Association of polymorphisms in the calpain I, calpain II and growth hormone genes with tenderness in bovine M. longissimus dorsi

Sustained Effects of Muscle Calpain System Genotypes on Tenderness Phenotypes of South African Beef Bulls during Ageing up to 20 Days

Simple Summary

When searching for genetic markers for the selection of more tender beef, it is important to maintain minimal environmental variation from pre-slaughter, right through to the ageing process, to ensure the accuracy of the obtained phenotypes. This is because beef quality traits have a large environmental component that can greatly alter the characteristics of the meat, which would not reflect a true genetic effect. We propose that variable ageing times are especially important in determining whether markers are associated with tenderization or not. Our analyses included candidate genes for the protein degrading enzyme system for calpains, because they contribute the most to tenderization. We were able to validate these markers in South African beef cattle, where they could be useful for selection. The timing of the collection of tenderness data was critical, as only a few (6/134) genetic markers sustained their association with tenderization over ageing to 20 days. A larger tenderization effect earlier in ageing, as shown here for the capn1_187 and capn1_4751 markers, would decrease the length of ageing. This would not only increase profits, but also decrease the energy needed during the storage and refrigeration of aged beef, decreasing the carbon footprint of beef production.

Abstract

The most important factor that determines beef tenderness is its proteolytic activity, and the balance between calpain-1 protease activity and calpastatin inhibition is especially important, while contributions can also arise from calpain-2 and, possibly, calpain-3. The meat ageing process itself affects these processes. To determine whether genotypes in the calpain–calpastatin system can enhance tenderness through a 20-day ageing period, South African purebred beef bulls (n = 166) were genotyped using the Illumina BovineHD SNP BeadChip through a gene-based association analysis targeting the cast, capn3, capn2 and capn1 genes. The Warner–Bratzler shear force (WBSF) and myofibril fragment length (MFL) of Longissimus thoracis et lumborum (LTL) steaks were evaluated between d 3 and d 20 of ageing, with protease enzyme activity in the first 20 h post-mortem. Although several of the 134 SNPs are associated with tenderness, only seven SNP in the cast, capn2 and capn1 genes sustained genetic associations, additive to the ageing-associated increases in tenderness for at least three of the four ageing periods. While most genomic associations were relatively stable over time, some genotypes within the SNP responded differently to ageing, resulting in altered genomic effects over time. The level of ageing at which genomic associations are performed is an important factor that determines whether SNPs affect tenderness phenotypes.

Associations between gene polymorphisms and selected meat traits in cattle - A review

Maintaining a high level of beef consumption requires paying attention not only to quantitative traits but also to the quality and dietary properties of meat. Growing consumer demands do not leave producers many options for how animals are selected for breeding and animal keeping. Meat and carcass fatness quality traits, which are influenced by multiple genes, are economically important in beef cattle breeding programs. The recent availability of genome sequencing methods and many previously identified molecular markers offer new opportunities for animal breeding, including the use of molecular information in selection programs. Many gene polymorphisms have thus far been analyzed and evaluated as potential candidates for molecular markers of meat quality traits. Knowledge of these markers can be further applied to breeding programs through marker-assisted selection. In this literature review, we discuss the most promising and well-described candidates and their associations with selected beef production traits.

RNA-seq of muscle from pigs divergent in feed efficiency and product quality identifies differences in immune response, growth, and macronutrient and connective tissue metabolism

BACKGROUND

Feed efficiency (FE) is an indicator of efficiency in converting energy and nutrients from feed into a tissue that is of major environmental and economic significance. The molecular mechanisms contributing to differences in FE are not fully elucidated, therefore the objective of this study was to profile the porcine Longissimus thoracis et lumborum (LTL) muscle transcriptome, examine the product quality from pigs divergent in FE and investigate the functional networks underpinning the potential relationship between product quality and FE.

RESULTS

RNA-Seq (n = 16) and product quality (n = 40) analysis were carried out in the LTL of pigs differing in FE status. A total of 272 annotated genes were differentially expressed with a P < 0.01. Functional annotation revealed a number of biological events related to immune response, growth, carbohydrate & lipid metabolism and connective tissue indicating that these might be the key mechanisms governing differences in FE. Five most significant bio-functions altered in FE groups were 'haematological system development & function', 'lymphoid tissue structure & development', 'tissue morphology', 'cellular movement' and 'immune cell trafficking'. Top significant canonical pathways represented among the differentially expressed genes included 'IL-8 signalling', 'leukocyte extravasation signalling, 'sphingosine-1-phosphate signalling', 'PKCθ signalling in T lymphocytes' and 'fMLP signalling in neutrophils'. A minor impairment in the quality of meat, in relation to texture and water-holding capacity, produced by high-FE pigs was observed. High-FE pigs also had reduced intramuscular fat content and improved nutritional profile in terms of fatty acid composition.

CONCLUSIONS

Ontology analysis revealed enhanced activity of adaptive immunity and phagocytes in high-FE pigs suggesting more efficient conserving of resources, which can be utilised for other important biological processes. Shifts in carbohydrate conversion into glucose in FE-divergent muscle may underpin the divergent evolution of pH profile in meat from the FE-groups. Moreover, altered amino acid metabolism and increased mobilisation & flux of calcium may influence growth in FE-divergent muscle. Furthermore, decreased degradation of fibroblasts in FE-divergent muscle could impact on collagen turnover and alter tenderness of meat, whilst enhanced lipid degradation in high-FE pigs may potentially underlie a more efficient fat metabolism in these animals.

Association of μ-Calpain and Calpastatin Polymorphisms with Meat Tenderness in a Brahman-Angus Population

Autogenous proteolytic enzymes of the calpain family are implicated in myofibrillar protein degradation. As a result, the μ-calpain gene and its specific inhibitor, calpastatin, have been repeatedly investigated for their association with meat quality traits in cattle; however, no functional mutation has been identified for these two genes. The objectives of this study were: (1) to assess breed composition effect on tenderness; (2) to perform a linkage disequilibrium (LD) analysis in μ-calpain and calpastatin genes as well as an association analyses with tenderness; and (3) to analyze putative functional SNPs inside the significant LD block for an effect on tenderness. Tenderness measurements and genotypes for 16 SNPs in μ-calpain gene and 28 SNPs in calpastatin gene from 673 steers were analyzed. A bioinformatic analysis identified “putative functional SNPs” inside the associated LD block – polymorphisms able to produce a physical and/or chemical change in the DNA, mRNA, or translated protein in silico. Breed composition had a significant (P < 0.0001) effect on tenderness where animals with more than 80% Angus composition had the most tender meat. One 11-kb LD-block and three LD-blocks of 37, 17, and 14 kb in length were identified in the μ-calpain and calpastatin genes, respectively. Out of these, the LD-block 3 in calpastatin, tagged by SNPs located at 7-98566391 and 7-98581038, had a significant effect on tenderness with the TG-CG diplotype being approximately 1 kg more tender than the toughest diplotype, TG-CG. A total of 768 SNPs in the LD-block 3 of calpastatin were included in the bioinformatic analysis, and 28 markers were selected as putative functional SNPs inside the LD-block 3 of calpastatin; however, none of them were polymorphic in this population. Out of 15 initial polymorphisms segregating inside the LD-block 3 of calpastatin in this population, markers ARSUSMARC116, Cast5, rs730723459, and rs210861835 were found to be significantly associated with tenderness.

Differences between sexes, muscles and aging times on the quality of meat from Wagyu × Angus cattle finished in feedlot

Our objectives were to assess quality parameters and chemical composition, and to evaluate the effects of sex, muscle and aging time on the quality of meats from Wagyu × Angus cross cattle reared under tropical conditions. Analyses were performed on the longissimus thoracis, semitendinosus and triceps brachii muscles obtained from chilled carcasses of a total of 30, 24-month-old, male (immunocastrated) and female animals (15 each sex). An effect of sex (P ≤ 0.05) was observed for subcutaneous fat thickness, marbling score, and ribeye area. The longissimus thoracis muscle from males was less (P < 0.0001) marbled than that from females, but males had greater subcutaneous fat thickness (P = 0.0001) and greater ribeye area (P = 0.0411) compared with females. No effect of sex (P ≥ 0.05) was observed for fat colour measures. An interaction effect of sex and muscle (P < 0.03) was detected for cooking loss, yellow intensity (b*), ash, and fat. Main effect of sex was not observed (P > 0.07) only for the ultimate pH and water-holding capacity. Greater shear force and moisture values were observed (P < 0.01) in meat from males than that from females, but a greater value of luminance (L*), red intensity (a*), chroma (C), hue (Ho), dry matter and protein was observed (P < 0.001) in meat from females than that from males. Main effect of muscle was not observed only for water-holding capacity (P = 0.13). Ultimate pH and shear force values were lesser (P < 0.001) in the longissimus thoracis muscle compared with other muscles. The triceps brachii muscle had the least (P ≤ 0.001) L* and Ho values among muscles, whereas the semitendinosus muscle had the greatest values of a* and C (P < 0.001). The semitendinosus muscle presented the greatest (P < 0.01) protein content compared with other muscles, although not differing in moisture and dry matter content from the triceps brachii muscle. An interaction effect of sex × aging time was observed for ultimate pH (P = 0.0110), meat colour parameters (except for Ho; P ≤ 0.01), and fat L* (P = 0.0025). Greater cooking loss, shear force, and fat a* values were observed (P < 0.01) in meat from males than that from females, but greater values of meat Ho, fat a* and Ho, dry matter, and protein were observed (P ≤ 0.03) in meat from females than that from males. Meat aging of longissimus thoracis reduced shear force. Based on these findings, we recommend that meat from Wagyu × Angus cross cattle should be aged during 7 days because, although differences between 7 and 14 days were observed in either aging times, meat subjected to this process is considered as very tender, based on shear force values. In addition, aging in a shorter period of time can reflect on costs by reducing particularly those related with energy, due to less refrigeration time.

CAPN1 gene as a potential marker for growth performance and carcass characteristics in pigs

The calcium-activated neutral proteinase 1 (CAPN1) gene, which encodes µ-calpain, is considered to be associated with the majority of meat-quality traits. The objective of the present study was to evaluate the effect of CAPN1 polymorphism on the most important slaughter, fattening and pork-quality traits. The genotype frequency of g.1429G>A polymorphism was estimated on 860 pigs represented by five breeds (Polish Landrace, Polish Large White, Pietrain, Duroc and Pulawska). In all breeds, the most frequent were pigs with an AA genotype (60–74%), with the exception of Duroc pigs where the largest number of GG animals was observed (14%). The results showed that g.1429G>A polymorphism significantly affected the number of days on test (P ≤ 0.05) and age at slaughter (P ≤ 0.01), the weight of ham and primary cuts (P ≤ 0.05, P ≤ 0.01 respectively), loin eye area (P ≤ 0.01) and average backfat thickness (P ≤ 0.05). The g.1429G>A single-nucleotide polymorphism showed no clear influence on complex pork-quality traits. At the present stage of research, the results obtained allow for the use of g.1429G>A polymorphism in CAPN1 gene as genetic marker in pig selection to improve several slaughter or fattening traits.

Association analysis of g.68G → A SNP in CAPN1 gene with carcass and meat quality traits in goose raised in organic <i>dehesa</i>

Abstract. Meat quality is an important concern for the poultry industry. Domestic geese products obtained from free-range systems usually have rather tough meat, and it is necessary to select them to improve meat tenderness. The relation of the calpain 1 (CAPN1) gene with the post-mortem tenderness process of meat has been demonstrated in several species. Thus, the objective of the present study was to identify polymorphisms in this gene and to perform an association analysis between these polymorphisms and related economic traits in goose raised in the dehesa ecosystem. For the analysis, 50 geese of 3 different subpopulations (20 Embden Anser anser; 20 Toulouse Anser anser; 10 F1 cross) were studied. The experimental protocols were followed complying with principles of animal welfare. A novel SNP was found in the CAPN1 gene, g.68G → A. This polymorphism was statistically associated with different carcass and meat quality traits such as thigh muscle width (P = 0.020) and the b* 10-day meat colour parameter (P = 0.024) for the global goose population. The association of this gene with meat tenderness (Warner–Bratzler shear force) was confirmed in the case of female individuals of the Toulouse breed (P = 0.043). The results suggest the possibility of using molecular markers in CAPN1 gene as a potential tool for improving carcass and meat quality traits in goose breeding programmes.

Análisis computacional del efecto de polimorfismos de genes del sistema μ-Calpaína/Calpastatina sobre la calidad de la carne bovina

<p>Los genes del sistema de enzimas μ-Calpaína/Calpastatina han sido ampliamente evaluados en estudios de asociación respecto de parámetros de calidad cárnica como la terneza; previamente se han identificado varios polimorfismos asociados con la variación fenotípica en poblaciones no relacionadas de bovinos. Usando herramientas computacionales se logró postular la asociación de cuatro polimorfismos encontrados en μ-Calpaína y 11 en Calpastatina que producen una alteración de los parámetros físico-químicos, tanto del ARNm (estabilidad y polimorfismo conformacional), como de la proteína (punto isoeléctrico, potencial electroestático y superficie molecular). Es importante poder establecer el soporte biológico de polimorfismos genéticos asociados con parámetros fenotípicos que mejoren la productividad animal, lo que hace que la aproximación in silico se convierta en una herramienta útil para tal fin.</p>

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.

Impact of polymorphism of the regulatory subunit of the μ-calpain (CAPN1S) on the proteolysis process and meat tenderness of young cattle

The objective of this study was to estimate the impact of the polymorphism of μ-calpain (CAPN1S) gene on protein changes of the cattle muscle tissue and its tenderness during 10-day cold storage. The analysis was performed on the longest dorsal and lumbar muscles collected from 76 bulls 6 to 12 months of age. Polymorphism identification of the above-mentioned gene was conducted using the PCR-RFLP technique. Its effect on the course of the proteolysis process was assessed by monitoring changes in proportions of tissue proteins during 10-day process of meat ageing. Special attention was focused on changes in native titin (T1) share and products of its degradation (proteins of molecular weight (m.w.) of 2400 and 200 kDa), α-actinin and protein of 37 kDa as well as myosin heavy chains (MHC). In the case of the last proteins, their polymorphism was evaluated as well. Meat tenderness was estimated measuring the value of shear force and sensorially. The highest tenderness was ascertained for the heterozygote. Its improvement was associated with a significant decrease in proportions of proteins of molecular weight of approximately 37 kDa accompanied by an increase of those with 200 kDa molecular weight. Muscles derived from cattle of CT genotype were characterised by the highest proportions of type 2a MHC isoform. Value differences between proportions determined for the heterozygote and CC and TT homozygotes of the CAPN1S gene were statistically significant. Therefore, it can be presumed that the process of meat tenderisation was especially connected with MHC polymorphism.

Association of polymorphisms in candidate genes with colour, water-holding capacity, and composition traits in bovine M. longissimus and M. semimembranosus

The objective of this study was to determine the association of single nucleotide polymorphisms (SNP) in selected candidate genes with sensory and technological meat quality traits in commercial cattle. SNP in seven candidate genes were genotyped in 130 crossbred Bos taurus cattle using PCR-RFLP. Reported associations between calpastatin (CAST) and Warner-Bratzler shear force and carboxypeptidase E (CPE) and intra-muscular fat were not confirmed. However, SNP in CAST, amp-activated protein kinase, gamma-3 subunit (PRKAG3), growth hormone receptor (GHR) and stearoyl coA desaturase (SCD) genes were significantly associated with colour traits (p<0.05). The PRKAG3 SNP was additionally associated with cook loss in M. longissimus thoracis et lumborum (p<0.05) and tended towards association in M. semimembranosus (p<0.1). An association with pH was identified for the SCD SNP (p<0.001). The GHR polymorphism was influential on moisture and intra-muscular fat in M. semimembranosus and protein content in both muscles (p<0.05). Only CPE was associated with sensory traits (flavour in M. longissimus, p<0.01).

Evidence for a new allele at the SERCA1 locus affecting pork meat quality in part through the imbalance of Ca2+ homeostasis

Sarcoendoplasmic reticulum Ca2+-ATPase 1 (SERCA1) as a Ca2+ release channel plays a key role in the relaxation of skeletal muscle through pumping cytosolic Ca2+ into the SR (sarcoplasmic reticulum). In this study, a novel single nucleotide polymorphism (SNP) in exon 8 (C > T) was detected by tetra-primer ARMS-PCR and the tissue expression pattern of SERCA1 was analyzed in eleven tissues. A model of primary skeletal muscle cells in vitro exposed to dexamethasone (DEX, a synthetic corticosteroid) was also employed to determine whether stress hormones cause an increase in intracellular Ca2+ concentration that is associated with alteration in SERCA1 and in turn subsequently affect meat quality. The results showed that the CC genotype has lower content intramuscular fat and higher water than pig carrying the genotype CT and CC. In addition, the additive effects were both significantly (P < 0.05) and allele T seemed to be associate with increase in intramuscular fat, while decrease in water content. Accompanied with previous studies, the high abundance of porcine SERCA1 was found in skeletal muscle tissue. DEX markedly down-regulated the expression of SERCA1, leading to Ca2+ overload. Furthermore, the imbalance of Ca2+ homeostasis up-regulated the transcription level of Calpain1. Taken together, we demonstrated a novel mechanism that the changes in expression of SERCA1 potential disturb the normal Ca2+ channel as well as the balance of Ca2+ homeostasis and which in turn finally activated Ca2+-dependent proteases such as Calpain1 which could affect meat quality.

New single nucleotide polymorphisms in the mu-calpain gene in Spanish maternal beef breeds

Calpains play an important role in the postmortem tenderization process of meat and several SNP in the mu-calpain gene (CAPN1) have been reported to be associated with tenderness in beef cattle. Our objectives were to identify the previously reported CAPN1 331G>C SNP and to detect new polymorphisms in this gene in Spanish maternal beef breeds. A fragment (exon 8 to 10) of the bovine CAPN1 gene was sequenced and genotyped in a sample of the main Spanish maternal beef breeds including Retinta, Morucha, and Avilenã Negra-Ibérica. These breeds are characterized for their high meat quality, their adaptation to adverse environmental conditions, and their good maternal aptitude. This adaptation makes it possible to rear these breeds in the south and west of Spain, where drought and feed shortages occur frequently. Six SNP in the mu-calpain gene were found, five of which (CAPN1 80C>T, 302C>G, 310G>A, 445C>T, 524A>C) have not been reported previously. Sequences obtained for these five newly found SNP were submitted to GenBank (Accessions EU386166 to EU386183).

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSION

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