.05) in genotype frequency among breeds in Fragment 1 and extremely significant differences (P < 0.01) in Fragments 2–4. We found a significant association between Fragment 2 genotype and muscle fiber number, Arg and Thr (P < 0.05); between Fragment 3 genotype and living weight, carcass weight, breast muscle weight, abdominal fat weight, and abdominal fat percentage (P < 0.05); between Fragment 4 genotype and Thr, Phe, and inosinic acid (P < 0.05). It was concluded that H-FABP was the major gene influencing slaughter performance and meat quality or was linked with the major gene in these strains and that the C783T mutation could be used as a candidate molecular genetic marker for breeding selection. The combination M1C2–B2B2–D1D1 is an ideal model for breeding in these strains because it can improve slaughter and meat quality traits.     

Deciphering signature of selection affecting beef quality traits in Angus cattle

Artificial selection towards a desired phenotype/trait has modified the genomes of livestock dramatically that generated breeds that greatly differ in morphology, production and environmental adaptation traits. Angus cattle are among the famous cattle breeds developed for superior beef quality. This paper aimed at exploring genomic regions under selection in Angus cattle that are associated with meat quality traits and other associated phenotypes. The whole genome of 10 Angus cattle was compared with 11 Hanwoo (A-H) and 9 Jersey (A-J) cattle breeds using a cross-population composite likelihood ratio (XP-CLR) statistical method. The top 1% of the empirical distribution was taken as significant and annotated using UMD3.1. As a result, 255 and 210 genes were revealed under selection from A–H and A–J comparisons, respectively. The WebGestalt gene ontology analysis resulted in sixteen (A–H) and five (A–J) significantly enriched KEGG pathways. Several pathways associated with meat quality traits (insulin signaling, type II diabetes mellitus pathway, focal adhesion pathway, and ECM-receptor interaction), and feeding efficiency (olfactory transduction, tight junction, and metabolic pathways) were enriched. Genes affecting beef quality traits (e.g., FABP3, FTO, DGAT2, ACS, ACAA2, CPE, TNNI1), stature and body size (e.g., PLAG1, LYN, CHCHD7, RPS20), fertility and dystocia (e.g., ESR1, RPS20, PPP2R1A, GHRL, PLAG1), feeding efficiency (e.g., PIK3CD, DNAJC28, DNAJC3, GHRL, PLAG1), coat color (e.g., MC1-R) and genetic disorders (e.g., ITGB6, PLAG1) were found to be under positive selection in Angus cattle. The study identified genes and pathways that are related to meat quality traits and other phenotypes of Angus cattle. The findings in this study, after validation using additional or independent dataset, will provide useful information for the study of Angus cattle in particular and beef cattle in general.     

Effects of DGAT1 gene on meat and carcass fatness quality in Chinese commercial cattle

This study was designed to investigate the candidate single nucleotide polymorphisms (SNPs) in the exon’s region of bovine diacylglycerol O-acyltransferase (DGAT1) gene using bioinformatics and experimental methods. A total of 17 SNPs were screened from public data resources and DNA sequencing. Three SNPs (c.572A>G, c.1241C>T and c.1416T>G) of these candidate SNPs were genotyped by created restriction site-polymerase chain reaction (CRS-PCR) methods. The gene-specific SNP markers and their effects on meat and carcass fatness quality traits were evaluated in Chinese commercial cattle. The c.572A>G and c.1416T>G significantly effected on backfat thickness, longissimus muscle area, marbling score, fat color and Warner-Bratzler shear force. No significant association was detected between the c.1241C>T and measured traits. Results from this study suggested that the SNP markers may be effective for the marker-assisted selection of meat and carcass fatness quality traits, and added new evidence that DGAT1 gene is an important candidate gene for the improvement of meat and carcass fatness quality in beef cattle industry.     

Genome-wide association and pathway analysis of carcass and meat quality traits in Piemontese young bulls

A key concern in beef production is how to improve carcass and meat quality traits. Identifying the genomic regions and biological pathways that contribute to explaining variability in these traits is of great importance for selection purposes. In this study, genome wide-association (GWAS) and pathway-based analyses of carcass traits (age at slaughter (AS), carcass weight (CW), carcass daily gain (CDG), conformation score and rib-eye muscle area) and meat quality traits (pH, Warner-Bratzler shear force, purge loss, cooking loss and colour parameters (lightness, redness, yellowness, chroma, hue)) were conducted using genotype data from the ‘GeneSeek Genomic Profiler Bovine LD’ array in a cohort of 1166 double-muscled Piemontese beef cattle. The genome wide-association analysis was based on the GRAMMAR-GC approach and identified 37 significant single nucleotide polymorphisms (SNPs), which were associated with 12 traits (P<5 × 10⁻⁵). In particular, 14 SNPs associated with CW, CDG and AS were located at 38.57 to 38.94 Mb on Bos taurus autosome 6 and mapped within four genes, that is, Leucine Aminopeptidase 3, Family with Sequence Similarity 184 Member B, Non-SMC Condensin I Complex Subunit G and Ligand-Dependent Nuclear Receptor Corepressor-Like. Strong pairwise linkage disequilibrium was found in this region. For meat quality traits, most associations were 1 SNP per trait, except for a signal on BTA25 (at ~11.96 Mb), which was significant for four of the five meat colour parameters assessed. Gene-set enrichment analyses yielded significant results for six traits (right-sided hypergeometric test, false discovery rate <0.05). In particular, several pathways related to transmembrane transport (i.e., oxygen, calcium, ion and cation) were overrepresented for meat colour parameters. The results obtained provide useful information for genomic selection for beef production and quality in the Piemontese breed.     

Genetic diversity of MYH 3 gene associated with growth and carcass traits in Chinese Qinchuan cattle

MYH₃, whose function is to convert chemical energy to mechanical energy through ATP hydrolysis, is mainly expressed in skeletal muscle at various stages and is indispensable in the procedure of development of skeletal muscle and heart. In the study, genetic variations and genotypes of MYH ₃ gene in a total of 365 Qinchuan cattles were analyzed by polymerase chain reaction-restriction fragment length polymorphism, as well as verified the effect on growth and carcass traits. After PCR products were digested by restriction enzymes, eight SNPs were identified and individuals were genotyped. It showed that the SNPs at nucleotides were all in low linkage disequilibrium, therefore no dominated haplotype was found in the population. The result of statistic analysis indicated seven SNPs were significantly associated with growth and carcass traits (P < 0.05, N = 365) except locus G13791A. To sum up, the result of the study proved that polymorphisms in MYH3 gene are associated with the growth performance of Chinese Qinchuan cattle, so the variations of the gene could be used as possible molecular assisted-makers in the beef cattle breeding program and management.     

A genome‐wide scan for selection signatures in Nellore cattle

Brazilian Nellore cattle (Bos indicus) have been selected for growth traits for over more than four decades. In recent years, reproductive and meat quality traits have become more important because of increasing consumption, exports and consumer demand. The identification of genome regions altered by artificial selection can potentially permit a better understanding of the biology of specific phenotypes that are useful for the development of tools designed to increase selection efficiency. Therefore, the aims of this study were to detect evidence of recent selection signatures in Nellore cattle using extended haplotype homozygosity methodology and BovineHD marker genotypes (>777 000 single nucleotide polymorphisms) as well as to identify corresponding genes underlying these signals. Thirty‐one significant regions (P < 0.0001) of possible recent selection signatures were detected, and 19 of these overlapped quantitative trait loci related to reproductive traits, growth, feed efficiency, meat quality, fatty acid profiles and immunity. In addition, 545 genes were identified in regions harboring selection signatures. Within this group, 58 genes were associated with growth, muscle and adipose tissue metabolism, reproductive traits or the immune system. Using relative extended haplotype homozygosity to analyze high‐density single nucleotide polymorphism marker data allowed for the identification of regions potentially under artificial selection pressure in the Nellore genome, which might be used to better understand autozygosity and the effects of selection on the Nellore genome.