Variation at the Calpain 3 gene is associated with meat tenderness in zebu and composite breeds of cattle

Bibliometric Analysis of Research on the Main Genes Involved in Meat Tenderness

Simple Summary

A bibliometric analysis was carried out to know the evolution of research on genes associated with meat tenderness, of interest for the development of selection programs. Since 1993, studies have been limited to a few researchers in high-income countries due to the costs associated with the techniques. The main findings showed that the scientific production had a discontinuous growth because science experienced a significant change since approximately 2010. Marker-assisted selection was widely used, evaluating mainly CAPN (calpain) and CAST (calpastatin) genes for their contribution to meat tenderness, especially in cattle. However, the effects are small; therefore, genomic selection was implemented by genotyping thousands of single nucleotide polymorphisms (SNPs) for further explanation of genetic variation. The results shown are important for scholars to identify emerging methodologies and gaps in the literature and to know who the prolific authors and institutions in the field for possible collaborations, etc., are.

Abstract

Tenderness is one of the main characteristics of meat because it determines its price and acceptability. This is the first bibliometric study on the trend of research on the role of genes in meat tenderness. A total of 175 original and English-language articles published up to 2021 were retrieved from Scopus. The bibliometric analysis was carried out with VOSviewer (version 1.6.18, Eck and Waltman, Leiden, Netherlands) and complemented with the Analyze search results service from Scopus. Erroneous and duplicate data were eliminated, and incomplete information was added to standardize the results. Scientific production was evaluated by means of quantity, quality and structure indicators. As a first glance, 8.816% of authors have published more than 50% of papers mainly related to genes encoding the calpain (CAPN)-calpastatin (CAST) system and single nucleotide polymorphisms (SNPs). Among other findings, a strong link was found between the contribution of the main countries (led by the United States with) and their institutions (led by the USDA Agricultural Research Service with) to their gross domestic product. Most studies on the topic are published in the Journal of Animal Science, and other journals with high impact according to the number of citations and different metrics. Finally, when evaluating the most cited articles, the occurrence and association of the main keywords, it was confirmed that research is focused on the role of CAPN and CAST genes and of SNPs in beef tenderness. The change in science was emphasized; although marker-assisted selection is still used, genes have an infinitesimal effect on complex traits. Therefore, since about 2010, new research groups adopted genomic selection to evaluate dense panels of SNPs and better explain genetic variation in meat tenderness.

Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus

Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis-regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes.

Molecular genetic characterisation and expression profiling of calpain 3 transcripts in red sea bream (Pagrus major)

Calpains (CAPNs) belong to the papain superfamily of cysteine proteases, and they are calcium-dependent cytoplasmic cysteine proteases that regulate a variety of physiological processes. We obtained the sequence of CAPN3 from an NGS-based analysis of Pagrus major (PmCAPN3) and confirmed the conserved molecular biological properties in the predicted amino acid sequence. The amino acid sequence and predicted domains of CAPN3 were found to be highly conserved in all of the examined species, and one catalytic domain and four calcium binding sites were identified. In healthy P. major, the PmCAPN3 mRNA was most abundantly expressed in the muscle and skin, and ubiquitously expressed in the other tissues used in the experiment. After artificial infections with fish pathogens, significant changes in its expression levels were found in immune-related tissues, most of showed upregulation. In particular, the highest level of expression was found in the liver, a tissue associated with protease activity. Taken together, these results suggest a physiological activity for PmCAPN3 in P. major and reveal functional possibilities that have not yet been reported in the immune system.

Genomewide association mapping and pathway analysis of meat tenderness in Polled Nellore cattle

Brazil is one of the world's largest beef exporters, although the product has a low price due to quality issues. The meat exported by Brazil is considered medium and low quality by international buyers, mainly due to lack of tenderness. The predominant Zebu breeds (80% Nellore) are known for producing tougher beef than taurine breeds. Nonetheless, some studies have shown that there is substantial genetic variability for tenderness within the Nellore breed, although it is a difficult trait to improve by conventional selection methods. Therefore, the aim of this study was to perform a genomewide association study (GWAS) and a gene set enrichment analysis to identify genomic regions and biologically relevant pathways associated with meat tenderness in Polled Nellore cattle. Data consisted of Warner-Bratzler shear force values of LM from 427 Polled Nellore animals divided into 3 experimental slaughters (years 2005, 2008, and 2010). The animals were genotyped with either the Illumina BovineHD BeadChip (777k, on 61 samples) or the GGP Indicus HD chip (77k, on 366 samples). Single nucleotide polymorphisms were excluded when the call rate was <90%, the Hardy-Weinberg proportions -value was <1% (Fisher exact test, Bonferroni adjusted), and the minor allele frequency was <1%. Imputation from the GGP Indicus HD chip to the Illumina BovineHD BeadChip was performed using the FImput program. Genomewide association analysis was performed using the Efficient Mixed Model Association eXpedited (EMMAx) and the population parameters previously determined (P3D) methods. The GWAS was complemented with a gene set enrichment analysis performed using the FatiGO procedure. Significant markers ( < 0.0001) explaining a larger proportion of variation than other significant SNPs were located on chromosomes 3, 13, 17, 20, 21, and 25, indicating QTL associated with meat tenderness throughout the genome. Additionally, gene set analysis identified 22 Gene Ontology functional terms and 2 InterPro entries that showed significant enrichment of genes associated with tenderness. The functional categories included protein tyrosine and serine/threonine kinase activity, calcium ion binding, lipid metabolic process, and growth factors, among others. These results help to elucidate the genetic architecture and metabolic pathways underlying this trait, which is of extreme economic and social importance to Brazil, because Nellore is the dominant beef cattle breed in the country.

Experimental Verification of CAPN1 and CAST Gene Polymorphisms in Different Generations of Da-Heng Broilers

The micromolar calcium activated neutral protease (CAPN1) and calpastatin (CAST) have been widely regarded as genes related to muscle growth and meat tenderness. The objective of this study was to verify the association of SNPs of CAPN1 and CAST genes with carcass and tenderness traits and search the possible change patterns of SNPs in CAPN1 and CAST genes in six generations of broiler breeding process for growth rate, efficiency, and reproduction, during the third generation and the ninth generation, respectively. We found that, for CAPN1, genetic effects between SNPs (G3535A, C7198A) and meat tenderness were similar in different generations, while SNP3 (G7324A) was a novel polymorphism and had significant association with carcass and tenderness traits (P < 0.05) in this study. Furthermore, there was significant association between SNP4 (G9950A) and carcass indexes instead of tenderness traits (P < 0.05) which was consistent in the two generations. Moreover, although SNP6 (G37868A) of CAST had no relevance to carcass traits or tenderness traits in the third generation, it showed significant association with LW and CW in the ninth generation (P < 0.05).

Accuracy of genomic breeding values for meat tenderness in Polled Nellore cattle

Zebu () cattle, mostly of the Nellore breed, comprise more than 80% of the beef cattle in Brazil, given their tolerance of the tropical climate and high resistance to ectoparasites. Despite their advantages for production in tropical environments, zebu cattle tend to produce tougher meat than Bos taurus breeds. Traditional genetic selection to improve meat tenderness is constrained by the difficulty and cost of phenotypic evaluation for meat quality. Therefore, genomic selection may be the best strategy to improve meat quality traits. This study was performed to compare the accuracies of different Bayesian regression models in predicting molecular breeding values for meat tenderness in Polled Nellore cattle. The data set was composed of Warner-Bratzler shear force (WBSF) of longissimus muscle from 205, 141, and 81 animals slaughtered in 2005, 2010, and 2012, respectively, which were selected and mated so as to create extreme segregation for WBSF. The animals were genotyped with either the Illumina BovineHD (HD; 777,000 from 90 samples) chip or the GeneSeek Genomic Profiler (GGP Indicus HD; 77,000 from 337 samples). The quality controls of SNP were Hard-Weinberg Proportion -value ≥ 0.1%, minor allele frequency > 1%, and call rate > 90%. The FImpute program was used for imputation from the GGP Indicus HD chip to the HD chip. The effect of each SNP was estimated using ridge regression, least absolute shrinkage and selection operator (LASSO), Bayes A, Bayes B, and Bayes Cπ methods. Different numbers of SNP were used, with 1, 2, 3, 4, 5, 7, 10, 20, 40, 60, 80, or 100% of the markers preselected based on their significance test (-value from genomewide association studies [GWAS]) or randomly sampled. The prediction accuracy was assessed by the correlation between genomic breeding value and the observed WBSF phenotype, using a leave-one-out cross-validation methodology. The prediction accuracies using all markers were all very similar for all models, ranging from 0.22 (Bayes Cπ) to 0.25 (Bayes B). When preselecting SNP based on GWAS results, the highest correlation (0.27) between WBSF and the genomic breeding value was achieved using the Bayesian LASSO model with 15,030 (3%) markers. Although this study used relatively few animals, the design of the segregating population ensured wide genetic variability for meat tenderness, which was important to achieve acceptable accuracy of genomic prediction. Although all models showed similar levels of prediction accuracy, some small advantages were observed with the Bayes B approach when higher numbers of markers were preselected based on their -values resulting from a GWAS analysis.

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.

Adaptive traits of indigenous cattle breeds: The Mediterranean Baladi as a case study

Generally taken, breeds of Bos taurus ancestry are considered more productive, in comparison with Bos indicus derived breeds that present enhanced hardiness and disease resistance, low nutritional requirements and higher capability of feed utilization. While breeds of B. taurus have been mostly selected for intensive production systems, indigenous cattle, developed mostly from indicine and African taurines, flourish in extensive habitats. Worldwide demographic and economic processes face animal production with new challenges - the increasing demand for animal food products. Intensification of animal husbandry is thus a desired goal in stricken parts of the world. An introduction of productive traits to indigenous breeds might serve to generate improved biological and economic efficiencies. For this to succeed, the genetic merit of traits like efficiency of feed utilization and product quality should be revealed, encouraging the conservation initiatives of indigenous cattle populations, many of which are already extinct and endangered. Moreover, to overcome potential genetic homogeneity, controlled breeding practices should be undertaken. The Baladi cattle are a native local breed found throughout the Mediterranean basin. Purebred Baladi animals are rapidly vanishing, as more European breeds are being introduced or used for backcrosses leading to improved production. The superiority of Baladi over large-framed cattle, in feedlot and on Mediterranean pasture, with respect to adaptability and efficiency, is highlighted in the current review.

Mediterranean river buffalo CSN1S1 gene: search for polymorphisms and association studies

The aim of the present study was to investigate the variability at CSN1S1 locus of the Italian Mediterranean river buffalo and to study possible allele effects on milk yield and its composition. Effects of parity, calving season and month of production were also evaluated. Three single-nucleotide polymorphisms were detected. The first mutation, located at position 89 of the 17th exon (c.628C>T), is responsible for the amino acid change p.Ser178 (B allele)/Leu178 (A allele). The other two polymorphisms, detected at the positions 144 (c.882G>A) and 239 (c.977A>G) of 19th exon, respectively, are silent (3ʹ UTR, untranslated region). Associations between the CSN1S1 genotypes and milk production traits were investigated using 4122 test day records of 503 lactations from 175 buffalo cows. Milk yield, fat and protein percentages were analysed using a mixed linear model. A significant association between the c.628C>T SNP and the protein percentage was found. In particular, the CC genotype showed an average value ~0.04% higher than the CT and TT genotypes. The allele substitution effect of cytosine into thymine was –0.014, with a quite low (0.3%) protein percentage contribution to total phenotypic variance. A large dominance effect was detected. Characterisation of the CSN1S1 transcripts and a method based on MboI amplification created restriction site PCR for a rapid genotyping of c.628C>T are provided.

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.

A New Insight into the Role of Calpains in Post-mortem Meat Tenderization in Domestic Animals: A review

Tenderness is the most important meat quality trait, which is determined by intracellular environment and extracellular matrix. Particularly, specific protein degradation and protein modification can disrupt the architecture and integrity of muscle cells so that improves the meat tenderness. Endogenous proteolytic systems are responsible for modifying proteinases as well as the meat tenderization. Abundant evidence has testified that calpains (CAPNs) including calpain I (CAPN1) and calpastatin (CAST) have the closest relationship with tenderness in livestock. They are involved in a wide range of physiological processes including muscle growth and differentiation, pathological conditions and post-mortem meat aging. Whereas, Calpain3 (CAPN3) has been established as an important activating enzyme specifically expressed in livestock's skeletal muscle, but its role in domestic animals meat tenderization remains controversial. In this review, we summarize the role of CAPN1, calpain II (CAPN2) and CAST in post-mortem meat tenderization, and analyse the relationship between CAPN3 and tenderness in domestic animals. Besides, the possible mechanism affecting post-mortem meat aging and improving meat tenderization, and current possible causes responsible for divergence (whether CAPN3 contributes to animal meat tenderization or not) are inferred. Only the possible mechanism of CAPN3 in meat tenderization has been confirmed, while its exact role still needs to be studied further.

A marker-derived gene network reveals the regulatory role of PPARGC1A, HNF4G, and FOXP3 in intramuscular fat deposition of beef cattle

High intramuscular fat (IMF) awards price premiums to beef producers and is associated with meat quality and flavor. Studying gene interactions and pathways that affect IMF might unveil causative physiological mechanisms and inform genomic selection, leading to increased accuracy of predictions of breeding value. To study gene interactions and pathways, a gene network was derived from genetic markers associated with direct measures of IMF, other fat phenotypes, feedlot performance, and a number of meat quality traits relating to body conformation, development, and metabolism that might be plausibly expected to interact with IMF biology. Marker associations were inferred from genomewide association studies (GWAS) based on high density genotypes and 29 traits measured on 10,181 beef cattle animals from 3 breed types. For the network inference, SNP pairs were assessed according to the strength of the correlation between their additive association effects across the 29 traits. The co-association inferred network was formed by 2,434 genes connected by 28,283 edges. Topological network parameters suggested a highly cohesive network, in which the genes are strongly functionally interconnected. Pathway and network analyses pointed towards a trio of transcription factors (TF) as key regulators of carcass IMF: PPARGC1A, HNF4G, and FOXP3. Importantly, none of these genes would have been deemed as significantly associated with IMF from the GWAS. Instead, a total of 313 network genes show significant co-association with the 3 TF. These genes belong to a wide variety of biological functions, canonical pathways, and genetic networks linked to IMF-related phenotypes. In summary, our GWAS and network predictions are supported by the current literature and suggest a cooperative role for the 3 TF and other interacting genes including CAPN6, STC2, MAP2K4, EYA1, COPS5, XKR4, NR2E1, TOX, ATF1, ASPH, TGS1, and TTPA as modulators of carcass and meat quality traits in beef cattle.

A post-transcriptional mechanism regulates calpastatin expression in bovine skeletal muscle

The objective of this study was to investigate whether single nucleotide polymorphisms (SNP) in the calpain 1 (CAPN1), calpain 3 (CAPN3) and calpastatin (CAST) genes, which have been shown to be associated with shear force and tenderness differences in the skeletal muscle of cattle, contribute to phenotypic variation in muscle tenderness by modulating the transcriptional activity of their respective gene. The mRNA expression of the calpain and CAST genes was assessed in the longissimus lumborum muscle (LLM) of cattle from two herds located in distinct production zones on the east (New South Wales, NSW) and west (Western Australia, WA) of Australia. The cattle in the herds were mainly Brahman cattle (Bos indicus) with smaller populations of Angus cattle (Bos taurus). There were 191 steers in the WA herd and 107 steers and 106 heifers in the NSW herd. These herds were established by choosing cattle from the diverse population which had different single nucleotide polymorphism (SNP) genotypes at the CAPN1, CAPN3 and CAST loci. Using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), the transcriptional activities of the CAPN1 and the CAST genes, but not the CAPN3 gene, were found to differ between favorable, positively associated with tenderness, and unfavorable, negatively associated with tenderness, allelic variants of these genes. These findings suggest that the muscle shear force and consumer taste panel differences in tenderness explained by the CAPN1 and CAST gene markers are a consequence of alterations in their mRNA levels, which may ultimately influence the protein activity of these genes, thereby altering the rate and(or) the extent of postmortem proteolysis in skeletal muscle. Of particular importance were the significantly lower type II and type III CAST 5' splice variant mRNA levels that were detected in the LLM muscle of Brahman and Angus cattle with 2 favourable alleles of the CAST:c.2832A > G polymorphism. Moreover, a reduction in the abundance of an alternative polyadenylated variant of the CAST transcript, terminated at the proximal polyadenylation site, provides a unique insight into the potential involvement of a post-transcriptional regulatory mechanism which may influence protein expression levels in bovine skeletal muscle.

MicroRNAs in domestic livestock

microRNAs (miRNAs) are a class of small noncoding RNA that bind to complementary sequences in the untranslated regions of multiple target mRNAs resulting in posttranscriptional regulation of gene expression. The recent discovery and expression-profiling studies of miRNAs in domestic livestock have revealed both their tissue-specific and temporal expression pattern. In addition, breed-dependent expression patterns as well as single nucleotide polymorphisms in either the miRNA or in the target mRNA binding site have revealed associations with traits of economic importance and highlight the potential use of miRNAs in future genomic selection programs.

Milk fatty acid variability: effect of some candidate genes involved in lipid synthesis

In this work, the genetic variation of milk FA was investigated in three different bovine breeds, the Jersey, the Piedmontese and the Valdostana, and at different lactation stages. All animals were genotyped for 21 Single Nucleotide Polymorphisms located within nine candidate genes involved in lipid synthesis: diacylglycerol acyltransferase 1 and 2 (DGAT1, 2); stearoyl-CoA desaturase (SCD); growth hormone receptor (GHR); fatty acid synthase (FASN); acyl-CoA dehydrogenase (ACAD); fatty acid binding protein (FABP4); lipoprotein lipase (LPL); and leptin gene (LEP). The highest milk-fat Jersey breed also showed the highest content of saturated FA. Throughout lactation, the breeds showed a similar variation in the FA, with a decrease in the short-chain, this was accompanied by a general increase in the long chain FA at the end of lactation. The increase in long chain saturated FA was particularly evident in the case of the Jersey. The effect of SCD gene on the C14 desaturation index was confirmed; the DGAT1 gene was polymorphic only in the Jersey breed, but its effect was confirmed only on milk fat content; three further potential candidate genes were identified: first, the FABP4 gene, which was found to influence medium and long chain FA in all the breeds, but not the desaturation indices; second, the FASN gene, which was found to influence the amount of PUFA in the Piedmontese and the Valdostana, and third, the LPL gene, which was found to affect fat content in the Piedmontese.

Gene expression phenotypes for lipid metabolism and intramuscular fat in skeletal muscle of cattle

Gene expression phenotypes were evaluated for intramuscular fat (IMF) in bovine skeletal muscle as an alternative to traditional estimates of IMF%. Gene expression data from a time course of LM development in high- and low-marbling Bos taurus cattle crosses were compared to identify genes involved in intramuscular adipocyte lipid metabolism with developmentally similar gene expression profiles. Three sets of genes were identified: triacylglyceride (TAG) synthesis and storage, fatty acid (FA) synthesis, and PPARγ-related genes. In an independent analysis in the LM of 48 Bos indicus cattle, TAG and FA gene sets were enriched in the top 100 genes of which expression was most correlated with IMF% (P = 1.2 × 10(-24) and 3.5 × 10(-9), respectively). In general, genes encoding enzymes involved in the synthesis of FA and TAG in the intramuscular adipocytes were present in the top 100 genes. In B. indicus, effects of a steroid hormone growth promotant (HGP), 2 experimental sites [New South Wales (NSW) and Western Australia (WA)], and 3 tenderness genotypes on the expression levels of genes in the TAG gene set and the correlation of gene expression with IMF% were investigated. Although correlation between expression of 12 individual TAG genes and IMF% was observed in HGP-treated animals in both experimental sites (mean r = 0.43), correlation was not observed for untreated animals at the NSW site (mean r = -0.07, P < 3 × 10(-6)). However, TAG genes showed an average 1.6-fold (P < 0.0004) reduction in expression in the LM of HGP-treated cattle relative to untreated cattle, an effect consistent across both experimental sites. Cattle possessing the favored tenderness calpain 1 and 3 and calpastatin alleles exhibited a greater (P = 0.008) reduction in expression in NSW (1.8-fold reduction, P = 0.0002) compared with WA (1.2-fold reduction, P = 0.03). Tenderness genotype had no impact (P > 0.05) on the correlation of TAG genes with IMF%. In general, the interactions among genotype, treatment and location, and TAG gene set gene expression were consistent with the interactions among the same factors and IMF% detected using 255 animals, of which the 48 in this study were a subset. Thus, the TAG gene set constitutes a gene expression phenotype able to predict effects of different genotypes and treatments on IMF% using much smaller groups than current approaches, even in animals with very low IMF%.

Quantitative genomics of 30 complex phenotypes in Wagyu x Angus F₁ progeny

In the present study, a total of 91 genes involved in various pathways were investigated for their associations with six carcass traits and twenty-four fatty acid composition phenotypes in a Wagyu×Angus reference population, including 43 Wagyu bulls and their potential 791 F₁ progeny. Of the 182 SNPs evaluated, 102 SNPs that were in Hardy-Weinberg equilibrium with minor allele frequencies (MAF>0.15) were selected for parentage assignment and association studies with these quantitative traits. The parentage assignment revealed that 40 of 43 Wagyu sires produced over 96.71% of the calves in the population. Linkage disequilibrium analysis identified 75 of 102 SNPs derived from 54 genes as tagged SNPs. After Bonferroni correction, single-marker analysis revealed a total of 113 significant associations between 44 genes and 29 phenotypes (adjusted P<0.05). Multiple-marker analysis confirmed single-gene associations for 10 traits, but revealed two-gene networks for 9 traits and three-gene networks for 8 traits. Particularly, we observed that TNF (tumor necrosis factor) gene is significantly associated with both beef marbling score (P=0.0016) and palmitic acid (C16:0) (P=0.0043), RCAN1 (regulator of calcineurin 1) with rib-eye area (P=0.0103), ASB3 (ankyrin repeat and SOCS box-containing 3) with backfat (P=0.0392), ABCA1 (ATP-binding cassette A1) with both palmitic acid (C16:0) (P=0.0025) and oleic acid (C18:1n9) (P=0.0114), SLC27A1(solute carrier family 27 A1) with oleic acid (C18:1n9) (P=0.0155), CRH (corticotropin releasing hormone) with both linolenic acid (OMEGA-3) (P=0.0200) and OMEGA 6:3 RATIO (P=0.0054), SLC27A2 (solute carrier family 27 A2) with both linoleic acid (OMEGA-6) (P=0.0121) and FAT (P=0.0333), GNG3 (guanine nucleotide binding protein gamma 3 with desaturase 9 (P=0.0115), and EFEMP1 (EGF containing fibulin-like extracellular matrix protein 1), PLTP (phospholipid transfer protein) and DSEL (dermatan sulfate epimerase-like) with conjugated linoleic acid (P=0.0042-0.0044), respectively, in the Wagyu x Angus F₁ population. In addition, we observed an interesting phenomenon that crossbreeding of different breeds might change gene actions to dominant and overdominant modes, thus explaining the origin of heterosis. The present study confirmed that these important families or pathway-based genes are useful targets for improving meat quality traits and healthful beef products in cattle.

Functional genomic analysis of variation on beef tenderness induced by acute stress in angus cattle

Beef is one of the leading sources of protein, B vitamins, iron, and zinc in human food. Beef palatability is based on three general criteria: tenderness, juiciness, and flavor, of which tenderness is thought to be the most important factor. In this study, we found that beef tenderness, measured by the Warner-Bratzler shear force (WBSF), was dramatically increased by acute stress. Microarray analysis and qPCR identified a variety of genes that were differentially expressed. Pathway analysis showed that these genes were involved in immune response and regulation of metabolism process as activators or repressors. Further analysis identified that these changes may be related with CpG methylation of several genes. Therefore, the results from this study provide an enhanced understanding of the mechanisms that genetic and epigenetic regulations control meat quality and beef tenderness.

Haplotype analysis improved evidence for candidate genes for intramuscular fat percentage from a genome wide association study of cattle

In genome wide association studies (GWAS), haplotype analyses of SNP data are neglected in favour of single point analysis of associations. In a recent GWAS, we found that none of the known candidate genes for intramuscular fat (IMF) had been identified. In this study, data from the GWAS for these candidate genes were re-analysed as haplotypes. First, we confirmed that the methodology would find evidence for association between haplotypes in candidate genes of the calpain-calpastatin complex and musculus longissimus lumborum peak force (LLPF), because these genes had been confirmed through single point analysis in the GWAS. Then, for intramuscular fat percent (IMF), we found significant partial haplotype substitution effects for the genes ADIPOQ and CXCR4, as well as suggestive associations to the genes CEBPA, FASN, and CAPN1. Haplotypes for these genes explained 80% more of the phenotypic variance compared to the best single SNP. For some genes the analyses suggested that there was more than one causative mutation in some genes, or confirmed that some causative mutations are limited to particular subgroups of a species. Fitting the SNPs and their interactions simultaneously explained a similar amount of the phenotypic variance compared to haplotype analyses. Haplotype analysis is a neglected part of the suite of tools used to analyse GWAS data, would be a useful method to extract more information from these data sets, and may contribute to reducing the missing heritability problem.

Muscle transcriptomic analyses in Angus cattle with divergent tenderness

Beef tenderness contributes significantly to variation of beef palatability, and is largely influenced by various genetic and environmental factors. To identify candidate genes and pathways related to beef tenderness, we analyzed the longissimus dorsi (LD) muscle of Angus cattle that had different degrees of tenderness, measured by Warner-Bratzler shear force (WBSF). Microarray and RT-PCR analyses identified 53 genes that were differentially expressed in LD samples categorized as either tough or tender, including myosin, heavy chain 3 skeletal muscle embryonic (MYH3), myosin heavy chain 8 skeletal muscle perinatal (MYH8), guanylate binding protein 5 (GBP5), fatty acid binding protein 4 (FABP4), Stearoyl-coenzyme A desaturase (SCD), Fatty acid synthase (FASN), ubiquitin-like with PHD and ring finger domains 1 (UHRF1). Most of these genes are involved in lipid metabolism and skeletal muscle contraction. Employing Gene ontology (GO) and Ingenuity Pathway Analysis (IPA), several GO terms and pathways were found to be related to hydrolase, peptidase and GTPase activity, lipid metabolism, small molecule biochemistry, molecular transport, and tissue development. Overall, this analysis provides insight into the metabolic relationships between muscle biology and beef quality.

Temperament and hypothalamic-pituitary-adrenal axis function are related and combine to affect growth, efficiency, carcass, and meat quality traits in Brahman steers

Associations between temperament, stress physiology, and productivity were studied in yearling Brahman steers (n = 81). Steers differed in calpain system gene marker status; 41 were implanted with a hormonal growth promotant at feedlot entry. Temperament was assessed with repeated measurements of flight speed (FS) and crush score (CS) during 6 mo of backgrounding at pasture and 117 d of grain finishing. Adrenal responsiveness was assessed with ACTH challenge, with plasma samples collected immediately before and 60 min after challenge. Steers with higher FS and CS had higher prechallenge plasma cortisol, glucose, lactate, and nonesterified fatty acid concentrations. The ACTH-induced cortisol response was unrelated to FS or CS, but glucose remained higher after challenge in flightier steers. The hormonal growth promotant reduced adrenal responsiveness; tenderness genotype had no effect. When temperament assessments and cortisol concentrations before and after challenge were combined in a principal components analysis, four vectors accounting for 38%, 25%, 18%, and 9% of the variation were identified. The first vector had significant loadings on temperament and prechallenge cortisol; increasing scores were associated with increased plasma glucose, lactate, and nonesterified fatty acid and with reductions in BW and feedlot growth rates, carcass fatness, and muscle pH. The second vector loaded only on ACTH-induced cortisol response; increased scores related to increased residual feed intake, number of daily feed sessions, and meat marbling score. The third and fourth vectors had different loadings on FS and CS and appeared to identify different aspects of temperament measured by FS or CS. Fewer associations were found between the third or fourth vectors and productivity traits, possibly because of lower variance accounted for by these vectors. In conclusion, temperament was related to prechallenge cortisol but not to ACTH-induced cortisol response. Principal components analysis separated these traits into separate components, which in turn had different relations with productivity traits. The largest component of temperament was described similarly by FS and CS, but there were smaller components that these described differently. There were some temperament-related differences in the metabolic status of the steers which were not related to the variation in cortisol, suggesting involvement of the sympatho-adrenal-medullary axis in these temperament-related effects.

A genome-wide association study of meat and carcass traits in Australian cattle

Chromosomal regions containing DNA variation affecting the traits intramuscular fat percentage (IMF), meat tenderness measured as peak force to shear the LM (LLPF), and rump fat measured at the sacro-iliac crest in the chiller (CHILLP8) were identified using a set of 53,798 SNP genotyped on 940 taurine and indicine cattle sampled from a large progeny test experiment. Of these SNP, 87, 64, and 63 were significantly (P < 0.001) associated with the traits IMF, LLPF, and CHILLP8, respectively. A second, nonoverlapping sample of 1,338 taurine and indicine cattle from the same large progeny test experiment genotyped for 335 SNP, including as a positive control the calpastatin (CAST) c.2832A > G SNP, was used to confirm these locations. In total, 37 SNP were significantly (P < 0.05) associated with the same trait and with the same favorable homozygote in both data sets, representing 27 chromosomal regions. For the trait IMF, the effect of SNP in the confirmation data set was predicted from the discovery set by multiplying the estimated allele effect of each SNP in the discovery set by the number of copies of the reference allele of each SNP in the confirmation set. These weighted effects were then summed over all SNP to generate a molecular breeding value (MBV) for each animal in the confirmation data set. Using a bivariate analysis of MBV and IMF phenotypes of animals in the confirmation set, a panel of 14 SNP explained 5.6 and 15.6% of the phenotypic and genetic variance of IMF, respectively, in the confirmation data set. The amount of variation did not increase as more SNP were added to the MBV and instead decreased to 1.2 and 3.8% of the phenotypic and genetic variance of IMF, respectively, when 329 SNP were included in the analysis.

Detection of chromosome segments of zebu and taurine origin and their effect on beef production and growth

Cattle in breeds formed by recent crossing of Bos taurus (Bt) and Bos indicus (Bi) subspecies should contain chromosomes that are a composite of Bt and Bt segments. Using data from a 50K SNP chip, we were able to identify whether a chromosome segment of 11 SNP in a composite animal descended from a Bt or a Bi ancestor. When the method was tested in purebred Bt or Brahman cattle, about 94% of segments were assigned correctly. About 10% of the genome in Australian Brahman cattle appears to be of Bt origin, as might be expected from their history. We then examined the effect of the origin of each chromosome segment on BW in a population of 515 Bt × Bi composite cattle and found 67 chromosome segments with a significant (P<0.01) effect. We confirmed these effects by examining these 67 segments in a population of Brahman cattle and in a population of mixed breeds including composite breeds such as Santa Gertrudis and Brahman cattle. About 66% of the 67 segments had an effect in the same direction in the confirmation analyses as in the discovery population. However, the effect on BW and other traits of chromosome segment origin is small, indicating that we had low power to detect these effects with the number of animals available. Consequently, when chromosome segment origin was used in genomic selection to predict BW, the accuracy was low (0.08). Chromosome segments that had a positive effect on BW tend to be at greater frequency in composite breeds than chromosome segments with a negative effect on BW.

Cattle temperament: persistence of assessments and associations with productivity, efficiency, carcass and meat quality traits

Relationships between temperament and a range of performance, carcass, and meat quality traits in young cattle were studied in 2 experiments conducted in New South Wales (NSW) and Western Australia (WA), Australia. In both experiments, growth rates of cattle were assessed during backgrounding on pasture and grain finishing in a feedlot. Carcass and objective meat quality characteristics were measured after slaughter. Feed intake and efficiency during grain finishing were also determined in NSW. Brahman (n = 82 steers and 82 heifers) and Angus (n = 25 steers and 24 heifers) cattle were used in the NSW experiment. In NSW, temperament was assessed by measuring flight speed [FS, m/s on exit from the chute (crush)] on 14 occasions, and by assessing agitation score during confinement in the crush (CS; 1 = calm to 5 = highly agitated) on 17 occasions over the course of the experiment. Brahman (n = 173) and Angus (n = 20) steers were used in the WA experiment. In WA, temperament was assessed by measuring FS on 2 occasions during backgrounding and on 2 occasions during grain feeding. At both sites, a hormonal growth promotant (Revalor-H, Virbac, Milperra, New South Wales, Australia) was applied to one-half of the cattle at feedlot entry, and the Brahman cattle were polymorphic for 2 calpain-system markers for beef tenderness. Temperament was not related (most P > 0.05) to tenderness gene marker status in Brahman cattle and was not (all P > 0.26) modified by the growth promotant treatment in either breed. The Brahman cattle had greater individual variation in, and greater correlations within and between, repeated assessments of FS and CS than did the Angus cattle. Correlations for repeated measures of FS were greater than for repeated assessments of CS, and the strength of correlations for both declined over time. Average FS or CS for each experiment and location (NSW or WA × backgrounding or finishing) were more highly correlated than individual measurements, indicating that the average values were a more reliable assessment of cattle temperament than any single measure. In Brahman cattle, increased average FS and CS were associated with significant (P < 0.05) reductions in backgrounding and feedlot growth rates, feed intake and time spent eating, carcass weight, and objective measures of meat quality. In Angus cattle, the associations between temperament and growth rates, feed intake, and carcass traits were weaker than in Brahmans, although the strength of relationships with meat quality were similar.

Exploring polymorphisms and effects of candidate genes on milk fat quality in dairy sheep

The aim of the present study was to investigate the genetic control of the fatty acid (FA) composition in milk from 3 breeds of sheep: Altamurana, Gentile di Puglia, and Sarda. Single nucleotide polymorphisms within genes, encoding enzymes putatively involved in the synthesis and metabolism of milk fat, were selected for analysis, and the allele substitution effects were determined for 16 genes, which were polymorphic in the 3 sheep breeds, upon the milk fat composition. Four genes (alpha-1-antichymotrypsin-2; diacylglycerol O-acyltransferase homolog-2; propionyl Coenzyme A carboxylase, beta polypeptide; and insulin-like growth factor-I) play a role in the desaturation of stearic FA into polyunsaturated fatty acids. Furthermore, 2 genes (growth hormone receptor and zona pellucida glycoprotein-2) affect the variability of the total fat content in addition to the butyric and stearic FA profile, and the fatty acid synthetase gene has an influence on the medium-chain FA. Milk FA profiles play an important role in dairy sheep farming because they have a large effect on cheese characteristics and also because sheep milk may be marketed as a source of nutraceuticals because it contains higher levels of conjugated linoleic acid than milk from other ruminants. The current study evaluated the global effects of a large number of single nucleotide polymorphisms and haplotypes on traits that are not commonly investigated in sheep but that are potentially very useful for improving milk quality.

DNA variation in the gene ELTD1 is associated with tick burden in cattle

Ticks and tick-born diseases are major constraints on cattle production in tropical and subtropical regions in the world. Previously, we identified single nucleotide polymorphisms (SNPs) associated with tick resistance on bovine chromosome 3 at approximately 70 Mb. In this study, we genotyped a dairy (n = 1133) and a beef (n = 774) sample to confirm the association of the intronic SNP rs29019303 and its gene (ELTD1) with tick burden. We genotyped 18 additional SNPs in a region of 181 kb and found that rs29019303 was significantly (P < 0.05) associated with tick burden in both samples with the same favourable allele. A second SNP in this same genomic region was also significantly associated with tick burden in each sample. The associations using haplotypes were stronger than for single markers, including a haplotype of nine tag SNPs that was highly significantly (P = 0.0008) associated with tick counts in the dairy animals. This haplotype and two others were significant after Bonferroni correction for multiple testing. The estimated size of the effects was close to 0.9% of the residual variance in both samples tested.

Genetic and environmental effects on meat quality

In order for livestock industries to consistently produce high quality meat, there must be an understanding of the factors that cause quality to vary, as well as the contribution of genetics. A brief overview of meat tenderness is presented to understand how genotype and environment may interact to influence this trait. Essentially, meat tenderness is determined from the contribution of connective tissue, sarcomere length determined pre-rigor and rate of proteolysis during ageing, as well as contributions from intramuscular fat and post-mortem energy metabolism. The influence of mutations in myostatin, the callipyge gene, the Carwell or rib eye muscle gene as well as the calpain system on meat tenderness is presented. Specific examples of interactions between the production or processing environment and genetics are presented for both sheep and cattle. The day-to-day variation in tenderness is evident across experiments and this variation needs to be controlled in order to consistently produce tender meat.

The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

Background

Food supply from the ocean is constrained by the shortage of domesticated and selected fish. Development of genomic models of economically important fishes should assist with the removal of this bottleneck. European sea bass Dicentrarchus labrax L. (Moronidae, Perciformes, Teleostei) is one of the most important fishes in European marine aquaculture; growing genomic resources put it on its way to serve as an economic model.

Results

End sequencing of a sea bass genomic BAC-library enabled the comparative mapping of the sea bass genome using the three-spined stickleback Gasterosteus aculeatus genome as a reference. BAC-end sequences (102,690) were aligned to the stickleback genome. The number of mappable BACs was improved using a two-fold coverage WGS dataset of sea bass resulting in a comparative BAC-map covering 87% of stickleback chromosomes with 588 BAC-contigs. The minimum size of 83 contigs covering 50% of the reference was 1.2 Mbp; the largest BAC-contig comprised 8.86 Mbp. More than 22,000 BAC-clones aligned with both ends to the reference genome. Intra-chromosomal rearrangements between sea bass and stickleback were identified. Size distributions of mapped BACs were used to calculate that the genome of sea bass may be only 1.3 fold larger than the 460 Mbp stickleback genome.

Conclusions

The BAC map is used for sequencing single BACs or BAC-pools covering defined genomic entities by second generation sequencing technologies. Together with the WGS dataset it initiates a sea bass genome sequencing project. This will allow the quantification of polymorphisms through resequencing, which is important for selecting highly performing domesticated fish.

A genome-wide scan for signatures of recent selection in Holstein cattle

The data from the newly available 50 K SNP chip was used for tagging the genome-wide footprints of positive selection in Holstein-Friesian cattle. For this purpose, we employed the recently described Extended Haplotype Homozygosity test, which detects selection by measuring the characteristics of haplotypes within a single population. To assess formally the significance of these results, we compared the combination of frequency and the Relative Extended Haplotype Homozygosity value of each core haplotype with equally frequent haplotypes across the genome. A subset of the putative regions showing the highest significance in the genome-wide EHH tests was mapped. We annotated genes to identify possible influence they have in beneficial traits by using the Gene Ontology database. A panel of genes, including FABP3, CLPN3, SPERT, HTR2A5, ABCE1, BMP4 and PTGER2, was detected, which overlapped with the most extreme P-values. This panel comprises some interesting candidate genes and QTL, representing a broad range of economically important traits such as milk yield and composition, as well as reproductive and behavioural traits. We also report high values of linkage disequilibrium and a slower decay of haplotype homozygosity for some candidate regions harbouring major genes related to dairy quality. The results of this study provide a genome-wide map of selection footprints in the Holstein genome, and can be used to better understand the mechanisms of selection in dairy cattle breeding.

Variation at CPE but not CEBPA appears to be associated with intramuscular fat deposition in the longissimus muscle of cattle

An important step in the localisation of quantitative trait loci is the confirmation of trait-marker associations in independent studies. In this report, we test three single nucleotide polymorphisms (SNP) of two genes for associations to intramuscular fat (IMF) measurements in cattle. We genotyped SNP of carboxypeptidase E (CPE) and ccaat/enhancer binding protein, α (CEBPA) in a sample of a total of 813 cattle of taurine, composite and indicine breeds. All three polymorphisms showed significant differences between breeds, with the widest range found in CEBPA:g.271A > C where the A allele frequency ranged from P = 0.07 in Brahman to 0.88 in Shorthorn. The taurine breeds showed high linkage disequilibrium between the pair of CPE SNP, with all four breeds showing r2 = 1.0. The Brahman and Santa Gertrudis showed r2 ≤ 0.17. Both CPE:g.445C > T and CPE:g.601C > T SNP showed significant allele substitution effects to IMF in animals of taurine ancestry, with an allele substitution effect of α = 0.22, P = 0.020 for CPE:g.445C > T, explaining 0.4% of the phenotypic variance.