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* USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE;
and
AgResearch, Ruakura Research Center, PB3123, Hamilton, New Zealand; and
and
AgResearch, Molecular Biology Unit, Dunedin, New Zealand
3 Correspondence:
Spur 18D, P.O. Box 166 (phone: 402-762-4366; fax: 402-762-4390; E-mail:
smith{at}email.marc.usda.gov).
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Abstract |
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 Top Abstract IntroductionMaterials and MethodsResultsDiscussionImplicationsReferences |
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Key Words: Calpain • Genetic Polymorphism • Meat • Quantitative Trait Loci
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Introduction |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionImplicationsReferences |
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The micromolar calcium-activated neutral protease (CAPN1) gene encodes a cysteine protease, µ-calpain, that degrades myofibrillar proteins under postmortem conditions and appears to be the primary enzyme in the postmortem tenderization process (Koohmaraie, 1992; 1994; 1996). Regulation of µ-calpain activity has been correlated with variation in meat tenderness (Geesink and Koohmaraie, 1999). Bovine CAPN1 has been mapped to the telomeric end of BTA29 (Smith et al., 2000a), and recently, a QTL for tenderness was found to be segregating in this region of BTA29 in two resource populations (Casas et al., 2000; Morris et al., 2001). The moderate effect (0.4 standard deviation) of this QTL on Warner-Bratzler shear force, a mechanical measurement of tenderness (AMSA, 1995) in the U.S. Meat Animal Research Center (MARC) population supported the evaluation of CAPN1 as a candidate gene for tenderness within this population. Our objective was to determine if genetic variation within the candidate gene CAPN1 could be associated with the meat tenderness values of two resource populations exhibiting meat tenderness QTL on BTA29.
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Materials and Methods |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionImplicationsReferences |
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A random shotgun library was prepared from a Bacterial Artificial Chromosome (BAC) clone (Smith et al., 2000a; Warren et al., 2000) containing the CAPN1 gene by partial digestion of ~5 µg of BAC DNA, with the restriction enzyme CviJI (0.3 units per µL) essentially as described (Gingrich et al., 1996). Briefly, the DNA was incubated with enzyme in a 50-µL volume for 20 min, the resulting DNA smear was separated on a 1% agarose gel, and fragments in the 1 to1.5 kb range were isolated using a commercial kit (Novagen, Madison, WI). The eluted fragments were ligated to a pBluescript vector (Stratagene, La Jolla, CA) that had been linearized with restriction enzyme EcoRV and treated with alkaline phosphatase. Ligated fragments were transformed into Top 10 competent cells (Invitrogen, Valencia, CA). Sequencing was performed on PCR-derived templates as described (Smith et al., 2000b), using T7 and T3 as universal sequencing primers on an ABI 3700 and ABI 377 sequencers.
The sequences from BAC subclones were analyzed with the sequence assembly algorithm Phrap (Ewing and Green 1998; Ewing et al., 1998) to detect overlaps and form contigs. The previously published (Smith et al., 2000a) partial sequence of the bovine CAPN1 gene was included in the data set to seed formation of contigs surrounding the gene. Sequence comparisons of the contig sequences with human genomic sequence surrounding the human CAPN1 gene (GenBank accession number NT_030106.2) and the E. coli genome were performed using BLASTN (Altshul et al., 1990; 1997).
Animal Sequencing and Single Nucleotide Polymorphisms Identification
Primers (Table 1
) for PCR amplification were designed from the CAPN1 gene sequence (GenBank accession AF252504 and AF248054) to obtain overlapping DNA fragments of 1 to 2 kb in predicted length. Production of amplicons for direct sequencing was performed in a 20-µL volume with Amplitaq Gold or HotStar Taq polymerase enzyme following the protocols supplied by the manufacturers (Applied Biosystems, Inc.; Qiagen, Inc). Sequencing was performed using one-fourth reaction volumes with BigDye Terminator as recommended by the manufacturer (Applied Biosytems, Inc.) and analyzed on an ABI 3700 sequencer. Amplicons were sequenced with the amplification primers.
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Resource Populations
The MARC resource family used in this study has been previously described (Casas et al., 1998). Briefly, a half-sib family was developed using a Piedmontese x Angus sire. A total of 209 offspring were produced by matings primarily to MARC III dams (1/4 Angus, 1/4 Hereford, 1/4 Pinzgauer, and 1/4 Red Poll). Dams were artificially inseminated, and the offspring were born during the spring of 1995. Calves were weaned at an average of 200 d and raised from weaning to slaughter on a corn-corn silage diet. Steers were slaughtered at a commercial beef processing facility after 194 to 312 d on feed, and heifers were slaughtered after 207 to 287 d on feed. Meat tenderness was measured in all animals on the longissimus thoracis as Warner-Bratzler shear force (kg) at 3 and 14 d postmortem after belt cooking as described by Wheeler et al. (1998). This family was used to detect QTL based on differences between the two paternal alleles for growth, carcass composition, and meat quality traits (Casas et al., 2000; 2001).
The New Zealand AgResearch resource family used in this study was the progeny of a Limousin x Australian Jersey sire. The bull’s semen was imported into New Zealand for insemination of New Zealand Limousin and New Zealand Jersey cows (mainly grade animals), thus providing backcross animals of two types for a joint New Zealand-Australian DNA marker study. Importation into New Zealand of semen from this and two other bulls from the Australian "Mapping Project" (Pitchford et al., 1998), provided common genetic links between New Zealand and Australian grandparents for the joint study. The cows in New Zealand were inseminated in 1995 and 1996, and calves were born in 1996 and 1997 in industry and research herds. Heifer and steer calves were collected after weaning and grown out on a research property (Tokanui Station) near AgResearch’s headquarters. Further details of trial design and animal management (live calves and at slaughter) are given by Morris et al. (2001). Briefly, animals were preallocated to slaughter groups at 22 to 28 mo of age, over 18 kill days in 1998 and 10 kill days in 1999, with preallocation based on breed of calf, sire, and balanced as far as possible for live weight before the first slaughter day. The right striploin (longissimus lumbarum) was removed for tenderness measurement before stimulation of the remainder of the carcass. Each striploin was maintained at 15°C after removal. Five steak portions from the unstimulated striploin were cut for the cooking and shear force measurements with the first steak processed at rigor mortis and the remainder at 1.3, 2.0, 2.3, and 4.0 d postmortem. A different technique for measuring shear force was used in the AgResearch population as shear force was measured by MIRINZ tenderometer (Fraserhurst and MacFarlane, 1983).
Haplotype Analysis
Haplotypes inherited from the sires were established based on a selection of 10 SNP representing genetic variation within the Piedmontese x Angus sire. Two SNP representing predicted amino acid changes, two SNP representing silent substitutions within the coding region, and six SNP representing intron variation were selected out of 38 total SNP heterozygous in the Piedmontese x Angus sire. Six of the SNP selected reside on the half of the gene 5' to the approximately 100-kb intron 10, while the remaining four are located in the half 3' to intron 10 (Figure 1). The haplotypes inherited by the sire from the Piedmontese grandsire and Angus grandam were identified by inferring the haplotypes based on offspring that were homozygous for all of the SNP tested and comparing these genotype patterns with markers used in the QTL analysis. All offspring from the MARC family were genotyped for the 10 SNP, offspring from the New Zealand family were genotyped for eight of these SNP informative in the Jersey x Limousin sire.
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Dam alleles were predicted based on the sire’s haplotype and the SNP genotypes of the progeny. The effect of the allele inherited from the dam was estimated simultaneously with the effect of the paternally inherited haplotype in the MARC population using multiple regression of SAS (SAS Inst. Inc., Cary, NC). Variation associated with the maternally inherited alleles was partitioned separately from that associated with paternal alleles in order to isolate novel variation from previously reported differences associated with paternal alleles (Casas et al., 2000). The two SNP predicting valine or isoleucine (V530/I530) and glycine or alanine (G316/A316) were evaluated. The analysis provided least squares means by using a model that included the effects of sex (steers or heifers) and days on feed as a covariate.
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Results |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionImplicationsReferences |
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The first step in the evaluation of CAPN1 as a candidate was to obtain sufficient sequence to enable identification of SNP within the entire coding region of the bovine gene. Partial sequence (11,055 bp) of the bovine CAPN1 gene (Smith et al., 2000a) was available; however, the reported CAPN1 sequence excluded sequences between exon 9 and exon 11. To obtain this sequence, a subclone library was made from a BAC containing the CAPN1 gene. Clones were sequenced from both ends to generate 5,947 sequence reads, a predicted 10-fold coverage of the BAC. Analysis of the sequences assembled 4,133 of the reads into 362 sequence contigs, with the remainder being low quality sequence reads or failing to show overlap with other sequences.
The three largest bovine contigs (containing 1,776 reads), were examined by BLAST analysis. The first contig contained exons 1 to 10 of the bovine CAPN1 gene, the second contig contained exons 11 to 22 of the bovine CAPN1 gene, and the third contig shared homology to the human CAPN1 intron 10 (estimated to be approximately 100 kb based on the draft human sequence). The three contigs containing CAPN1 genomic sequence represented a total length of 43,848 bp. No matches or overlaps were found from the remaining contigs that added sequence information.
The two contigs containing coding portions of the bovine CAPN1 gene added significant new sequence, relative to the previous report by Smith et al. (2000a), within and around the exons as indicated by filled rectangles in Figure 1
. Furthermore, two significant aspects of CAPN1 gene architecture were revealed that had not been identified in the previous study. The additional sequence upstream of the 100-kb intron revealed a 130-bp intron in exon 9, that had not been detected by the exon primer-based PCR approach used previously (Smith et al., 2000a). Thus, the portion of the bovine CAPN1 gene upstream from the 100-kb intron includes 10 exons, rather than the nine as previously reported. The second aspect involved the first intron downstream of the large intron which had been reported to be approximately 4 kb, but the new sequence data demonstrated that this intron is divided into a 2,791-bp intron, 12-bp exon, and an 891-bp intron (Figure 1). Therefore, the half of the gene downstream of the large intron includes 12 exons, rather than 10 as previously reported. In summary, the data indicate that the bovine CAPN1 gene consists of 22 exons and 21 introns. This is the same arrangement observed for the human gene by comparison of the human cDNA (accession NM_005186) and the draft genome (Lander et al., 2001) sequences (data not shown). The updated sequence information was sufficient to support primer design to scan all exons of the gene. No effort was made to completely sequence the ~100-kb intron 10. In all, more than 28 kb of sequence containing the entire coding region of the bovine CAPN1 gene was determined.
Single-Nucleotide Polymorphism Iidentification in MARC Quantitative Trait Locus Population.
The hypothesis that CAPN1 variation underlies the QTL effect observed in the MARC resource population predicts the presence of sequence variation between the two alleles of the Piedmontese x Angus sire of the population (sire PA). To identify this variation, a set of PCR primers was designed to amplify and sequence the coding region of the gene (Table 1). A total of 12.5 kb of the gene was encompassed by 35 amplicons. All 22 exons were completely sequenced to identify coding region variation, and all but the two largest introns were included to identify sufficient numbers of SNP to support construction of haplotypes. This procedure identified 38 SNP in sire PA, of which five were in exons. Two of the five exon SNP predicted amino acid variation in the µ-calpain protein, including a GCC alanine codon in exon 9 vs a GGC glycine codon (amino acid number 316), and a GTC valine codon in exon 14 vs an ATC isoleucine codon (amino acid number 530).
A set of microsatellite markers had been used previously to define the sire allele with effect on shear force measurement of meat tenderness. However, mapping the CAPN1 gene to the QTL interval (Smith et al., 2000a) did not define which allele of the gene would associate with decreased meat tenderness (increased shear force), nor did the previous analysis establish haplotypes to permit this analysis. Therefore, the haplotypes of the sire were determined by genotyping of the progeny to identify homozygotes of each haplotype and permit unambiguous assignment of SNP alleles to each haplotype. This analysis demonstrated that one sire allele contained alanine at position 316 (allele A316) and valine at position 530 (allele V530), whereas the other sire allele contained glycine (allele G316) and isoleucine (allele I530) at those same two positions. A set of 10 SNP heterozygous in sire PA were chosen to genotype the entire resource population, to determine the haplotype associated with increased shear force. The SNP chosen and their alternative alleles in this bull are shown in Table 2, with the positions in the gene shown graphically in Figure 1. We arbitrarily define allele 1 of this sire as the GTTTCGATCG haplotype containing G316 and I530, and allele 2 as the ACCCTCGCTA haplotype containing A316 and V530 with each base designation representing the allele of each SNP in the order shown in Table 2. Alleles 1 and 2 were inherited from the Piedmontese and Angus parent of the sire, respectively. Consistent with the original microsatellite-based QTL analysis, the haplotype analysis revealed that the Piedmontese allele had an effect on meat tenderness in this population (Table 3). This result suggests that the G316 I530 haplotype is a marker for a functional allele of CAPN1 associated with increased shear force in this population.
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summarizes the analyses of the sire alleles and the dam alleles with regard to shear force mean differences and their significance as measured by the P value. The magnitude of effect is measured by both shear force mean differences in the two alleles tested and the calculated effect in standard deviations. The dam alleles containing I530 or V530 were analyzed separately from the dam alleles containing G316 or A316 as numbers of dams containing inferred genotypes for both markers were insufficient for haplotype analysis. The G316 allele inherited from the dams was present at 86% frequency and did not show an effect on meat tenderness. The I530 allele was present in the dams at 18% frequency and showed an effect on meat tenderness (increase in shear force d 14, P < 0.04), providing strong support for the hypothesis that this SNP is in linkage disequilibrium with a functional allele. Single Nucleotide Polymorphism Identification in AgResearch Quantitative Trait Locus Population.
A second resource population at AgResearch in New Zealand had been developed that showed evidence of a QTL on BTA29 (C. Morris, unpublished data). A reciprocal backcross population using a Jersey x Limousin sire (sire JL) revealed a significant QTL approximately centered at the map position of CAPN1, affecting MIRINZ tenderometer shear force. This resource population had a different breed composition and was raised in a different environment (New Zealand vs Nebraska), by a different production protocol, suggesting it represented a rigorous test for the association of particular CAPN1 haplotypes with meat tenderness across populations. The CAPN1 gene of the Jersey x Limousin sire was sequenced. No additional variation within the coding region was identified that would be predicted to alter the amino acid sequence of the protein. Genotypes from the 10 SNP used in the MARC population demonstrated that sire JL was heterozygous for eight of the 10, including the two predicting amino acid variation. Genotypes for the eight informative SNP were collected on the progeny of the resource population to define haplotypes of the bull and to determine which haplotype had the effect of increased shear force. The two haplotypes are shown in Table 2, with allele 1 arbitrarily defined as the allele containing G316 and I530. Use of these SNP markers in a QTL analysis of the New Zealand population demonstrated that allele 1 of sire JL is associated with decreased meat tenderness (i.e., increased shear force, P < 0.0001) in this Jersey x Limousin cross (Table 4). Allele 1 was derived from the Limousin grandsire and is highly similar to allele 1 of the MARC sire, providing support for the hypothesis that these SNP represent markers of functional alleles of CAPN1.
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. The analysis of the dam contributions revealed an effect for the G316 allele similar to that observed in the sire alleles of both resource populations. No effect was observed for the I530 allele when the dam contributions were analyzed as independent variables. The identification of two µ-calpain variants that show effects on meat tenderness in unrelated QTL populations led to examination of the gene in a wider source of germplasm to ascertain the depth of CAPN1 diversity in cattle. The same primers previously used to amplify overlapping portions of the gene were applied to sequence a sampling of 16 beef breeds and the Holstein dairy breed represented in the MARC bovine diversity panel (described in Heaton et al., 2001). An additional 134 SNP were detected in this panel, but none of the eleven present in exons were predicted to result in amino acid variation in the protein, nor were there any other obviously significant changes to the gene. The I530 allele was observed in all of the breeds in the diversity panel except Brangus and was present at an overall frequency of 30%. The G316 allele was observed in all of the breeds represented by the diversity panel and was present at an overall frequency of 86%. The A316 allele was not observed in Brahman, Simmental, Gelbvieh, Salers, Maine-Anjou, or Chianina breeds.
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Discussion |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionImplicationsReferences |
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No association with decreased meat tenderness was detected for the G316 allele contributed from the dams in the MARC resource population, in contrast to the effect observed in the sire alleles. The low frequency of A316 in the dams resulted in many of the progeny inheriting a V530 and G316 allele from the dam which is out of phase with the inheritance pattern from the sire. The inheritance of these two opposing alleles from the dam limits the conclusion that can be made when an effect is not observed. The I530 allele, however, showed a similar effect on shear force when the dam alleles were analyzed as had been observed in the sire alleles, providing strong support for the utility of this marker. Further strong support is provided by the discovery that the I530 allele also is correlated with increased shear force in the AgResearch population, which is comprised of different breeds, raised on a separate continent, and with different management variables. The association of I530 with decreased tenderness in three different genetic backgrounds as demonstrated by the MARC sire (Piedmontese x Angus), the MARC dams (Red Poll, Pinzgauer, Hereford, Angus) and the AgResearch sire (Jersey x Limousin) provides strong evidence for I530 as a functional marker. The association of the G316 allele with increased shear force in the AgResearch population was demonstrated when inherited from either the sire or the dams providing support for the utility of this marker in addition to the I530 marker. The association of G316 with increased shear force is demonstrated in three different genetic backgrounds as demonstrated by the MARC sire (Piedmontese x Angus), the AgResearch sire (Jersey x Limousin) from Australia, and the AgResearch dams (Jersey and Limousin) from New Zealand.
Although differences were not detected in the AgResearch dams between the I530 and V530 alleles, the low frequency of dams contributing I530 in the AgResearch population may have limited the ability to detect a difference in shear force values. In addition, tenderness measurements were taken only up to d 4 postmortem in this population. It is possible that differences are only detectable at d 14 postmortem as demonstrated by the MARC resource population. Similarly the low frequency of A316 in the MARC resource population may have hindered the detection of a difference between A316 and G316 alleles in the MARC dams.
The overall results provide strong evidence that I530 and G316 are informative markers for meat tenderness variation. Both I530 and V530 alleles were detected in all breeds present in the diversity panel except for Brangus (note the panel has only four Brangus bull samples, and the Brahman and Angus bull samples had both alleles), with no breed appearing fixed for the I530 allele. The observed frequency of I530 across the entire panel was 30%, sufficiently high to suggest that selection could impact variation in meat tenderness. The observed frequency of G316 across the entire panel was 86% with Brahman, Simmental, Gelbvieh, Salers, Maine-Anjou, and Chianina appearing fixed for the G316 allele. However, the low number of samples from each breed does not support the precise calculation of frequency within breeds.
In addition to utility as markers, it is possible that one or both of the amino acid variations reflect a mutation that causes a functional change in the µ-calpain protease. The µ-calpain isoform containing I530, G316, or both may be a functionally different protein that led to variation in myofibrillar proteolysis and resulted in a difference in shear force in the two QTL populations. The I530/V530 variation represents a relatively conservative substitution of nonpolar amino acids in Domain III of the protein, which currently has no known function in terms of the activity of the enzyme. However, it could potentially alter protein folding or stability, impacting autocatalysis or proteolytic activity. Moreover, a major change in the protein is unlikely to be necessary to effect the relatively small change in postmortem proteolysis underlying the variation in shear force measurement. A peptide search using NCBI BLAST of bovine Domain III revealed that human, mice, rat, rabbit, chicken, and monkey versions of µ-calpain all have isoleucine at position 530. In contrast, sequences for swine, sheep, zebrafish, and frog all have valine at this position, which is the most common allele in the beef diversity panel. The region of comparison was well conserved among species (> 90%) except for chicken (66%) and zebrafish (56%). More sequencing of these other species is necessary before any conclusions could be made regarding these potential differences. Similar to the I530 allele, the variation represented by the G316 and A316 alleles represent a relatively conservative substitution of non-polar amino acids. However, this variation is located in Domain II of the protein, which has been identified as the proteolysis domain. An alteration in the proteolysis domain could alter the activity of the protein, and thus effect meat tenderization. A peptide search using the region around this variation revealed that monkey, human, mice, rat, chicken, and frog versions of µ-calpain do not contain glycine or alanine. The region in general is less conserved (< 90%) for the species mentioned, and the presence of glycine, alanine, serine, asparagine, lysine, and glutamic acid demonstrate that this position is not highly conserved among species.
Our results demonstrate the association of the I530 and G316 alleles with meat tenderness in two separate populations as well as in the dam alleles of the MARC population and the AgResearch population, and are consistent with the hypothesis that variation in CAPN1 is responsible for the detection of the BTA29 QTL in the two resource populations.
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Implications |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionImplicationsReferences |
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Footnotes |
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2 Mention of trade names, proprietary products, or specific equipment does not constitute a guarantee or warranty of the product by the USDA and does not imply its approval to the exclusion of other products that also may be suitable.
Received for publication May 30, 2002. Accepted for publication July 16, 2002.
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