Table 1 - uploaded by Paul L Greenwood
Content may be subject to copyright.
Number of Brahman and Angus cattle by gender, HGP-status, and genotype (number of favorable alleles) for calpain-system gene markers in the New South Wales (NSW) and Western Australian (WA) experiments
Source publication
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 modulat...
Contexts in source publication
Context 1
... design for the Angus controls in NSW included contrasts of HGP status and gender, and was also chosen to maximize the accuracy of estimating the effect of CAPN1-316 marker status (Robinson et al., 2007). The number of Brahman and Angus animals within each allelic status for the 4 calpain system gene markers and within gender and HGP category in the NSW experiment are also presented in Table 1. ...
Context 2
... design for Angus cattle in- cluded a contrast of HGP status and was also chosen to maximize the accuracy of estimating CAPN1-316 mark- er effect. The number of Brahman and Angus animals within each allelic status for the 4 calpain system gene markers and within HGP category in the WA experiment are also shown in Table 1. Brahman cattle were sourced at weaning (6 to 8 mo of age) from 4 producers in the Northern Agricultural region of WA, and the Angus cattle from a commercial herd in the south-west of WA. ...
Context 3
... 5% higher of "total" CAST mRNA were detected in the LLM of HGP-implanted cattle than in non-implanted cattle (P = 0.01; Table 4 and 7). Table 4. Significance (P-values) of the terms fitted in the linear models 1 Dependent variable 2 Terms fitted (P-values) 2 Abbreviated mRNA transcript identifiers for CALP1 = calpain 1; CALP3 = calpain 3; CAST = 'total' calpastatin; RPLP0 = Ribosomal Protein, Large, P0; CASTII = type II calpastatin splice variant; CASTIII (ex3) = type III calpastatin splice variant containing exon 3; CASTIII (ex2-ex4) = type III calpastatin splice variant lacking exon 3; CASTpA1 = calpastatin proximal polyadenylation variant; and CASTpA2 = calpastatin distal polyadenylation variant. 3 The initial phase of the experiment screened 152 cattle from NSW and 191 cattle from WA. ...
Similar publications
Backfat thickness is a good predictor of carcass lean content, an economically important trait, and a main breeding target in pig improvement. In this study, the candidate genes and genomic regions associated with the tenth rib backfat thickness trait were identified in two independent pig populations, using a genome-wide association study of porci...
The KIF6 719Arg allele is an interesting genomic variant widely screened in various populations and is reported to be associated with the risk of Coronary Artery Disease (CAD) and statin treatment outcome. Recent population based clinical studies and large-scale meta-analyses pondered over the role of 719Arg variant in CAD risk and treatment respon...
Coronary artery disease (CAD) is the most common chronic inflammatory disease worldwide. NF-κB, a central regulator of inflammation, is involved in various inflammatory diseases. The aim of this study was to investigate the association between NFKB1 and NFKBIA polymorphisms and the susceptibility to CAD and their impact on plasma levels of IL-6 in...
Chronic lymphocytic leukemia (CLL) is the most common leukemia in the Western world and is characterized by a heterogeneous clinical course. This variability in clinical course has spiked the search for prognostic markers able to predict patient evolution at the moment of diagnosis. Markers demonstrated to be of value are the mutation status of the...
Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system that predominantly affects young adults. The genetic contributions to this multifactorial disease were underscored by a genome wide association study (GWAS) conducted by the International Multiple Sclerosis Genetic Consortium in a multinational cohort prompting th...
Citations
... The association between reduced levels of calpastatin protein in Longissimus lumborum from Brahman and the occurrence of the favorable allele (CAST:c.2832 A > G polymorphism) also points to its association with regulatory sequences which have a role in the post-transcriptional regulation of CAST mRNA transcripts (Nattrass et al., 2014). One available and promising tool is the use of calpastatin gene marker to assisted selection, which has no negative impact on other production or carcass characteristics (Cafe et al., 2010). ...
... The inhibitory effect of calpastatin is used to predict beef quality by the calpastatin activity (Geesink et al., 2006;Grant et al., 2005); however, it is necessary to consider the significant heterogeneity between calpastatin variants generated by alternative splicing (Raynaud et al., 2005). This variability is associated to the calpastatin inhibitory activity (Nattrass et al., 2014) and can be identified by their mRNAs and by the transcriptional activity of calpastatin (CAST) gene promoters. Different responses to stimuli among species may be partly responsible for variations in CAST expression (species, breeds, and individuals). ...
... Proteins in the calpain system, including calpastatin, have long half-lives (Zhang, Lane, & Mellgren, 1996); therefore, this condition is compatible with greater protein degradation, lower WBSF, and greater MFI associated to lower CAPN1 and greater CAST II mRNA abundances. The difference in calpastatin between biological types that reduces tenderness is associated to CAST gene allele modification (Curi et al., 2010) and, although genetic associations have not been addressed in our study, polymorphism in the CAST gene seems to be related to alterations of mRNA levels, mainly CAST II, as reported by Nattrass et al. (2014). These authors verified that animals with one or two favorable alleles to tenderness showed low mRNA levels to the CAST II variant in comparison to animals without favorable alleles, which in turn presented a 14% increase in mRNA levels and reduced tenderness. ...
The calpain system is the central player for meat tenderization and the calpastatin activity plays an important role in beef tenderness of Bos taurus indicus cattle. This study investigated whether dietary vitamin D3 induced gene expression of μ-calpain (CAPN1), total calpastatin (CAST T), and their variants (CAST I and II). Animals received none or 2 × 10⁶ IU of vitamin D3 for either 2 or 8 days before slaughter and were submitted to different conditions during feedlot: sun exposure or artificial shade. Steaks from Longissimus lumborum were fabricated, aged for 1, 7, and 21 days post-mortem, and later used for the analyses of shear force and the myofibrillar fragmentation index. Vitamin D3 did not influence mRNA abundance; however, it induced a greater CAST II transcript in animals supplemented 8 days before slaughter. There was a negative association between CAST II abundance and the shear force, which revealed an important modulation of the calpain system expression due to vitamin D supplementation. This result is an important tool for strategies to improve beef tenderness.
beef; Bos taurus indicus; calcium; calpastatin; tenderness
... Twenty-one isoforms of the human CAST gene are included in RefSeq (https ://www.ncbi.nlm. nih.gov/gene/831#), and similarly, several isoforms of bovine CAST [65] are found in RefSeq (https ://www. ncbi.nlm.nih.gov/gene/28103 ...
Abstract Background Variants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles. Results Whereas a relatively small number of molecular phenotypes were significantly heritable (h2 > 0, P
... Four alternative promoters direct the expression of four different transcripts isolated from different tissues, named Type I, II, III, and IV, which differ in their 5´ ends (Raynaud et al., 2005a). Moreover, differences in transcript length can also be originated by alternative polyadenylation sites and alternative exon splicing (Cong et al., 1998;Raynaud et al., 2005b;Nattrass et al., 2014). ...
... There is still little information about the expression of CAST isoforms with different polyadenylation sites in different muscles or breeds, and its potential effects on beef quality traits. Nattrass et al. (2014) quantified two polyadenylation variants of CAST (those designated here as short and long, respectively) in the longissimus lumborum muscle of Angus and Brahman steers. The steers had been genotyped for the CAST:c.2832 ...
Calpastatin activity has a key role in the tenderization process that occurs during post-mortem storage of meat under refrigerated conditioning. The regulation of calpastatin (CAST) expression is highly complex, the gene has four putative promoters and at least three different polyadenylation sites, and it is also alternatively spliced. We investigated the presence of alternative polyadenylation (APA) isoforms of CAST transcripts in three muscles (infraspinatus, triceps brachii and semitendinosus) of two bovine breeds (Angus and Brahman). The 3´ RACE-PCR was used to specifically amplify the different APA sites. The amplified fragments were cloned and sequenced. Sequencing confirmed the existence of three expected polyadenylation sites corresponding to short, medium and long polyadenylated transcripts. Also, transcripts with a novel APA site were found in the three muscles of both breeds. Because the same APAs isoforms were found between muscles and breeds, we could hypothesize a possible contribution to the relative abundance of different isoforms, probably in coordination with promoter preference and alternative splicing. This knowledge would be useful in the design of future experiments to analyze differential expression of CAST isoforms and their contribution to the definition of beef tenderness.
... Four alternative promoters direct the expression of four different transcripts isolated from different tissues, named Type I, II, III, and IV, which differ in their 5´ ends (Raynaud et al., 2005a). Moreover, differences in transcript length can also be originated by alternative polyadenylation sites and alternative exon splicing (Cong et al., 1998;Raynaud et al., 2005b;Nattrass et al., 2014). ...
... There is still little information about the expression of CAST isoforms with different polyadenylation sites in different muscles or breeds, and its potential effects on beef quality traits. Nattrass et al. (2014) quantified two polyadenylation variants of CAST (those designated here as short and long, respectively) in the longissimus lumborum muscle of Angus and Brahman steers. The steers had been genotyped for the CAST:c.2832 ...
... The favorable A allele has been shown to produce a more energetically unstable mRNA (Leal-Gutiérrez, et al., 2018). This is substantiated by reports of Brahman animals with the AA genotype having approximately 14% lower mRNA expression than the GG genotype (Nattrass et al. 2014), suggesting less calpastatin protein being produced and therefore less postmortem µ-calpain inhibition. ...
Beef palatability is a complex concept and could be described through an array of features such as tenderness, juiciness and flavor traits. Improving the eating experience when consuming beef and the ability to accurately inform the consumers of the expected eating quality when the product is purchased are critical challenges. In this review, we discuss the current knowledge of quantitative and molecular genetic aspects of palatability and discuss implications of genetic manipulation for the cattle industry.
... Niciura et al (48) encontraron que la expresión del gen CAST fue dos veces mayor en el músculo de los animales homocigotos para el genotipo GG con respecto a los animales con genotipo AG en el marcador CAST T1. Natrass et al (49) determinaron esta relación en ganado Bos indicus y Bos taurus y encontraron diferencias en la expresión de los genes de la CAPN1 y la CAST entre las variantes favorables y desfavorables de estos marcadores (marcadores CAPN1 4751 y CAST T1), sugiriendo un efecto polimórfico en la expresión génica. Estos hallazgos sugieren que las diferencias en la terneza de la carne explicadas por los marcadores genéticos podrían ser una consecuencia de la alteración en los niveles de ARNm, actividad, velocidad y (o) extensión de la proteólisis post mortem en el músculo esquelético. ...
... Niciura et al (48) found that CAST was expressed twice as much in muscle of homozygous GG as in heterozygous AG in the CAST T1 marker. Natrass et al (49) investigated this relationship in Bos indicus and Bos taurus cattle and found differences in CAPN1 and CAST gene expression between favourable and unfavourable allelic variants of these genes (CAPN1 4751 and CAST T1 markers), indicating a polymorphic effect on gene expression. These findings suggest that differences in tenderness explained by gene markers could be a consequence of the alteration in their mRNA levels, protein activity and rate and (or) the extent of postmortem proteolysis in skeletal muscle. ...
a terneza de la carne es considerada como el atributo de mayor importancia en el concepto de calidad de carne. El proceso de tenderización de la carne post mortem es principalmente el resultado de la degradación de proteínas clave de las fibras musculares, mediado por las proteasas del sistema calpaína. Este sistema proteico está compuesto por tres moléculas: dos proteasas calcio-dependientes y su inhibidor específico. Numerosos estudios han demostrado que el sistema calpaína desempeña un papel central en la proteólisis postmortem y en la tenderización de la carne. El objetivo de esta revisión es describir los últimos descubrimientos bioquímicos y moleculares en relación con este sistema proteolítico y su relación con la terneza de la carne bovina. Se describen los hallazgos de polimorfismos de ADN y de expresión de ARNm y proteínas, como herramientas para predecir la terneza de la carne. La comprensión de las bases moleculares de la tenderización de la carne puede ser de utilidad para la industria cárnica, permitiendo la modificación de las prácticas de manipulación antes del sacrificio y los tratamientos post mortem, mejorando la calidad de la carne bovina.
... However, the mRNA expression of genes does not always explain the differences in myofibrillar proteolysis in skeletal muscle of Bos taurus and Bos indicus cattle ( Giusti et al. 2013). Thus, due to inconsistencies regarding mRNA levels of CAPN1 and myofibrillar proteolysis of skeletal muscle in Bos taurus and Bos indicus, a post-transcriptional regulatory mechanism such as a change in the abundance of an alternative polyadenylated variant of the CAST transcript has been proposed ( Nattrass et al. 2014). However, the molecular factors underlying the differences in proteolysis between Bos taurus and Bos indicus animals are still not fully understood. ...
... The next question to be answered is what causes the differences in myofibrillar proteolysis in skeletal muscle of Bos taurus and Bos indicus. To answer that question a great body of evidence has been amassed to evaluate the mRNA abundance and/or the allelic as well as genotype frequencies of CAPN1 and CAST and their polymorphism to assess the possible mechanisms related to myofibrillar proteolysis in the skeletal muscle ( Curi et al. 2009Curi et al. , 2010Giusti et al. 2013;Nattrass et al. 2014). Although most of these studies were developed to investigate beef tenderness, their results may reflect the effects of these genes on proteolysis in a live skeletal muscle tissue. ...
... Although most of these studies were developed to investigate beef tenderness, their results may reflect the effects of these genes on proteolysis in a live skeletal muscle tissue. Nattrass et al. (2014) speculated that the level of gene expression of CAPN1 and CAST would ultimately influence the activity of the proteins encoded by these genes (Calpain and Calpastatin), thus leading to the difference in the extent of skeletal muscle proteolysis. However, a genome scan performed by Tizioto et al. (2013) found a small effect of single nucleotide polymorphisms (SNPs) in CAPN1 and CAST in proteolysis and consequently Warner-Bratzler shear force on beef from Nellore cattle. ...
The present study aimed to explore the molecular factors underlying differences in Calpain/Calpastatin proteolytic system in Nellore and Angus cattle. Longissimus muscle samples were collected in Nellore ( n = 6; body weight (BW) = 373 ± 37·3 kg) and Angus ( n = 6; BW = 383 ± 23·9 kg) cattle at slaughter for analysis of gene and protein expression, and Calpastatin enzyme activity. Additionally, the myofibrillar fragmentation index was used to quantify the extension of proteolysis in longissimus muscle samples. A greater myofibrillar fragmentation was observed in skeletal muscle of Angus compared with Nellore cattle. Conversely, no differences were found between breeds for mRNA expression of Calpain 1 ( CAPN1 ) and Calpastatin ( CAST ). Similarly, no differences were observed for the abundance of Calpain and Calpastatin proteins between skeletal muscles of Nellore and Angus cattle. Despite the lack of differences in mRNA and protein abundance, a greater activity of Calpastatin was observed in skeletal muscle of Nellore compared with Angus cattle. These data indicate that the greater proteolysis in skeletal muscle of Angus compared with Nellore cattle is mainly driven by a greater Calpastatin activity rather than Calpain or Calpastatin mRNA and protein expression.
... Pleiotropy could be important both to understand genetic architecture of complex traits and also to characterize more completely the underlying biology and phenotypic consequences of associated loci. However, we did not detect any SNP on CAST or CAPN1, which regulates calpastatin expression in bovine skeletal muscle, and were strongly associated with SF as previous report (Nattrass et al. 2014;Tizioto et al. 2014). ...
Improving meat quality is the best way to enhance profitability and strengthen competitiveness in beef industry. Identification of genetic variants that control beef quality traits can help breeders design optimal breeding programs to achieve this goal. We carried out a genome-wide association study for meat quality traits in 1141 Simmental cattle using the Illumina Bovine HD 770K SNP array to identify the candidate genes and genomic regions associated with meat quality traits for beef cattle, including fat color, meat color, marbling score, longissimus muscle area, and shear force. In our study, we identified twenty significant single-nucleotide polymorphisms (SNPs) (p < 1.47 × 10(-6)) associated with these five meat quality traits. Notably, we observed several SNPs were in or near eleven genes which have been reported previously, including TMEM236, SORL1, TRDN, S100A10, AP2S1, KCTD16, LOC506594, DHX15, LAMA4, PREX1, and BRINP3. We identified a haplotype block on BTA13 containing five significant SNPs associated with fat color trait. We also found one of 19 SNPs was associated with multiple traits (shear force and longissimus muscle area) on BTA7. Our results offer valuable insights to further explore the potential mechanism of meat quality traits in Simmental beef cattle.
... Among the SFNB-containing genes found (S2 Table), some noteworthy genes include PPARG (peroxisome proliferator-activated receptor gamma), which is the main regulator of adipogenesis and which is involved in intramuscular fat deposition (marbling) [26][27][28][29][30] and has been associated with age of puberty [31] in cattle. The genes found also included CAST genes (calpastatins) and calpain (CAPN) inhibitors, which are both accountable for post-mortem muscle fiber proteolysis and associated with shear force and tenderness in the skeletal muscles [32,33]. ...
High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus) samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/ Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.
