Mutations in calpastatin and μ-calpain are associated with meat tenderness, flavor and juiciness in Hanwoo (Korean cattle): molecular modeling of the effects of substitutions in the calpastatin/μ-calpain complex

Improving the textural and microstructural quality of cow meat by black chokeberry, grape, and hawthorn vinegar-based marination

This study was designed to investigate the effects of vinegar-based marinades on pH, technological properties, color, microstructure, texture, and sensory characteristics of 9-year-old Holstein meat which had tough texture. To marinate the Longissimus lumborum steaks, three different marinades were prepared depending on the different additions of vinegar: black chokeberry (BV), grape (GV), and hawthorn vinegars (HV). The group with water (without vinegar) was prepared as a control sample (C). The steak samples were dipped into the vinegar-based marinades and stored at 4°C for 24 h. Vinegar-based marinades decreased the pH and cooking loss of the samples (p < .05). The highest a* values were determined in the BV group, while the samples marinated with vinegar-based marinades had lower L* values than the control group (p < .05). The samples marinated with grape vinegar marinade had the lowest hardness, WBSF, and WBSE values (p < .05). SEM images and sensory analysis results also supported these texture results. The results suggest that grape vinegar-based marinade may be a promising natural tenderizer to improve textural characteristics of tough meats.

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.

Exploring and Identifying Candidate Genes and Genomic Regions Related to Economically Important Traits in Hanwoo Cattle

The purpose of the current review was to explore and summarize different studies concerning the detection and characterization of candidate genes and genomic regions associated with economically important traits in Hanwoo beef cattle. Hanwoo cattle, the indigenous premium beef cattle of Korea, were introduced for their marbled fat, tenderness, characteristic flavor, and juiciness. To date, there has been a strong emphasis on the genetic improvement of meat quality and yields, such as backfat thickness (BFT), marbling score (MS), carcass weight (CW), eye muscle area (EMA), and yearling weight (YW), as major selection criteria in Hanwoo breeding programs. Hence, an understanding of the genetics controlling these traits along with precise knowledge of the biological mechanisms underlying the traits would increase the ability of the industry to improve cattle to better meet consumer demands. With the development of high-throughput genotyping, genomewide association studies (GWAS) have allowed the detection of chromosomal regions and candidate genes linked to phenotypes of interest. This is an effective and useful tool for accelerating the efficiency of animal breeding and selection. The GWAS results obtained from the literature review showed that most positional genes associated with carcass and growth traits in Hanwoo are located on chromosomes 6 and 14, among which LCORL, NCAPG, PPARGC1A, ABCG2, FAM110B, FABP4, DGAT1, PLAG1, and TOX are well known. In conclusion, this review study attempted to provide comprehensive information on the identified candidate genes associated with the studied traits and genes enriched in the functional terms and pathways that could serve as a valuable resource for future research in Hanwoo breeding programs.

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.

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.

A Gene-Set Enrichment and Protein-Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle

Non-synonymous SNPs and protein coding SNPs within the promoter region of genes (regulatory SNPs) might have a significant effect on carcass traits. Imputed sequence level data of 10,215 Hanwoo bulls, annotated and filtered to include only regulatory SNPs (450,062 SNPs), were used in a genome-wide association study (GWAS) to identify loci associated with backfat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). A total of 15, 176, and 1 SNPs were found to be significantly associated (p < 1.11 × 10-7) with BFT, CWT, and EMA, respectively. The significant loci were BTA4 (CWT), BTA6 (CWT), BTA14 (CWT and EMA), and BTA19 (BFT). BayesR estimated that 1.1%~1.9% of the SNPs contributed to more than 0.01% of the phenotypic variance. So, the GWAS was complemented by a gene-set enrichment (GSEA) and protein-protein interaction network (PPIN) analysis in identifying the pathways affecting carcass traits. At p < 0.005 (~2,261 SNPs), 25 GO and 18 KEGG categories, including calcium signaling, cell proliferation, and folate biosynthesis, were found to be enriched through GSEA. The PPIN analysis showed enrichment for 81 candidate genes involved in various pathways, including the PI3K-AKT, calcium, and FoxO signaling pathways. Our finding provides insight into the effects of regulatory SNPs on carcass traits.

Validation Study of SNPs in CAPN1-CAST Genes on the Tenderness of Muscles (Longissimus thoracis and Semimembranosus) in Hanwoo (Korean Cattle)

Simple Summary

For meat tenderness, single nucleotide polymorphisms (SNPs) in the μ-calpain (CAPN1) and calpastatin (CAST) genes have been reported to be associated with Warner-Bratzler shear force (WBSF) in different cattle populations, including Korean Hanwoo cattle. In this study, we validated the association of seven SNPs in CAPN1 and CAST genes with meat tenderness in two different muscle cuts tenderness in the Longissimus thoracis (LT) and Semimembranosus (SM) muscles. Two SNPs in CAPN1 and one SNPs in CAST genes showed association with WBSF of both muscle types. Furthermore, of twelve reconstructed haplotypes, six demonstrated significant associations with WBSF values. These findings may be one of the strong evidences that CAPN1 and CAST gene mutations are strongly associated with WBSF. The information of significantly-associated SNPs and the resulted haplotypes could be utilized in the Hanwoo breeding program for further genetic improvement of tenderness traits.

Abstract

Previous studies demonstrated that polymorphisms in the μ-calpain (CAPN1) and calpastatin (CAST) genes had significant effects on meat tenderness in different cattle populations. The aim of this study was to validate the potential association of seven single nucleotide polymorphisms (SNPs) harbored in these two candidate genes with meat tenderness in the Longissimus thoracis (LT) and Semimembranosus (SM) muscles. A total of 1000 animals were genotyped using TaqMan SNP genotyping arrays, and the meat tenderness of two muscle (LT and SM at 7 days post-slaughter) was assessed based on Warner-Bratzler WBSF (WBSF) testing. We observed significant associations of the CAPN1:c.580T>C, CAPN1:c.658T>C and CAST:c.1985G>C polymorphisms (p < 0.05) with the WBSF values in the LT and SM muscles. Additive effects of the C allele in CAPN1:c.580T>C and CAST:c.1985G>C were associated with an increase of 0.16 and 0.15 kg, and 0.08 and 0.26 kg WBSF in the LT and SM, respectively; CAPN1:c.658T>C had negative effects on the WBSFs. Furthermore, six reconstructed haplotypes demonstrated significant associations with WBSF values (p < 0.05). In conclusion, the significant associations identified between the SNPs in CAPN1, CAST and WBSF values could be utilized in marker-assisted selection programs in order to improve the beef tenderness of Hanwoo cattle.

Effects of polymorphisms in CAPN1 and CAST genes on meat tenderness of Chinese Simmental cattle

Considerable evidence has demonstrated that the μ -calpain (CAPN1) gene and its inhibitor calpastatin (CAST) gene are major factors affecting meat quality. Marker-assisted selection (MAS) has been widely used to improve beef quality traits. Therefore, the objective of the present study was to investigate the single nucleotide polymorphisms (SNPs) of bovine CAPN1 and CAST genes using 367 animals representing the four main Chinese cattle breeds and to explore the effects of these SNPs on meat quality traits. Two SNPs within CAPN1 and one SNP in CAST were successfully identified in cattle. Genetic diversity analyses suggested that most SNPs in the four breeds exhibited a moderate genetic diversity. Moreover, associations between individual markers and meat quality traits were analyzed in Chinese Simmental cattle. The CAPN1 4558 A > G locus was found to be significantly associated with shear force value (SFV) and marbling score (BMS), and CAPN1 4684 C > T exerted a significant effect on SFV, while the CAST genotype was not significantly associated with any of the measured traits. SFV, commonly used to measure meat tenderness, represents an important quality trait as it contributes to the flavor of cooked meat. This work confirms the effect of CAPN1 on beef tenderness and lays an important foundation for future cattle breeding.

A whole-genome sequence based association study on pork eating quality traits and cooking loss in a specially designed heterogeneous F6 pig population

To determine the genetic basis of pork eating quality traits and cooking loss, we herein performed a genome-wide association study (GWAS) for tenderness, juiciness, oiliness, umami, overall liking and cooking loss by using whole genome sequences of heterogeneous stock F6 pigs which were generated by crossing 4 typical western pig breeds (Duroc, Landrace, Large White and Pietrain) and 4 typical Asian pig breeds (Erhualian, Laiwu, Bamaxiang and Tibetan). We identified 50 associated loci (QTLs) and most of them are novel. Seven loci also showed pleiotropic associations with different traits. In addition, we identified multiple promising candidate genes for these traits, including PAK1 and AQP11 for cooking loss, EP300 for tenderness, SDK1 for juiciness, FITM2 and 5-linked MYH genes for oiliness, and TNNI2 and TNNT3 for overall liking. Our results provide not only a better understanding of the genetic basis for meat quality, but also a potential application in future breeding for these complex traits.

A Review of Selected Genes with Known Effects on Performance and Health of Cattle

There are genetic conditions that influence production in dairy and beef cattle. The objective of this review was to describe relevant genetic conditions that have been associated with productivity and health in cattle. Genes or genomic regions that have been identified as a candidate for the condition will be included, and the genetic basis of the condition will be defined. Genes and genetic conditions included in this review are bovine leukocyte adhesion deficiency, deficiency of the uridine monophosphate synthase, bovine chronic interstitial nephritis, horn development, myostatin, complex vertebral malformation, leptin, osteopetrosis, apoptosis peptide activating factor 1, chondrodysplastic dwarfism, caseins, calpastatin, umbilical hernia, lactoglobulin, citrullinemia, cholesterol deficiency, prions, thyroglobulin, diacylglycerol acyltransferase, syndactyly, maple syrup urine disease, slick hair, Factor XI deficiency, and μ-Calpain. This review is not meant to be comprehensive, and relevant information is provided to ascertain genetic markers associated with the conditions.

Genome-wide Association Study for Warner-Bratzler Shear Force and Sensory Traits in Hanwoo (Korean Cattle)

Significant SNPs associated with Warner-Bratzler (WB) shear force and sensory traits were confirmed for Hanwoo beef (Korean cattle). A Bonferroni-corrected genome-wide significant association (p<1.3×10⁻⁶) was detected with only one single nucleotide polymorphism (SNP) on chromosome 5 for WB shear force. A slightly higher number of SNPs was significantly (p<0.001) associated with WB shear force than with other sensory traits. Further, 50, 25, 29, and 34 SNPs were significantly associated with WB shear force, tenderness, juiciness, and flavor likeness, respectively. The SNPs between p = 0.001 and p = 0.0001 thresholds explained 3% to 9% of the phenotypic variance, while the most significant SNPs accounted for 7% to 12% of the phenotypic variance. In conclusion, because WB shear force and sensory evaluation were moderately affected by a few loci and minimally affected by other loci, further studies are required by using a large sample size and high marker density.

Homology modeling study of bovine μ-calpain inhibitor-binding domains

The activated mammalian CAPN-structures, the CAPN/CAST complex in particular, have become an invaluable target model using the structure-based virtual screening of drug candidates from the discovery phase to development for over-activated CAPN linked to several diseases, such as post-ischemic injury and cataract formation. The effect of Ca²⁺-binding to the enzyme is thought to include activation, as well as the dissociation, aggregation, and autolysis of small regular subunits. Unfortunately, the Ca²⁺-activated enzyme tends to aggregate when provided as a divalent ion at the high-concentration required for the protease crystallization. This is also makes it very difficult to crystallize the whole-length enzyme itself, as well as the enzyme-inhibitor complex. Several parameters that influence CAPN activity have been investigated to determine its roles in Ca²⁺-modulation, autoproteolysis, phosphorylation, and intracellular distribution and inhibition by its endogenous inhibitor CAST. CAST binds and inhibits CAPN via its CAPN-inhibitor domains (four repeating domains 1–4; CAST1–4) when CAPN is activated by Ca²⁺-binding. An important key to understanding CAPN1 inhibition by CAST is to determine how CAST interacts at the molecular level with CAPN1 to inhibit its protease activity. In this study, a 3D structure model of a CAPN1 bound bovine CAST4 complex was built by comparative modeling based on the only known template structure of a rat CAPN2/CAST4 complex. The complex model suggests certain residues of bovine CAST4, notably, the TIPPKYQ motif sequence, and the structural elements of these residues, which are important for CAPN1 inhibition. In particular, as CAST4 docks near the flexible active site of CAPN1, conformational changes at the interaction site after binding could be directly related to CAST4 inhibitory activity. These functional interfaces can serve as a guide to the site-mutagenesis in research on bovine CAPN1 structure-function relationships for the design of small molecules inhibitors to prevent uncontrolled and unspecific degradation in the proteolysis of key protease substrates.