Identification of genomic regions and pathways associated with traits related to rumen acidosis in feedlot Nellore cattle

There may be an increased risk of metabolic disorders, such as rumen acidosis, in cattle fed high-concentrate diets, particularly those from Bos taurus indicus genotypes, which have shown to be more sensitive to ruminal acidification. Therefore, this study aimed to estimate (co)variance components and identify genomic regions and pathways associated with ruminal acidosis in feedlot Nellore cattle fed high-concentrate diets. It was utilized a dataset containing a total of 642 Nellore bulls that were genotyped from seven feedlot nutrition studies. The GGP Indicus 35k panel was used with the single step genome-wide association study methodology in which the effects of the markers were obtained from the genomic values estimated by the GBLUP model. A bivariate model to estimate genetic correlations between the economically important traits and indicator traits for acidosis was used. The traits evaluated in this study that were nutritionally related to rumen acidosis included average daily gain (ADG), final body weight, time spent eating (TSE), time spent ruminating, rumenitis score (RUM), rumen absorptive surface area (ASA), rumen keratinized layer thickness (KER) and hot carcass weight (HCW). The identified candidate genes were mainly involved in the negative or non-regulation of the apoptotic process, salivary secretion, and transmembrane transport. The genetic correlation between HCW and ASA was low positive (0.27 ± 0.23), and between ADG and ASA was high moderate (0.58 ± 0.59). A positive genetic correlation between RUM and all performance traits was observed, and TSE correlated negatively with HCW (-0.33 ± 0.21), ASA (-0.75 ± 0.48), and KER (-0.40 ± 0.27). The genetic association between economically important traits and indicator traits for acidosis suggested that Nellore cattle may be more sensitive to acidosis in feedlot systems.

Sequence-based GWAS meta-analyses for beef production traits

BACKGROUND

Combining the results of within-population genome-wide association studies (GWAS) based on whole-genome sequences into a single meta-analysis (MA) is an accurate and powerful method for identifying variants associated with complex traits. As part of the H2020 BovReg project, we performed sequence-level MA for beef production traits. Five partners from France, Switzerland, Germany, and Canada contributed summary statistics from sequence-based GWAS conducted with 54,782 animals from 15 purebred or crossbred populations. We combined the summary statistics for four growth, nine morphology, and 15 carcass traits into 16 MA, using both fixed effects and z-score methods.

RESULTS

The fixed-effects method was generally more informative to provide indication on potentially causal variants, although we combined substantially different traits in each MA. In comparison with within-population GWAS, this approach highlighted (i) a larger number of quantitative trait loci (QTL), (ii) QTL more frequently located in genomic regions known for their effects on growth and meat/carcass traits, (iii) a smaller number of genomic variants within the QTL, and (iv) candidate variants that were more frequently located in genes. MA pinpointed variants in genes, including MSTN, LCORL, and PLAG1 that have been previously associated with morphology and carcass traits. We also identified dozens of other variants located in genes associated with growth and carcass traits, or with a function that may be related to meat production (e.g., HS6ST1, HERC2, WDR75, COL3A1, SLIT2, MED28, and ANKAR). Some of these variants overlapped with expression or splicing QTL reported in the cattle Genotype-Tissue Expression atlas (CattleGTEx) and could therefore regulate gene expression.

CONCLUSIONS

By identifying candidate genes and potential causal variants associated with beef production traits in cattle, MA demonstrates great potential for investigating the biological mechanisms underlying these traits. As a complement to within-population GWAS, this approach can provide deeper insights into the genetic architecture of complex traits in beef cattle.

The Effect of MSTN Mutation on Bile Acid Metabolism and Lipid Metabolism in Cattle

Myostatin (MSTN) is a negative regulator of skeletal muscle genesis during development. MSTN mutation leads to increased lean meat production and reduced fat deposition in livestock. However, the mechanism by which MSTN promotes myogenesis by regulating metabolism is not clear. In this study, we compared the metabolomics of the livers of wild-type (WT) and MSTN mutation cattle (MT), and found changes in the content and proportion of fatty acids and bile acids in MT cattle. The differential metabolites were enriched in sterol synthesis and primary bile acid synthesis. We further analyzed the expression of genes involved in the regulation of lipid and bile acid metabolism, and found that the loss of MSTN may alter lipid synthesis and bile acid metabolism. This study provides new basic data for MSTN mutations in beef cattle breeding.

Relationship between Some Myostatin Variants and Meat Production Related Calving, Weaning and Muscularity Traits in Charolais Cattle

The slaughter value of live cattle can be assessed during visual conformation scoring, as well as by examining different molecular genetic information, e.g., the myostatin gene, which can be responsible for muscle development. In this study, the F94L, Q204X, nt267, nt324 and nt414 alleles of the myostatin gene (MSTN) were examined in relation to birth weight (BIW), calving ease (CAE), 205-day weaning weight (CWW), muscle score of shoulder (MSS), muscle score of back (MSB), muscle score of thigh (MST), roundness score of thigh (RST), loin thickness score (LTS), and overall muscle development percentage (OMP) of Charolais weaned calves in Hungary. Multi-trait analysis of variance (GLM) and weighted linear regression analysis were used to process the data. Calves carrying the Q204X allele in the heterozygous form achieved approximately 0.14 points higher MSB, MST and LTS, and 1.2% higher OMP, and gained 8.56 kg more CWW than their counterparts not carrying the allele (p < 0.05). As for the F94L allele, there was a difference of 4.08 kg in CWW of the heterozygous animals, but this difference could not be proved statistically. The other alleles had no significant effect on the evaluated traits.

Polymorphism of Genes and Their Impact on Beef Quality

The single-nucleotide polymorphism (SNP) form of genes is a valuable source of information regarding their suitability for use as specific markers of desirable traits in beef cattle breeding. For several decades, breeding work focused on improving production efficiency through optimizing the feed conversion ratio and improving daily gains and meat quality. Many research teams previously undertook research work on single-nucleotide polymorphism in myostatin (MSTN), thyroglobulin (TG), calpain (CAPN), and calpastatin (CAST) proteins. The literature review focuses on the most frequently addressed issues concerning these genes in beef cattle production and points to a number of relevant studies on the genes' polymorphic forms. The four genes presented are worth considering during breeding work as a set of genes that can positively influence productivity and production quality.

Effect of Myostatin Gene Mutation on Slaughtering Performance and Meat Quality in Marchigiana Bulls

Simple Summary

The aim of this work was the evaluation of slaughtering performance in a sample of 78 Marchigiana bulls with different allelic situation at the myostatin locus; in addition, the qualitative composition of meat samples collected from Longissimus thoracis muscle was evaluated. At the myostatin gene, 67 homozygotes normal, 11 heterozygotes, and no double-muscled homozygote bulls were detected. Heterozygote bulls showed high values in final live weight and dressing yield; moreover, they were characterized by a low incidence of fat at steak dissection, as well as in meat chemical composition. A better muscular conformation in heterozygote bulls’ carcasses was highlighted, with a higher incidence of their carcasses in class E and evident convexity of round, back, and shoulder muscular masses compared to the carcasses of Marchigiana bulls which were normal at the myostatin gene.

Abstract

The myostatin gene also called Growth Differentiation Factor 8 gene (GDF8) is one of the most investigated loci that can be responsible for several quantitative and qualitative carcass and meat traits in double-muscled beef cattle. The objective of the study was to bring to light the effect of the myostatin polymorphism on slaughtering performance and meat quality in Marchigiana beef cattle. The experiment was carried out on 78 bulls reared according to the “cow-calf” extensive managing system. At the end of the fattening period, in vivo and carcass data were recorded. From each carcass, a steak of Longissimus thoracis was taken and used to determine the meat’s analytical composition and colorimetric properties. Finally, from each steak a sample of Longissimus thoracis was collected, then used for DNA extraction and genotyping at the myostatin locus. The heterozygous bulls showed slight superiority in the carcass data (e.g., hot carcass weight: 426.09 kg—heterozygotes vs. 405.32 kg—normal) and meat quality parameters, although not always with statistical significance. Only fat and ashes content were significantly affected by the myostatin genotype (heterozygotes: 2.01%, 1.26%; normal: 3.04%, 1.15%). The greater muscularity of heterozygous animals compared to normal ones could be a starting point to improving productive efficiency in Marchigiana beef cattle.

Myostatin: Basic biology to clinical application

Myostatin is a member of the transforming growth factor (TGF)-β superfamily. It is expressed by animal and human skeletal muscle cells where it limits muscle growth and promotes protein breakdown. Its effects are influenced by complex mechanisms including transcriptional and epigenetic regulation and modulation by extracellular binding proteins. Due to its actions in promoting muscle atrophy and cachexia, myostatin has been investigated as a promising therapeutic target to counteract muscle mass loss in experimental models and patients affected by different muscle-wasting conditions. Moreover, growing evidence indicates that myostatin, beyond to regulate skeletal muscle growth, may have a role in many physiologic and pathologic processes, such as obesity, insulin resistance, cardiovascular and chronic kidney disease. In this chapter, we review myostatin biology, including intracellular and extracellular regulatory pathways, and the role of myostatin in modulating physiologic processes, such as muscle growth and aging. Moreover, we discuss the most relevant experimental and clinical evidence supporting the extra-muscle effects of myostatin. Finally, we consider the main strategies developed and tested to inhibit myostatin in clinical trials and discuss the limits and future perspectives of the research on myostatin.

Identification of genomic regions that exhibit sexual dimorphism for size and muscularity in cattle

Sexual dimorphism, the phenomenon whereby males and females of the same species are distinctive in some aspect of appearance or size, has previously been documented in cattle for traits such as growth rate and carcass merit using a quantitative genetics approach. No previous study in cattle has attempted to document sexual dimorphism at a genome level; therefore, the objective of the present study was to determine whether genomic regions associated with size and muscularity in cattle exhibited signs of sexual dimorphism. Analyses were undertaken on 10 linear-type traits that describe the muscular and skeletal characteristics of both males and females of five beef cattle breeds: 1,444 Angus (AA), 6,433 Charolais (CH), 1,129 Hereford, 8,745 Limousin (LM), and 1,698 Simmental. Genome-wide association analyses were undertaken using imputed whole-genome sequence data for each sex separately by breed. For each single-nucleotide polymorphism (SNP) that was segregating in both sexes, the difference between the allele substitution effect sizes for each sex, in each breed separately, was calculated. Suggestively (P ≤ 1 × 10-5) sexually dimorphic SNPs that were segregating in both males and females were detected for all traits in all breeds, although the location of these SNPs differed by both trait and breed. Significantly (P ≤ 1 × 10-8) dimorphic SNPs were detected in just three traits in the AA, seven traits in the CH, and three traits in the LM. The vast majority of all segregating autosomal SNPs (86% in AA to 94% in LM) had the same minor allele in both males and females. Differences (P ≤ 0.05) in allele frequencies between the sexes were observed for between 36% (LM) and 66% (AA) of the total autosomal SNPs that were segregating in both sexes. Dimorphic SNPs were located within a number of genes related to muscularity and/or size including the NAB1, COL5A2, and IWS1 genes on BTA2 that are located close to, and thought to be co-inherited with, the MSTN gene. Overall, sexual dimorphism exists in cattle at the genome level, but it is not consistent by either trait or breed.

The Blonde d'Aquitaine T3811>G3811 mutation in the myostatin gene: association with growth, carcass, and muscle phenotypes in veal calves

The mutation T3811 → G3811 (TG3811) discovered in the myostatin gene of the Blonde d'Aquitaine breed is suspected of contributing to the outstanding muscularity of this breed. An experiment was designed to estimate the effect of this mutation in an F2 and back-cross Blonde d'Aquitaine × Holstein population. By genotyping all known mutations in the myostatin gene, it was ensured that the TG3811 mutation was indeed the only known mutation segregating in this population. Fifty-six calves (43 F2, 13 back-cross) were intensively fattened and slaughtered at 24.0 ± 1.4 wk of age. The effects of the mutation were estimated by comparing the calves with the [T/T] (n = 18), [T/G] (n = 30), and [G/G] (n = 8) genotypes. Highly significant substitution effects (P < 0.001), above + 1.2 phenotypic SD, were shown on carcass yield and muscularity scores. Birth weight (P < 0.001) was positively affected by the mutation (+0.8 SD) but not growth rate (P = 0.97), while carcass length (P = 0.03), and fatness (P ≤ 0.03) were negatively affected (-0.5 to -0.7 SD). The characteristics of the Triceps brachii muscle were affected by the mutation (P < 0.001), with lower ICDH activity (oxidative) and a higher proportion of myosin type 2X muscle fibers (fast twitch). The effects of the TG3811 mutation were similar to those of other known myostatin mutations, although the Blonde d'Aquitaine animals, which are predominantly [G/G] homozygous, do not exhibit extreme double muscling.

Genome-wide association study of economically important traits in Charolais and Limousin beef cows

Genomic selection has proven effective for advancing genetic gain for key profit traits in dairy cattle production systems. However, its impact to-date on genetic improvement programs for beef cattle has been less effective. Despite this, the technology is thought to be particularly useful for low heritability traits such as those associated with reproductive efficiency. The objective of this study was to identify genetic variants associated with key determinants of reproductive and overall productive efficiency in beef cows. The analysis employed a large dataset derived from the national genetic evaluation program in Ireland for two of the most predominant beef breeds, viz. Charolais (n = 5 244 cows) and Limousin (n = 7 304 cows). Single nucleotide polymorphisms (SNPs) were identified as being statistically significantly associated (adj. P < 0.05) with both reproductive and productive traits for both breed types. However, there was little across breed commonality, with only two SNPs (rs110240246 and rs110344317; adj. P < 0.05) located within the genomic regions of the LCORL and MSTN genes respectively, identified in both Charolais and Limousin populations, associated with traits including carcass weight, cull-cow weight and live-weight. Significant SNPs within the MSTN gene were also associated with both reproduction and production related traits within each breed. Finally, traits including calving difficulty, calf mortality and calving interval were associated with SNPs within genomic regions comprising genes involved in cellular growth and lipid metabolism. Genetic variants identified as associated with both important reproductive efficiency and production related traits from this study warrant further analyses for their potential incorporation into breeding programmes to support the sustainability of beef cattle production.

Associations of CAST, CAPN1 and MSTN Genes Polymorphism with Slaughter Value and Beef Quality – A Review

The slaughter value of cattle and beef quality are influenced by many factors, which can generally be divided into antemortem (breed, sex, age, housing system, diet, pre-slaughter handling) and postmortem (post-slaughter processing, chilling temperature, packaging). Studies of many authors have shown that meat quality traits can be also influenced by the individual genetic background of an animal. Numerous studies have been conducted worldwide to determine the functions of various genes as well as polymorphisms with potential effects on fattening and slaughter value of cattle and on beef quality. This study reviews the most important research done on the associations of polymorphisms in the calpain, calpastatin and myostatin genes with carcass traits and beef quality. Knowledge about the genes and chromosome regions associated with desired meat quality characteristics may prove very helpful when selecting pairs for mating and estimating the breeding value of offspring, mainly because it is difficult to improve meat quality traits based on conventional selection methods due to their low heritability and polygenic regulation. Furthermore, meat quality evaluation is expensive and can only be carried out after slaughter.

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.

Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds

BACKGROUND

Linear type traits, which reflect the muscular characteristics of an animal, could provide insight into how, in some cases, morphologically very different animals can yield the same carcass weight. Such variability may contribute to differences in the overall value of the carcass since primal cuts vary greatly in price; such variability may also hinder successful genome-based association studies. Therefore, the objective of our study was to identify genomic regions that are associated with five muscularity linear type traits and to determine if these significant regions are common across five different breeds. Analyses were carried out using linear mixed models on imputed whole-genome sequence data in each of the five breeds, separately. Then, the results of the within-breed analyses were used to conduct an across-breed meta-analysis per trait.

RESULTS

We identified many quantitative trait loci (QTL) that are located across the whole genome and associated with each trait in each breed. The only commonality among the breeds and traits was a large-effect pleiotropic QTL on BTA2 that contained the MSTN gene, which was associated with all traits in the Charolais and Limousin breeds. Other plausible candidate genes were identified for muscularity traits including PDE1A, PPP1R1C and multiple collagen and HOXD genes. In addition, associated (gene ontology) GO terms and KEGG pathways tended to differ between breeds and between traits especially in the numerically smaller populations of Angus, Hereford, and Simmental breeds. Most of the SNPs that were associated with any of the traits were intergenic or intronic SNPs located within regulatory regions of the genome.

CONCLUSIONS

The commonality between the Charolais and Limousin breeds indicates that the genetic architecture of the muscularity traits may be similar in these breeds due to their similar origins. Conversely, there were vast differences in the QTL associated with muscularity in Angus, Hereford, and Simmental. Knowledge of these differences in genetic architecture between breeds is useful to develop accurate genomic prediction equations that can operate effectively across breeds. Overall, the associated QTL differed according to trait, which suggests that breeding for a morphologically different (e.g. longer and wider versus shorter and smaller) more efficient animal may become possible in the future.

Genetic parameters and genome-wide association study regarding feed efficiency and slaughter traits in Charolais cows

Residual energy intake (REI) on two successive diets (hay and maize based) and slaughter traits, including visceral organs, were phenotyped in 584 adult purebred Charolais cows. To investigate the relationships between these traits and their genetic determinism, we first estimated the genetic parameters, including correlations, using REML modeling under WOMBAT software. The animals were then genotyped on the BovineSNP50 SNPchip before being imputed to the 600K density and genome wide association study was performed with GCTA software. We found low heritability for REI (h2 = 0.12 in each of the diet phases). Although the phenotypic correlation between the two diet phases was moderate (0.36), the genetic correlation was high (0.83), indicating a common genetic determinism for feed efficiency regardless of the diet. Correlations between REI and slaughter traits were negative regarding muscle-related traits and positive for fat-related traits, indicating that efficient animals generally had a more muscular carcass. It was also seen that feed efficiency was genetically and phenotypically correlated with smaller organs when expressed as a proportion of their empty body weight. From the GWAS analysis, seven QTLs were found to be associated with a trait at the genome-wide level of significance and 18 others at the chromosome-wide level. One important QTL was detected in BTA 2, reflecting the essential effect of the myostatin gene on both carcass composition and relative organ weight. Three QTLs were detected for REI during the maize diet phase on BTA 13, 19, and 28, the latter being significant at the genome-wide level. The QTLs on BTA 19 mapped into the TANC2 gene and the QTLs on BTA 28 into the KIF1BP gene, which are both known to interact with the same protein (KIF1A). However, no obvious functional link between these genes and feed efficiency could be made. Among the other QTLs detected, one association on BTA 4 with liver proportion mapped to the candidate gene WASL, which has previously been shown to be differentially expressed in liver cells and linked to feed restriction or cancer development. No QTLs were found to be common between feed efficiency and any slaughter traits.

Reaffirmation of known major genes and the identification of novel candidate genes associated with carcass-related metrics based on whole genome sequence within a large multi-breed cattle population

Background

The high narrow sense heritability of carcass traits suggests that the underlying additive genetic potential of an individual should be strongly correlated with both animal carcass quality and quantity, and therefore, by extension, carcass value. Therefore, the objective of the present study was to detect genomic regions associated with three carcass traits, namely carcass weight, conformation and fat cover, using imputed whole genome sequence in 28,470 dairy and beef sires from six breeds with a total of 2,199,926 phenotyped progeny.

Results

Major genes previously associated with carcass performance were identified, as well as several putative novel candidate genes that likely operate both within and across breeds. The role of MSTN in carcass performance was re-affirmed with the segregating Q204X mutation explaining 1.21, 1.11 and 5.95% of the genetic variance in carcass weight, fat and conformation, respectively in the Charolais population. In addition, a genomic region on BTA6 encompassing the NCAPG/LCORL locus, which is a known candidate locus associated with body size, was associated with carcass weight in Angus, Charolais and Limousin. Novel candidate genes identified included ZFAT in Angus, and SLC40A1 and the olfactory gene cluster on BTA15 in Charolais. Although the majority of associations were breed specific, associations that operated across breeds included SORCS1 on BTA26, MCTP2 on BTA21 and ARL15 on BTA20; these are of particular interest due to their potential informativeness in across-breed genomic evaluations. Genomic regions affecting all three carcass traits were identified in each of the breeds, although these were mainly concentrated on BTA2 and BTA6, surrounding MSTN and NCAPG/LCORL, respectively. This suggests that although major genes may be associated with all three carcass traits, the majority of genes containing significant variants (unadjusted p-value < 10^− 4) may be trait specific associations of small effect.

Conclusions

Although plausible novel candidate genes were identified, the proportion of variance explained by these candidates was minimal thus reaffirming that while carcass performance may be affected by major genes in the form of MSTN and NCAPG/LCORL, the majority of variance is attributed to the additive (and possibly multiplicative) effect of many polymorphisms of small effect.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6071-9) contains supplementary material, which is available to authorized users.

Cellular development in muscle differs between Angus steers from low and high muscle score selection lines1

This study assessed cellular characteristics of longissimus lumborum (LL) and semitendinosus (ST) muscles in steers genetically selected for low (Low) or high (High) muscling using live muscle scoring, and High steers with 1 copy of the loss-of-function 821 del11 MSTN allele (HighHet). We hypothesized High and HighHet have altered muscle cellular characteristics and mechanisms influencing muscling compared with Low steers. Angus steers 25 mo old comprising 14 High, 19 Low, and 11 HighHet were backgrounded to 20 mo of age, grain finished for 150 d, and then slaughtered. Body and carcass weights did not differ due to muscling line (P = 0.46). Weight of LL was 16% greater (P = 0.004) and total protein in LL was 18% greater (P = 0.012) in HighHet than Low steers. ST weight in HighHet was 10% and 13% greater than in High and Low steers (P = 0.007), respectively, and of total ST protein 12% and 17% greater in HighHet than High or Low (P = 0.002). Cross-sectional area (CSA) of LL was greater in HighHet than in High and greater in High than in Low (85.0 vs. 77.0 vs. 70.4 cm2, P < 0.001). Apparent number of myofibers and myofibers per unit CSA did not differ between the muscling lines in LL (P = 0.14) or ST (P = 0.47). Myofiber CSA was greater in the ST of Low than of High and HighHet for type 1 (36% and 31% respectively, P = 0.005) and 2A (22% and 25%, P < 0.001). HighHet steers had greater area of glycolytic (type 2X) relative to more oxidative myofiber types within LL (P = 0.02; 11% and 43% more than High and Low, respectively) and ST (P < 0.001; 27% and 75%). Concentration of RNA in LL was 13% and 10% greater (P = 0.005) in High than in Low and HighHet, respectively, and total amount of RNA in LL was 22% greater in High and 20% greater in HighHet than in Low (P < 0.001). The LL of High steers had less protein to RNA (P = 0.03; 57.4 vs. 65.6) and more RNA to DNA (P = 0.007; 9.03 vs. 7.83) than Low. HighHet steers had 11% more DNA in ST than High (P = 0.04) and 19% more RNA in ST than Low (P = 0.012). The shift towards glycolytic myofibers was consistent with loadings in a principal component that explained 39% of the variation in LL and 38% in ST. Overall, these findings show that selection for increased muscling using live cattle muscle scoring, and 1 copy of the 821 del11 MSTN allele, results in more glycolytic muscle. They also suggest that increased muscling of the High compared with Low steers may be associated with increased translational capacity in the LL.

Survey of allele specific expression in bovine muscle

Allelic imbalance is a common phenomenon in mammals that plays an important role in gene regulation. An Allele Specific Expression (ASE) approach can be used to detect variants with a cis-regulatory effect on gene expression. In cattle, this type of study has only been done once in Holstein. In our study we performed a genome-wide analysis of ASE in 19 Limousine muscle samples. We identified 5,658 ASE SNPs (Single Nucleotide Polymorphisms showing allele specific expression) in 13% of genes with detectable expression in the Longissimus thoraci muscle. Interestingly we found allelic imbalance in AOX1, PALLD and CAST genes. We also found 2,107 ASE SNPs located within genomic regions associated with meat or carcass traits. In order to identify causative cis-regulatory variants explaining ASE we searched for SNPs altering binding sites of transcription factors or microRNAs. We identified one SNP in the 3’UTR region of PRNP that could be a causal regulatory variant modifying binding sites of several miRNAs. We showed that ASE is frequent within our muscle samples. Our data could be used to elucidate the molecular mechanisms underlying gene expression imbalance.

Cattle phenotypes can disguise their maternal ancestry

Background

Cattle are bred for, amongst other factors, specific traits, including parasite resistance and adaptation to climate. However, the influence and inheritance of mitochondrial DNA (mtDNA) are not usually considered in breeding programmes. In this study, we analysed the mtDNA profiles of cattle from Victoria (VIC), southern Australia, which is a temperate climate, and the Northern Territory (NT), the northern part of Australia, which has a tropical climate, to determine if the mtDNA profiles of these cattle are indicative of breed and phenotype, and whether these profiles are appropriate for their environments.

Results

A phylogenetic tree of the full mtDNA sequences of different breeds of cattle, which were obtained from the NCBI database, showed that the mtDNA profiles of cattle do not always reflect their phenotype as some cattle with Bos taurus phenotypes had Bos indicus mtDNA, whilst some cattle with Bos indicus phenotypes had Bos taurus mtDNA. Using D-loop sequencing, we were able to contrast the phenotypes and mtDNA profiles from different species of cattle from the 2 distinct cattle breeding regions of Australia. We found that 67 of the 121 cattle with Bos indicus phenotypes from NT (55.4%) had Bos taurus mtDNA. In VIC, 92 of the 225 cattle with Bos taurus phenotypes (40.9%) possessed Bos indicus mtDNA. When focusing on oocytes from cattle with the Bos taurus phenotype in VIC, their respective oocytes with Bos indicus mtDNA had significantly lower levels of mtDNA copy number compared with oocytes possessing Bos taurus mtDNA (P < 0.01). However, embryos derived from oocytes with Bos indicus mtDNA had the same ability to develop to the blastocyst stage and the levels of mtDNA copy number in their blastocysts were similar to blastocysts derived from oocytes harbouring Bos taurus mtDNA. Nevertheless, oocytes originating from the Bos indicus phenotype exhibited lower developmental potential due to low mtDNA copy number when compared with oocytes from cattle with a Bos taurus phenotype.

Conclusions

The phenotype of cattle is not always related to their mtDNA profiles. MtDNA profiles should be considered for breeding programmes as they also influence phenotypic traits and reproductive capacity in terms of oocyte quality.

Electronic supplementary material

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Genome-wide association study for behavior, type traits, and muscular development in Charolais beef cattle

Behavior, type traits, and muscular development are of interest for beef cattle breeding. Genome-wide association studies (GWAS) enable the identification of candidate genes, which enables gene-based selection and provides insight in the genetic architecture of these traits. The objective of the current study was to perform a GWAS for 3 behavior traits, 12 type traits, and muscular development in Charolais cattle. Behavior traits, including aggressiveness at parturition, aggressiveness during gestation period, and maternal care, were scored by farmers. Type traits, including udder conformation, teat, feet and legs, and locomotion, were scored by trained classifiers. Data used in the GWAS consisted of 3,274 cows with phenotypic records and genotyping information for 44,930 SNP. When SNP had a false discovery rate (FDR) smaller than 0.05, they were referred to as significant. When SNP had a FDR between 0.05 and 0.20, they were referred to as suggestive. Four significant and 12 suggestive regions were detected for aggressiveness during gestation, maternal care, udder balance, teat thinness, teat length, foot angle, foot depth, and locomotion. These 4 significant and 12 suggestive regions were not supported by other significant SNP in close proximity. No SNP with major effects were detected for behavior and type traits, and SNP associations for these traits were spread across the genome, suggesting that behavior and type traits were influenced by many genes, each explaining a small part of genetic variance. The GWAS identified 1 region on chromosome 2 significantly associated with muscular development, which included the myostatin gene (), which is known to affect muscularity. No other regions associated with muscular development were found. Results showed that the myostatin region associated with muscular development had pleiotropic effects on udder volume, teat thinness, rear leg, and leg angle.

Multi-breed and multi-trait co-association analysis of meat tenderness and other meat quality traits in three French beef cattle breeds

Background

Studies to identify markers associated with beef tenderness have focused on Warner–Bratzler shear force (WBSF) but the interplay between the genes associated with WBSF has not been explored. We used the association weight matrix (AWM), a systems biology approach, to identify a set of interacting genes that are co-associated with tenderness and other meat quality traits, and shared across the Charolaise, Limousine and Blonde d’Aquitaine beef cattle breeds.

Results

Genome-wide association studies were performed using ~500K single nucleotide polymorphisms (SNPs) and 17 phenotypes measured on more than 1000 animals for each breed. First, this multi-trait approach was applied separately for each breed across 17 phenotypes and second, between- and across-breed comparisons at the AWM and functional levels were performed. Genetic heterogeneity was observed, and most of the variants that were associated with WBSF segregated within rather than across breeds. We identified 206 common candidate genes associated with WBSF across the three breeds. SNPs in these common genes explained between 28 and 30 % of the phenotypic variance for WBSF. A reduced number of common SNPs mapping to the 206 common genes were identified, suggesting that different mutations may target the same genes in a breed-specific manner. Therefore, it is likely that, depending on allele frequencies and linkage disequilibrium patterns, a SNP that is identified for one breed may not be informative for another unrelated breed. Well-known candidate genes affecting beef tenderness were identified. In addition, some of the 206 common genes are located within previously reported quantitative trait loci for WBSF in several cattle breeds. Moreover, the multi-breed co-association analysis detected new candidate genes, regulators and metabolic pathways that are likely involved in the determination of meat tenderness and other meat quality traits in beef cattle.

Conclusions

Our results suggest that systems biology approaches that explore associations of correlated traits increase statistical power to identify candidate genes beyond the one-dimensional approach. Further studies on the 206 common genes, their pathways, regulators and interactions will expand our knowledge on the molecular basis of meat tenderness and could lead to the discovery of functional mutations useful for genomic selection in a multi-breed beef cattle context.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-016-0216-y) contains supplementary material, which is available to authorized users.

Structural and Dynamic Characterization of the C313Y Mutation in Myostatin Dimeric Protein, Responsible for the "Double Muscle" Phenotype in Piedmontese Cattle

The knowledge of the molecular effects of the C313Y mutation, responsible for the “double muscle” phenotype in Piedmontese cattle, can help understanding the actual mechanism of phenotype determination and paves the route for a better modulation of the positive effects of this economic important phenotype in the beef industry, while minimizing the negative side effects, now inevitably intersected. The structure and dynamic behavior of the active dimeric form of Myostatin in cattle was analyzed by means of three state-of-the-art Molecular Dynamics simulations, 200-ns long, of wild-type and C313Y mutants. Our results highlight a role for the conserved Arg333 in establishing a network of short and long range interactions between the two monomers in the wild-type protein that is destroyed upon the C313Y mutation even in a single monomer. Furthermore, the native protein shows an asymmetry in residue fluctuation that is absent in the double monomer mutant. Time window analysis on further 200-ns of simulation demonstrates that this is a characteristic behavior of the protein, likely dependent on long range communications between monomers. The same behavior, in fact, has already been observed in other mutated dimers. Finally, the mutation does not produce alterations in the secondary structure elements that compose the characteristic TGF-β cystine-knot motif.

A comparison of methods for whole-genome QTL mapping using dense markers in four livestock species

Background

With dense genotyping, many choices exist for methods to detect quantitative trait loci (QTL) in livestock populations. However, no across-species study has been conducted on the performance of different methods using real data. We compared three methods that correct for relatedness either implicitly or explicitly: linkage and linkage disequilibrium haplotype-based analysis (LDLA), efficient mixed-model association (EMMA) analysis, and Bayesian whole-genome regression (BayesC). We analyzed one chromosome in each of five datasets (dairy cattle, beef cattle, sheep, horses, and pigs) using real genotypes based on dense single nucleotide polymorphisms and phenotypes. The P values corrected for multiple testing or Bayes factors greater than 150 were considered to be significant. To complete the real data study, we also simulated quantitative trait loci (QTL) for the same datasets based on the real genotypes. Several scenarios were chosen, with different QTL effects and linkage disequilibrium patterns. A pseudo-null statistical distribution was chosen to make the significance thresholds comparable across methods.

Results

For the real data, the three methods generally agreed within 1 or 2 cM for the locations of QTL regions and disagreed when no signals were significant (e.g. in pigs). For certain datasets, LDLA had more significant signals than EMMA or BayesC, but they were concentrated around the same peaks. Therefore, the three methods detected approximately the same number of QTL regions. For the simulated data, LDLA was slightly less powerful and accurate than either EMMA or BayesC but this depended strongly on how thresholds were set in the simulations.

Conclusions

All three methods performed similarly for real and simulated data. No method was clearly superior across all datasets or for any particular dataset. For computational efficiency and ease of interpretation, EMMA is recommended, but using more than one method is suggested.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0087-7) contains supplementary material, which is available to authorized users.

A whole genome association study on meat palatability in hanwoo

A whole genome association (WGA) study was carried out to find quantitative trait loci (QTL) for sensory evaluation traits in Hanwoo. Carcass samples of 250 Hanwoo steers were collected from National Agricultural Cooperative Livestock Research Institute, Ansung, Gyeonggi province, Korea, between 2011 and 2012 and genotyped with the Affymetrix Bovine Axiom Array 640K single nucleotide polymorphism (SNP) chip. Among the SNPs in the chip, a total of 322,160 SNPs were chosen after quality control tests. After adjusting for the effects of age, slaughter-year-season, and polygenic effects using genome relationship matrix, the corrected phenotypes for the sensory evaluation measurements were regressed on each SNP using a simple linear regression additive based model. A total of 1,631 SNPs were detected for color, aroma, tenderness, juiciness and palatability at 0.1% comparison-wise level. Among the significant SNPs, the best set of 52 SNP markers were chosen using a forward regression procedure at 0.05 level, among which the sets of 8, 14, 11, 10, and 9 SNPs were determined for the respectively sensory evaluation traits. The sets of significant SNPs explained 18% to 31% of phenotypic variance. Three SNPs were pleiotropic, i.e. AX-26703353 and AX-26742891 that were located at 101 and 110 Mb of BTA6, respectively, influencing tenderness, juiciness and palatability, while AX-18624743 at 3 Mb of BTA10 affected tenderness and palatability. Our results suggest that some QTL for sensory measures are segregating in a Hanwoo steer population. Additional WGA studies on fatty acid and nutritional components as well as the sensory panels are in process to characterize genetic architecture of meat quality and palatability in Hanwoo.

Fine mapping of quantitative trait loci underlying sensory meat quality traits in three French beef cattle breeds

Improving the traits that underlie meat quality is a major challenge in the beef industry. The objective of this paper was to detect QTL linked to sensory meat quality traits in 3 French beef cattle breeds. We genotyped 1,059, 1,219, and 947 young bulls and their sires belonging to the Charolais, Limousin, and Blonde d'Aquitaine breeds, respectively, using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). After estimating relevant genetic parameters using VCE software, we performed a linkage disequilibrium and linkage analysis on 4 meat traits: intramuscular fat content, muscle lightness, shear force, and tenderness score. Heritability coefficients largely ranged between 0.10 and 0.24; however, they reached a maximum of 0.44 and 0.50 for intramuscular fat content and tenderness score, respectively, in the Charolais breed. The 2 meat texture traits, shear force and tenderness score, were strongly genetically correlated (-0.91 in the Charolais and Limousin breed and -0.86 in the Blonde d'Aquitaine breed), indicating that they are 2 different measures of approximately the same trait. The genetic correlation between tenderness and intramuscular fat content differed across breeds. Using a significance threshold of 5 × 10(-4) for QTL detection, we found more than 200 significant positions across the 29 autosomal chromosomes for the 4 traits in the Charolais and Blonde d'Aquitaine breeds; in contrast, there were only 78 significant positions in the Limousin breed. Few QTL were common across breeds. We detected QTL for intramuscular fat content located near the myostatin gene in the Charolais and Blonde d'Aquitaine breeds. No mutation in this gene has been reported for the Blonde d'Aquitaine breed; therefore, it suggests that an unknown mutation could be segregating in this breed. We confirmed that, in certain breeds, markers in the calpastatin and calpain 1 gene regions affect tenderness. We also found new QTL as several QTL on chromosome 3 that are significantly associated with meat tenderness in the Blonde d'Aquitaine breed. Overall, these results greatly contribute to the goal of building a panel of markers that can be used to select animals of high meat quality.

Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing

Background

The advent of large-scale gene expression technologies has helped to reveal in eukaryotic cells, the existence of thousands of non-coding transcripts, whose function and significance remain mostly poorly understood. Among these non-coding transcripts, long non-coding RNAs (lncRNAs) are the least well-studied but are emerging as key regulators of diverse cellular processes. In the present study, we performed a survey in bovine Longissimus thoraci of lincRNAs (long intergenic non-coding RNAs not overlapping protein-coding transcripts). To our knowledge, this represents the first such study in bovine muscle.

Results

To identify lincRNAs, we used paired-end RNA sequencing (RNA-Seq) to explore the transcriptomes of Longissimus thoraci from nine Limousin bull calves. Approximately 14–45 million paired-end reads were obtained per library. A total of 30,548 different transcripts were identified. Using a computational pipeline, we defined a stringent set of 584 different lincRNAs with 418 lincRNAs found in all nine muscle samples. Bovine lincRNAs share characteristics seen in their mammalian counterparts: relatively short transcript and gene lengths, low exon number and significantly lower expression, compared to protein-encoding genes. As for the first time, our study identified lincRNAs from nine different samples from the same tissue, it is possible to analyse the inter-individual variability of the gene expression level of the identified lincRNAs. Interestingly, there was a significant difference when we compared the expression variation of the 418 lincRNAs with the 10,775 known selected protein-encoding genes found in all muscle samples. In addition, we found 2,083 pairs of lincRNA/protein-encoding genes showing a highly significant correlated expression. Fourteen lincRNAs were selected and 13 were validated by RT-PCR. Some of the lincRNAs expressed in muscle are located within quantitative trait loci for meat quality traits.

Conclusions

Our study provides a glimpse into the lincRNA content of bovine muscle and will facilitate future experimental studies to unravel the function of these molecules. It may prove useful to elucidate their effect on mechanisms underlying the genetic variability of meat quality traits. This catalog will complement the list of lincRNAs already discovered in cattle and therefore will help to better annotate the bovine genome.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-499) contains supplementary material, which is available to authorized users.

A systems biology approach using metabolomic data reveals genes and pathways interacting to modulate divergent growth in cattle

BACKGROUND

Systems biology enables the identification of gene networks that modulate complex traits. Comprehensive metabolomic analyses provide innovative phenotypes that are intermediate between the initiator of genetic variability, the genome, and raw phenotypes that are influenced by a large number of environmental effects. The present study combines two concepts, systems biology and metabolic analyses, in an approach without prior functional hypothesis in order to dissect genes and molecular pathways that modulate differential growth at the onset of puberty in male cattle. Furthermore, this integrative strategy was applied to specifically explore distinctive gene interactions of non-SMC condensin I complex, subunit G (NCAPG) and myostatin (GDF8), known modulators of pre- and postnatal growth that are only partially understood for their molecular pathways affecting differential body weight.

RESULTS

Our study successfully established gene networks and interacting partners affecting growth at the onset of puberty in cattle. We demonstrated the biological relevance of the created networks by comparison to randomly created networks. Our data showed that GnRH (Gonadotropin-releasing hormone) signaling is associated with divergent growth at the onset of puberty and revealed two highly connected hubs, BTC and DGKH, within the network. Both genes are known to directly interact with the GnRH signaling pathway. Furthermore, a gene interaction network for NCAPG containing 14 densely connected genes revealed novel information concerning the functional role of NCAPG in divergent growth.

CONCLUSIONS

Merging both concepts, systems biology and metabolomic analyses, successfully yielded new insights into gene networks and interacting partners affecting growth at the onset of puberty in cattle. Genetic modulation in GnRH signaling was identified as key modifier of differential cattle growth at the onset of puberty. In addition, the benefit of our innovative concept without prior functional hypothesis was demonstrated by data suggesting that NCAPG might contribute to vascular smooth muscle contraction by indirect effects on the NO pathway via modulation of arginine metabolism. Our study shows for the first time in cattle that integration of genetic, physiological and metabolomics data in a systems biology approach will enable (or contribute to) an improved understanding of metabolic and gene networks and genotype-phenotype relationships.

Modelling of beef sensory quality for a better prediction of palatability

Despite efforts by the industry to control the eating quality of beef, there remains a high level of variability in palatability, which is one reason for consumer dissatisfaction. In Europe, there is still no reliable on-line tool to predict beef quality and deliver consistent quality beef to consumers. Beef quality traits depend in part on the physical and chemical properties of the muscles. The determination of these properties (known as muscle profiling) will allow for more informed decisions to be made in the selection of individual muscles for the production of value-added products. Therefore, scientists and professional partners of the ProSafeBeef project have brought together all the data they have accumulated over 20 years. The resulting BIF-Beef (Integrated and Functional Biology of Beef) data warehouse contains available data of animal growth, carcass composition, muscle tissue characteristics and beef quality traits. This database is useful to determine the most important muscle characteristics associated with a high tenderness, a high flavour or generally a high quality. Another more consumer driven modelling tool was developed in Australia: the Meat Standards Australia (MSA) grading scheme that predicts beef quality for each individual muscle×specific cooking method combination using various information on the corresponding animals and post-slaughter processing factors. This system has also the potential to detect variability in quality within muscles. The MSA system proved to be effective in predicting beef palatability not only in Australia but also in many other countries. The results of the work conducted in Europe within the ProSafeBeef project indicate that it would be possible to manage a grading system in Europe similar to the MSA system. The combination of the different modelling approaches (namely muscle biochemistry and a MSA-like meat grading system adapted to the European market) is a promising area of research to improve the prediction of beef quality. In both approaches, the volume of data available not only provides statistically sound correlations between various factors and beef quality traits but also a better understanding of the variability of beef quality according to various criteria (breed, age, sex, pH, marbling etc.).

Candidate genes and single nucleotide polymorphisms associated with variation in residual feed intake in beef cattle

The candidate gene approach was used to identify genes associated with residual feed intake (RFI) in beef steers. The approach uses prior knowledge of gene functions to predict their biological role in the variation observed in a trait. It is suited to identify genes associated with complex traits where each gene has a relatively small effect. First, positional candidate genes were identified within the genomic positions of previously reported QTL associated with component traits related to RFI such as dry matter intake (DMI), growth, feed conversion ratio (FCR), average daily gain (ADG), and energy balance. Secondly, the positional candidate genes were prioritized into functional candidate genes according to their biological functions and their relationship with the biological processes associated with RFI including carbohydrate, fat and protein metabolism, thermoregulation, immunity and muscle activity. Single nucleotide polymorphisms (SNPs) located within the functional candidate genes were identified using mRNA sequences and prioritized into functional classes such as non-synonymous (nsSNP), synonymous (sSNP) or intronic SNP. A total of 117 nsSNP were considered as functional SNP and genotyped in steers at the University of Alberta ranch in Kinsella. Multiple marker association analysis in ASReml was performed using RFI data obtained from 531 beef steers. Twenty-five SNP were significantly associated with RFI (P < 0.05) accounting for 19.7% of the phenotypic variation. Using SIFT program to predict the effect of the SNP on the function of the corresponding protein, 3 of the 25 SNP were predicted to cause a significant effect on protein function (P < 0.05). One of the 3 SNP was located in the GHR gene and was also associated with a significant effect on the tertiary structure of the GHR protein (P < 0.05) as modeled using SWISSModel software. Least square means for each genotype were estimated and an over-dominance effect was observed for the SNP located in the GHR, CAST, ACAD11 and UGT3A1 genes. In addition, 2 other SNP showed a dominance effect and 3 genes had an additive effect. Gene network analysis performed in Ingenuity pathway analysis (IPA) software (Ingenuity Systems, www.ingenuity.com) indicated that the significant genes were involved in biological pathways such as lipid, protein and energy metabolism, electron transport and membrane signaling. The genes in this study, if validated in other beef cattle populations, may be useful for marker assisted selection for feed efficiency.

Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing

Background

Genetic information based on molecular markers has increasingly being used in cattle breeding improvement programmes, as a mean to improve conventionally phenotypic selection. Advances in molecular genetics have led to the identification of several genetic markers associated with genes affecting economic traits. Until recently, the identification of the causative genetic variants involved in the phenotypes of interest has remained a difficult task. The advent of novel sequencing technologies now offers a new opportunity for the identification of such variants. Despite sequencing costs plummeting, sequencing whole-genomes or large targeted regions is still too expensive for most laboratories. A transcriptomic-based sequencing approach offers a cheaper alternative to identify a large number of polymorphisms and possibly to discover causative variants. In the present study, we performed a gene-based single nucleotide polymorphism (SNP) discovery analysis in bovine Longissimus thoraci, using RNA-Seq. To our knowledge, this represents the first study done in bovine muscle.

Results

Messenger RNAs from Longissimus thoraci from three Limousin bull calves were subjected to high-throughput sequencing. Approximately 36–46 million paired-end reads were obtained per library. A total of 19,752 transcripts were identified and 34,376 different SNPs were detected. Fifty-five percent of the SNPs were found in coding regions and ~22% resulted in an amino acid change. Applying a very stringent SNP quality threshold, we detected 8,407 different high-confidence SNPs, 18% of which are non synonymous coding SNPs. To analyse the accuracy of RNA-Seq technology for SNP detection, 48 SNPs were selected for validation by genotyping. No discrepancies were observed when using the highest SNP probability threshold. To test the usefulness of the identified SNPs, the 48 selected SNPs were assessed by genotyping 93 bovine samples, representing mostly the nine major breeds used in France. Principal component analysis indicates a clear separation between the nine populations.

Conclusions

The RNA-Seq data and the collection of newly discovered coding SNPs improve the genomic resources available for cattle, especially for beef breeds. The large amount of variation present in genes expressed in Limousin Longissimus thoracis, especially the large number of non synonymous coding SNPs, may prove useful to study the mechanisms underlying the genetic variability of meat quality traits.

Detection of signatures of selective sweeps in the Blonde d'Aquitaine cattle breed

Identifying recent positive selection signatures in domesticated animals could provide information on genome response to strong directional selection from domestication and artificial selection and therefore could help in identifying mutations responsible for improved traits. We used genotyping data generated using Illumina's BovineSNP50 Genotyping BeadChips to identify selection signatures in the Blonde d'Aquitaine breed, a well-muscled French beef breed. For this purpose, we employed a hidden Markov model-based test, which detects selection by studying local variations in the allele frequency spectrum along the genome, within a single population. Three regions containing selective sweeps were identified. Annotation of genes located within these regions revealed interesting candidate genes. For example, myostatin (also known as GDF8), a known muscle growth factor inhibitor, is located within the selection signature region found on chromosome 2. In addition, we have identified chromosomal regions that show some evidence of selection within QTL regions for economically important traits. The results of this study could help to better understand the mechanisms related to the selection of the Blonde d'Aquitaine breed.

Cluster analysis application identifies muscle characteristics of importance for beef tenderness

BACKGROUND

An important controversy in the relationship between beef tenderness and muscle characteristics including biochemical traits exists among meat researchers. The aim of this study is to explain variability in meat tenderness using muscle characteristics and biochemical traits available in the Integrated and Functional Biology of Beef (BIF-Beef) database. The BIF-Beef data warehouse contains characteristic measurements from animal, muscle, carcass, and meat quality derived from numerous experiments. We created three classes for tenderness (high, medium, and low) based on trained taste panel tenderness scores of all meat samples consumed (4,366 observations from 40 different experiments). For each tenderness class, the corresponding means for the mechanical characteristics, muscle fibre type, collagen content, and biochemical traits which may influence tenderness of the muscles were calculated.

RESULTS

Our results indicated that lower shear force values were associated with more tender meat. In addition, muscles in the highest tenderness cluster had the lowest total and insoluble collagen contents, the highest mitochondrial enzyme activity (isocitrate dehydrogenase), the highest proportion of slow oxidative muscle fibres, the lowest proportion of fast-glycolytic muscle fibres, and the lowest average muscle fibre cross-sectional area. Results were confirmed by correlation analyses, and differences between muscle types in terms of biochemical characteristics and tenderness score were evidenced by Principal Component Analysis (PCA). When the cluster analysis was repeated using only muscle samples from m. Longissimus thoracis (LT), the results were similar; only contrasting previous results by maintaining a relatively constant fibre-type composition between all three tenderness classes.

CONCLUSION

Our results show that increased meat tenderness is related to lower shear forces, lower insoluble collagen and total collagen content, lower cross-sectional area of fibres, and an overall fibre type composition displaying more oxidative fibres than glycolytic fibres.

Effect of an exon 1 mutation in the myostatin gene on the growth traits of the Bian chicken

Myostatin (MSTN), or growth and differentiation factor 8 (GDF8), is a member of the transforming growth factor (TGF)-β superfamily. This family functions as a negative regulator of skeletal muscle development and growth in mammals. Single-nucleotide polymorphisms in exon 1 of the Bian chicken myostatin gene were detected by polymerase chain reaction-restriction fragment length polymorphism. A mutation (c.234G>A) in exon 1 was found. Female Bian chickens of genotypes AA and GA had significantly higher body weights than those of genotype GG (P < 0.05 or P < 0.01) from 6 to 18 weeks of age. These results suggested that the mutation c.234G>A in exon 1 could be used as a genetic marker for Bian chicken growth traits.

The challenge and limitations of combining data: a case study examining the relationship between intramuscular fat content and flavour intensity based on the BIF-BEEF database

The BIF-BEEF (Beef Integrated and Functional Biology) data warehouse for muscle biology to predict beef quality gathers data related to bovines, their carcasses and their beef. These data come mainly from three sources: the INRA database named FiLiCol, the European GEMQUAL program and the French QUALVIGENE program databases plus other minor sources. At the beginning of 2011, the BIF-BEEF data warehouse contained 331 745 measurements for 621 variables. Measurements were obtained on eight muscles and/or from 5197 animals (mainly young bulls) belonging to 20 different breeds (mainly Charolais, Limousin, Blonde d’Aquitaine, the three major French beef breeds) from experiments carried out over a 10-year period. A web interface was developed to extract data and to analyse them using basic statistical tools (correlation, variance analysis, etc) with R software. Clearly, since the various experiments were not designed initially to ultimately link together, it appeared very difficult to integrate some data which differ a lot by units, scales or laboratory methods. Ontology will help to address these issues. However, the usefulness of the BIF-BEEF data warehouse is described by studying the relationship in M. longissimus thoracis between intramuscular fat content (IMF) and flavour assessed by sensory panels. When data from different sources or different sensory panels were used, they were corrected for these fixed factors in the regression model. They were also corrected for known sources of variation (sex, breed and age of the animals). On average, the relationship between IMF and flavour was low (partial correlation coefficient r = 0.11) but significant. This relationship was no more significant for breeds with low IMF levels (such as Blonde d’Aquitaine) or for animals with the highest IMF such as steers or females.

Mutations in the myostatin gene leading to hypermuscularity in mammals: indications for a similar mechanism in fish?

The transforming growth factor β (TGF-β) superfamily encodes secreted factors that are important in regulating embryonic development and tissue homeostatis in adults. Myostatin (MSTN, encoded by MSTN) or 'growth and differentiation factor 8', a member of this superfamily, is a negative regulator of skeletal muscle growth and is highly conserved among animal species. In 1997, a mutation associated with the so-called double-muscling phenotype in cattle was found in the MSTN gene. During the years following the discovery of the first MSTN mutation, other mutations were found in cattle and other mammalian species, and MSTN became one of the most thoroughly studied genes in animals. The aim of this review is mainly to describe the functional mutations located in the MSTN genes of several mammalian species, leading to double muscling in these animals. Furthermore, in light of the increasing importance of fish genetics, the possibility of functional mutations in piscine MSTN with a similar effect as in mammals, and a genetic model for MSTN research in fish, will also be discussed.

Metabolomic profiles indicate distinct physiological pathways affected by two loci with major divergent effect on Bos taurus growth and lipid deposition

Identifying trait-associated genetic variation offers new prospects to reveal novel physiological pathways modulating complex traits. Taking advantage of a unique animal model, we identified the I442M mutation in the non-SMC condensin I complex, subunit G ( NCAPG) gene and the Q204X mutation in the growth differentiation factor 8 ( GDF8) gene as substantial modulators of pre- and/or postnatal growth in cattle. In a combined metabolomic and genotype association approach, which is the first respective study in livestock, we surveyed the specific physiological background of the effects of both loci on body-mass gain and lipid deposition. Our data provided confirming evidence from two historically and geographically distant cattle populations that the onset of puberty is the key interval of divergent growth. The locus-specific metabolic patterns obtained from monitoring 201 plasma metabolites at puberty mirror the particular NCAPG I442M and GDF8 Q204X effects and represent biosignatures of divergent physiological pathways potentially modulating effects on proportional and disproportional growth, respectively. While the NCAPG I442M mutation affected the arginine metabolism, the 204X allele in the GDF8 gene predominantly raised the carnitine level and had concordant effects on glycerophosphatidylcholines and sphingomyelins. Our study provides a conclusive link between the well-described growth-regulating functions of arginine metabolism and the previously unknown specific physiological role of the NCAPG protein in mammalian metabolism. Owing to the confirmed effect of the NCAPG/LCORL locus on human height in genome-wide association studies, the results obtained for bovine NCAPG might add valuable, comparative information on the physiological background of genetically determined divergent mammalian growth.