Validation Study of SNPs in CAPN1-CAST Genes on the Tenderness of Muscles (Longissimus thoracis and Semimembranosus) in Hanwoo (Korean Cattle)
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Animal and Phenotype Measurement
2.2. Genotyping
2.3. Statistical Analyses
3. Results and Discussion
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
- Shackelford, S.D.; Wheeler, T.L.; Meade, M.K.; Reagan, J.O.; Byrnes, B.L.; Koohmaraie, M. Consumer impressions of Tender Select beef. J. Anim. Sci. 2001, 79, 2605–2614. [Google Scholar] [CrossRef] [PubMed]
- Aberle, E.D.; Forrest, J.C.; Gerrard, D.E.; Mills, E.W. Principles of Meat Science, 4th ed.; Kendal/Hunt Publishing: Dubuque, IA, USA, 2001. [Google Scholar]
- Cho, S.H.; Kim, J.; Park, B.Y.; Seong, P.N.; Kim, G.H.; Jung, S.G.; Im, S.K.; Kim, D.H. Assessment of meat quality properties and development of a palatability prediction model for Korean Hanwoo steer beef. Meat Sci. 2010, 86, 236–242. [Google Scholar] [CrossRef] [PubMed]
- Van Eenennaam, A.L.; Li, J.; Thallman, R.M.; Quaas, R.L.; Dikeman, M.E.; Gill, C.A.; Franke, D.E.; Thomas, M.G. Validation of commercial DNA tests for quantitative beef quality traits. J. Anim. Sci. 2007, 85, 891–900. [Google Scholar] [CrossRef] [PubMed]
- White, S.N.; Casas, E.; Wheeler, T.L.; Shackelford, S.D.; Koohmaraie, M.; Riley, D.G.; Chase, C.C., Jr.; Johnson, D.D.; Keele, J.W.; Smith, T.P.L. A new single nucleotide polymorphism in CAPN1 extends the current tenderness marker test to include cattle of Bos indicus, Bos taurus, and crossbred descent. J. Anim. Sci. 2005, 83, 2001–2008. [Google Scholar] [CrossRef] [PubMed]
- Casas, E.; White, S.N.; Wheeler, T.L.; Shackelford, S.D.; Koohmaraie, M.; Riley, D.G.; Chase, C.C., Jr.; Johnson, D.D.; Smith, T.P.L. Effects of calpastatin and μ-calpain markers in beef cattle on tenderness traits. J. Anim. Sci. 2006, 84, 520–525. [Google Scholar] [CrossRef] [PubMed]
- Li, Y.X.; Jin, H.G.; Yan, C.G.; Seo, K.S.; Zhang, L.C.; Ren, C.Y.; Ji, X. Association of CAST gene polymorphisms with carcass and meat quality traits in Yanbian cattle of China. Mol. Biol. Rep. 2013, 40, 1875–1881. [Google Scholar] [CrossRef] [PubMed]
- Barendse, W.J. DNA Markers for Meat Tenderness. U.S. Patent 7625698, 12 January 2009. [Google Scholar]
- Wheeler, T.L.; Koohmaraie, M. Pre-rigor and post-rigor changes in tenderness of ovine longissimus muscle. J. Anim. Sci. 1994, 72, 32–1238. [Google Scholar] [CrossRef] [PubMed]
- Johnston, D.J.; Graser, H.U. 2010. Estimated gene frequencies of GeneSTAR markers and their size of effects on meat tenderness, marbling, and feed efficiency in temperate and tropical beef cattle breeds across a range of production systems. J. Anim. Sci. 2010, 88, 1917–1935. [Google Scholar] [CrossRef] [PubMed]
- Allais, S.; Journaux, L.; Leveziel, H.; Payet-Duprat, N.; Raynaud, P.; Hocquette, J.F.; Lepetit, J.; Rousset, S.; Denoyelle, C.; Bernard-Capel, C.; et al. Effects of polymorphisms in the calpastatin and μ-calpain genes on meat tenderness in 3 French beef breeds. J. Anim. Sci. 2011, 89, 1–11. [Google Scholar] [CrossRef] [PubMed]
- Curi, R.A.; Chardulo, L.A.L.; Mason, M.C.; Arrigoni, M.D.B.; Silveira, A.C.; de Oliveira, H.N. Effect of single nucleotide polymorphisms of CAPN1 and CAST genes on meat traits in Nellore beef cattle (Bos indicus) and in their crosses with Bos taurus. Anim. Genet. 2009, 40, 456–462. [Google Scholar] [CrossRef] [PubMed]
- Lee, S.H.; Kim, S.C.; Chai, H.H.; Cho, S.H.; Kim, H.C.; Lim, D.; Choi, B.H.; Dang, C.G.; Sharma, A.; Gondro, C.; et al. 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. Meat. Sci. 2014, 96, 1501–1508. [Google Scholar] [CrossRef] [PubMed]
- Wheeler, T.L.; Shackelford, S.D.; Koohmaraie, M. Relationship of beef longissimus tenderness classes to tenderness of gluteus medius, semimembranosus, and biceps femoris. J. Anim. Sci. 2000, 78, 2856–2861. [Google Scholar] [CrossRef] [PubMed]
- Stephens, M.; Smith, N.J.; Donnelly, P. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 2001, 68, 978–989. [Google Scholar] [CrossRef] [PubMed]
- Barrett, J.C.; Fry, B.; Maller, J.; Daly, M.J. Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics 2005, 21, 263–265. [Google Scholar] [CrossRef] [PubMed]
- Gilmour, A.R.; Gogel, B.J.; Cullis, B.R.; Thompson, R. ASReml User Guide Release 2.0; VSN International Ltd.: Hemel Hempstead, UK, 2006. [Google Scholar]
- Falconer, D.S.; Mackay, T.F.C. Introduction to Quantitative Genetics, 4th ed.; Prentice Hall: London, UK, 1996. [Google Scholar]
- Page, B.T.; Casas, E.; Quaas, R.L.; Thallman, R.M.; Wheeler, T.L.; Shackelford, S.D.; Koohmaraie, M.; White, S.N.; Bennett, G.L.; Keele, J.W.; et al. Association of markers in the bovine CAPN1 gene with meat tenderness in large crossbred populations that sample influential industry sires. J. Anim. Sci. 2004, 82, 3474–3481. [Google Scholar] [CrossRef] [PubMed]
- Morris, C.A.; Cullen, N.G.; Hickey, S.M.; Dobbie, P.M.; Veenvliet, B.A.; Manley, T.R.; Pitchford, W.S.; Kruk, Z.A.; Bottema, C.D.K.; Wilson, T. Genotypic effects of calpain 1 and calpastatin on the tenderness of cooked M. longissimus dorsi steaks from Jersey × Limousin, Angus and Hereford-cross cattle. Anim. Genet. 2006, 37, 411–414. [Google Scholar] [CrossRef] [PubMed]
- Barendse, W. Haplotype analysis improved evidence for candidate genes for intramuscular fat percentage from a genome wide association study of cattle. PLoS ONE 2011, 6, e29601. [Google Scholar] [CrossRef] [PubMed]
- Gill, J.L.; Bishop, S.C.; McCorquodale, C.; Williams, J.L.; Wiener, P. Association of selected SNP with carcass and taste panel assessed meat quality traits in a commercial population of Aberdeen Angus-sired beef cattle. Genet. Sel. Evol. 2009, 41, 36–42. [Google Scholar] [CrossRef] [PubMed]
- McClure, M.C.; Ramey, H.R.; Rolf, M.M.; McKay, S.D.; Decker, J.E.; Chapple, R.H.; Kim, J.W.; Taxis, T.M.; Weaber, R.L.; Schnabel, R.D.; et al. Genome-wide association analysis for quantitative trait loci influencing Warner–Bratzler shear force in five taurine cattle breeds. Anim. Genet. 2012, 43, 662–673. [Google Scholar] [CrossRef] [PubMed]
Traits | Longissimus thoracis (n = 1000) | Semimembranosus (n = 1000) | ||||||
---|---|---|---|---|---|---|---|---|
Mean | SD | Min | Max | Mean | SD | Min | Max | |
WBSF (kg) | 3.97 | 0.86 | 2.15 | 6.92 | 6.65 | 1.14 | 3.4 | 9.88 |
IMF (%) | 15.83 | 4.26 | 4.82 | 29.34 | 4.89 | 1.85 | 1.5 | 15.61 |
Age (months) | 30.8 | 1.45 | 21.2 | 36.6 |
Markers | Allele | MAF a | WBSF (kg) in Longissimus thoracis at 7 Days | WBSF (kg) in Semimembranosus at 7 Days | ||||||
---|---|---|---|---|---|---|---|---|---|---|
Effects | F-Value | p-Value | %Var | Effects | F-Value | p-Value | %Var | |||
CAST:c.182G>A (rs109727850) | A | 0.41 | −0.02 ± 0.04 | 0.33 | 0.561 | 0.03 | −0.03 ± 0.05 | 0.22 | 0.631 | 0.04 |
CAST:c.1526A>G (rs109384915) | G | 0.41 | −0.06 ± 0.05 | 1.91 | 0.170 | 0.28 | −0.04 ± 0.06 | 1.31 | 0.255 | 0.08 |
CAST:c.1985G>C (rs110914810) | C | 0.08 | 0.15 ± 0.07 | 4.70 | 0.032 * | 0.53 | 0.26 ± 0.09 | 8.57 | 0.004 ** | 0.99 |
CAPN1:c.580T>C (rs17872079) | C | 0.40 | 0.16 ± 0.06 | 28.32 | 1.33 × 10−7 ** | 1.98 | 0.08 ± 0.07 | 10.71 | 0.001 ** | 0.31 |
CAPN1:c.658T>C (rs17872093) | C | 0.34 | −0.09 ± 0.06 | 9.57 | 0.002 ** | 0.59 | −0.13 ± 0.07 | 10.31 | 0.001 ** | 0.76 |
CAPN1:c.948G>C (rs17872000) | C | 0.36 | −0.03 ± 0.06 | 0.43 | 0.508 | 0.07 | −0.05 ± 0.07 | 0.31 | 0.574 | 0.12 |
CAPN1:c.1589T>C (rs17871051) | C | 0.26 | 0.03 ± 0.04 | 0.65 | 0.420 | 0.06 | 0.07 ± 0.05 | 2.11 | 0.149 | 0.19 |
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Lee, H.J.; Jin, S.; Kim, H.-J.; Bhuiyan, M.S.A.; Lee, D.H.; Lee, S.H.; Jang, S.B.; Han, M.H.; Lee, S.H. Validation Study of SNPs in CAPN1-CAST Genes on the Tenderness of Muscles (Longissimus thoracis and Semimembranosus) in Hanwoo (Korean Cattle). Animals 2019, 9, 691. https://doi.org/10.3390/ani9090691
Lee HJ, Jin S, Kim H-J, Bhuiyan MSA, Lee DH, Lee SH, Jang SB, Han MH, Lee SH. Validation Study of SNPs in CAPN1-CAST Genes on the Tenderness of Muscles (Longissimus thoracis and Semimembranosus) in Hanwoo (Korean Cattle). Animals. 2019; 9(9):691. https://doi.org/10.3390/ani9090691
Chicago/Turabian StyleLee, Hyo Jun, Shil Jin, Hyoun-Joo Kim, Mohammad Shamsul Alam Bhuiyan, Doo Ho Lee, Soo Hyun Lee, Sung Bong Jang, Man Hye Han, and Seung Hwan Lee. 2019. "Validation Study of SNPs in CAPN1-CAST Genes on the Tenderness of Muscles (Longissimus thoracis and Semimembranosus) in Hanwoo (Korean Cattle)" Animals 9, no. 9: 691. https://doi.org/10.3390/ani9090691
APA StyleLee, H. J., Jin, S., Kim, H.-J., Bhuiyan, M. S. A., Lee, D. H., Lee, S. H., Jang, S. B., Han, M. H., & Lee, S. H. (2019). Validation Study of SNPs in CAPN1-CAST Genes on the Tenderness of Muscles (Longissimus thoracis and Semimembranosus) in Hanwoo (Korean Cattle). Animals, 9(9), 691. https://doi.org/10.3390/ani9090691