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Variation of the calpain 1 p.Ala316Gly genotypes in Turkish Grey Steppe and Anatolian Black bulls

Year 2022, Volume: 41 Issue: 1, 55 - 61, 26.07.2022
https://doi.org/10.30782/jrvm.1090467

Abstract

Calpain 1 (CAPN1) gene is known as the micromolar calcium-activated neutral protease gene and it degrades calcium-dependent cysteine protease, μ-calpain, which reduces myofibrillar proteins in postmortem conditions. This gene has important effects on muscle metabolism and development. Although this gene has been widely studied among various cattle breeds, there is limited information on Turkish native cattle. Therefore, the present study aimed at determining the genetic variability of the CAPN1 p.Ala316Gly polymorphism in some Turkish native cattle breeds. In this respect, 99 Turkish Grey Steppe and 41 Anatolian Black bulls were genotyped by the PCR-RFLP. The genotypic and allelic frequencies, the Hardy-Weinberg equilibrium (HWE), the population genetic parameters including gene heterozygosity (He), the polymorphism information content (PIC), the effective allele numbers (Ne), the fixation index (Fıs), and the level of possible variability realization (%V) were evaluated in this study. Moreover, biodiversity indexes including the Shannon-Weaver diversity index, Simpson's dominance index, and Gini coefficient were calculated. Results revealed that the GG genotype was remarkably predominant in both native breeds. On the other hand, it was observed that the CC genotype was absent in the total population. This resulted in notably low C allele frequency (0.13 and 0.12 in Turkish Grey Steppe and Anatolian Black, respectively). The Fisher’s exact test showed a deviation from HWE and population genetics parameters indicated remarkably low genetic variabilities in the studied breeds. This observation was supported by the low levels of biodiversity. Taken together, the CAPN1 marker showed low informativeness in Turkish Grey Steppe and Anatolian Black cattle but further analyzes are needed for the genetic characterization of the native cattle breeds in Turkey. Molecular genetic studies on native breeds should be encouraged to reveal broader perspectives regarding significant biological processes and to achieve a better understanding of complex traits such as growth, muscle development, and feed efficiency.

References

  • 1. Page B, Casas E, Heaton M, et al. Evaluation of single-nucleotide polymorphisms in CAPN1 for association with meat tenderness in cattle. Journal of Animal Science 2002;80(12):3077-3085.
  • 2. Smith T, Casas E, Rexroad Iii C, Kappes S, Keele J. Bovine CAPN1 maps to a region of BTA29 containing a quantitative trait locus for meat tenderness. Journal of Animal Science 2000;78(10):2589-2594.
  • 3. Ensembl genome browser. 2022 [cited 18.03.2022]; Available from: https://www.ensembl.org/index.html
  • 4. Casas E, White S, Riley D, et al. Assessment of single nucleotide polymorphisms in genes residing on chromosomes 14 and 29 for association with carcass composition traits in Bos indicus cattle. Journal of Animal Science 2005;83(1):13-19.
  • 5. Pintos D, Corva P. Association between molecular markers for beef tenderness and growth traits in Argentinian angus cattle. Animal Genetics 2011;42(3):329-332.
  • 6. Kappes SM, Keele JW, Stone RT, et al. A second-generation linkage map of the bovine genome. Genome Research 1997;7(3):235-249.
  • 7. Solinas-Toldo S, Lengauer C, Fries R. Comparative genome map of human and cattle. Genomics 1995;27(3):489-496.
  • 8. Warner R, Wheeler TL, Ha M, et al. Meat tenderness: Advances in biology, biochemistry, molecular mechanisms and new technologies. Meat Science 185 (2022):108657.
  • 9. White S, Casas E, Wheeler T, et al. A new single nucleotide polymorphism in CAPN1 extends the current tenderness marker test to include cattle of Bos indicus, Bos taurus, and crossbred descent. Journal of Animal Science 2005;83(9):2001-2008.
  • 10. Laben R, Shanks R, Berger P, Freeman A. Factors affecting milk yield and reproductive performance. Journal of Dairy Science 1982;65(6):1004-1015.
  • 11. Green MR, Sambrook J. Isolation of high-molecular-weight DNA from mammalian cells using proteinase K and phenol. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, New York, USA: Cold Spring Harbor Laboratory Press; 2012. p. 47-48.
  • 12. Falconer DS, Mackay TFC. Introduction to quantitative genetics, Pearson Education Ltd, Harlow, England; 1996.
  • 13. Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 1980;32(3):314-331.
  • 14. Crow JF, Kimura M. Properties of a finite population. An introduction to population genetics theory. Caldwell, New Jersey: The Blackburn Press; 1970. p. 319-365.
  • 15. Nei M, Roychoudhury A. Sampling variances of heterozygosity and genetic distance. Genetics 1974;76(2):379-390.
  • 16. Ardicli S, Dincel D, Samli H, Balci F. Effects of polymorphisms at LEP, CAST, CAPN1, GHR, FABP4 and DGAT1 genes on fattening performance and carcass traits in Simmental bulls. Archives Animal Breeding 2017;60(2):61-70.
  • 17. Li X, Ekerljung M, Lundström K, Lundén A. Association of polymorphisms at DGAT1, leptin, SCD1, CAPN1 and CAST genes with color, marbling and water holding capacity in meat from beef cattle populations in Sweden. Meat Science 2013;94(2):153-158.
  • 18. Ardicli S, Ustüner H, Arslan Ö, Kandazoğlu O. Variability of CAPN1 g. 5709 C> G and MYF5 g. 1911 A> G Polymorphisms in Beef Cattle Imported from Brazil to Turkey. Lalahan Hayvancılık Araştırma Enstitüsü Dergisi 2019;59(2):72-78.
  • 19. Curi RA, Chardulo LAL, Giusti J, Silveira AC, Martins CL, de Oliveira HN. Assessment of GH1, CAPN1 and CAST polymorphisms as markers of carcass and meat traits in Bos indicus and Bos taurus–Bos indicus cross beef cattle. Meat Science 2010;86(4):915-920.
  • 20. Kök S, Atalay S, Eken HS, Savasci M. The genetic characterization of Turkish grey cattle with regard to UoG Cast, CAPN1 316 and CAPN1 4751 markers. Pakistan Journal of Zoology 2017;49(1):281-287.
  • 21. Allais S, Journaux L, Levéziel H, et al. Effects of polymorphisms in the calpastatin and µ-calpain genes on meat tenderness in 3 French beef breeds. Journal of Animal Science 2011;89(1):1-11.
  • 22. Ardicli S, Samli H, Dincel D, Soyudal B, Balci F. Individual and combined effects of CAPN1, CAST, LEP and GHR gene polymorphisms on carcass characteristics and meat quality in Holstein bulls. Archives Animal Breeding 2017;60(3):303-313.
  • 23. Ardicli S, Samli H, Vatansever B, Soyudal B, Dincel D, Balci F. Comprehensive assessment of candidate genes associated with fattening performance in Holstein–Friesian bulls. Archives Animal Breeding 2019;62(1):9-32.
  • 24. Miquel MC, Villarreal E, Mezzadra C, et al. The association of CAPN1 316 marker genotypes with growth and meat quality traits of steers finished on pasture. Genetics and Molecular Biology 2009;32(3):491-496.
  • 25. Bonilla C, Rubio M, Sifuentes A, et al. Association of CAPN1 316, CAPN1 4751 and TG5 markers with bovine meat quality traits in Mexico. Genetics and Molecular Research 2010;9(4):2395-2405.
  • 26. Gill JL, Bishop SC, McCorquodale C, Williams JL, 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. Genetics Selection Evolution 2009;41(1):1-12.
  • 27. Van Eenennaam A, Li J, Thallman R, et al. Validation of commercial DNA tests for quantitative beef quality traits. Journal of Animal Science 2007;85(4):891-900.
  • 28. Bracamonte MP, Rincón AMS, Rivas EGC, Medhin AT, Gonzalez JCM. Polymorphism in Calpain gene of registered Brahman cattle from Mexico. Latin American Archives of Animal Production 2007;15(1):33-38.
  • 29. Carvalho TDd, Siqueira F, Torres Júnior RAdA, et al. Association of polymorphisms in the leptin and thyroglobulin genes with meat quality and carcass traits in beef cattle. Revista Brasileira de Zootecnia 2012;41(10):2162-2168.
  • 30. Menezes MPC, Martinez AM, Ribeiro MN, Pimenta Filho EC, Bermejo JVD. Genetic characterization of Brazilian native breeds of goats using 27 markers microsatellites. Revista Brasileira de Zootecnia 2006;35:1336-1341.
  • 31. Trakovická A, Moravčíková N, Kasarda R. Genetic polymorphisms of leptin and leptin receptor genes in relation with production and reproduction traits in cattle. Acta Biochimica Polonica 2013;60(4): 783-787.
  • 32. Machado MA, Azevedo ALS, Teodoro RL, et al. Genome wide scan for quantitative trait loci affecting tick resistance in cattle (Bos taurus× Bos indicus). BMC Genomics 2010;11(1):1-11.
  • 33. Konopiński MK. Shannon diversity index: a call to replace the original Shannon’s formula with unbiased estimator in the population genetics studies. PeerJ 2020;8:e9391.

Boz ve Yerli Kara Irkı Sığırlarda Kalpain 1 p.Ala316Gly Genotiplerine Ait Genetik Varyasyonun Değerlendirilmesi

Year 2022, Volume: 41 Issue: 1, 55 - 61, 26.07.2022
https://doi.org/10.30782/jrvm.1090467

Abstract

Kalpain 1 (CAPN1) geni, mikromolar kalsiyum–aktive nötral proteaz geni olarak bilinir ve postmortem koşullarda miyofibriler proteinleri indirgeyen kalsiyum bağımlı sistein proteazı, μ-kalpaini ayrıştırır. Bu genin kas metabolizması ve gelişimi üzerinde önemli etkileri vardır. Bu gen, çeşitli sığır ırkları arasında geniş çapta çalışılmış olmasına rağmen, Türk yerli sığırları hakkında sınırlı bilgi bulunmaktadır. Bu nedenle bu çalışma, bazı Türk yerli sığır ırklarında CAPN1 p.Ala316Gly polimorfizmine ait genetik varyasyonu belirlemeyi amaçlamıştır. Bu kapsamda 99 Boz ve 41 Yerli Kara ırkı erkek sığır PCR-RFLP metodu kullanılarak genotiplendirilmiştir. Genotipik ve alelik frekanslar, Hardy-Weinberg dengesi (HWE), heterozigotluk (He), polimorfizm bilgi içeriği (PIC), efektif alel sayısı (Ne), fiksasyon indeksi (Fıs), olası varyasyon gerçekleşme düzeyi (%V) dahil olmak üzere popülasyon genetik parametreleri değerlendirilmiştir. Ayrıca Shannon-Weaver indeksi, Simpson dominantlık indeksi ve Gini katsayısını içeren biyoçeşitlilik indeksleri hesaplanmıştır. Sonuçlar, GG genotipinin her iki yerli ırkta da oldukça baskın olduğunu ortaya koydu. Öte yandan, toplam popülasyonda CC genotipinin bulunmadığı gözlenmiştir. Bu durum dikkate değer düzeyde düşük C allel frekansıyla sonuçlanmıştır (Boz ve Yerli Kara için sırasıyla 0.13 ve 0.12). Fisher’ın kesin testi, HWE’den sapma oldğunu, popülasyon genetiği parametreleri ise, incelenen ırklarda oldukça düşük bir genetik varyasyon düzeyi olduğunu göstermiştir. Bu gözlem, düşük seviyedeki biyolojik çeşitlilik seviyeleri ile desteklenmiştir. Nitekim CAPN1 markörü, Boz ve Yerli Kara sığırları için düşük seviyede bilgilendiricilik göstermiştir ancak Türkiye’deki yerli sığır ırklarının genetik karakterizasyonu hakkında ileride yapılacak çalışmalara ihtiyaç vardır. Yerli ırklarda yapılacak moleküler genetik çalışmalar, önemli biyolojik süreçlerle ilgili daha geniş perspektifleri ortaya koymak ve büyüme, kas gelişimi ve yem verimliliği gibi kompleks özelliklerin daha iyi anlaşılmasını sağlamak için teşvik edilmelidir.

References

  • 1. Page B, Casas E, Heaton M, et al. Evaluation of single-nucleotide polymorphisms in CAPN1 for association with meat tenderness in cattle. Journal of Animal Science 2002;80(12):3077-3085.
  • 2. Smith T, Casas E, Rexroad Iii C, Kappes S, Keele J. Bovine CAPN1 maps to a region of BTA29 containing a quantitative trait locus for meat tenderness. Journal of Animal Science 2000;78(10):2589-2594.
  • 3. Ensembl genome browser. 2022 [cited 18.03.2022]; Available from: https://www.ensembl.org/index.html
  • 4. Casas E, White S, Riley D, et al. Assessment of single nucleotide polymorphisms in genes residing on chromosomes 14 and 29 for association with carcass composition traits in Bos indicus cattle. Journal of Animal Science 2005;83(1):13-19.
  • 5. Pintos D, Corva P. Association between molecular markers for beef tenderness and growth traits in Argentinian angus cattle. Animal Genetics 2011;42(3):329-332.
  • 6. Kappes SM, Keele JW, Stone RT, et al. A second-generation linkage map of the bovine genome. Genome Research 1997;7(3):235-249.
  • 7. Solinas-Toldo S, Lengauer C, Fries R. Comparative genome map of human and cattle. Genomics 1995;27(3):489-496.
  • 8. Warner R, Wheeler TL, Ha M, et al. Meat tenderness: Advances in biology, biochemistry, molecular mechanisms and new technologies. Meat Science 185 (2022):108657.
  • 9. White S, Casas E, Wheeler T, et al. A new single nucleotide polymorphism in CAPN1 extends the current tenderness marker test to include cattle of Bos indicus, Bos taurus, and crossbred descent. Journal of Animal Science 2005;83(9):2001-2008.
  • 10. Laben R, Shanks R, Berger P, Freeman A. Factors affecting milk yield and reproductive performance. Journal of Dairy Science 1982;65(6):1004-1015.
  • 11. Green MR, Sambrook J. Isolation of high-molecular-weight DNA from mammalian cells using proteinase K and phenol. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, New York, USA: Cold Spring Harbor Laboratory Press; 2012. p. 47-48.
  • 12. Falconer DS, Mackay TFC. Introduction to quantitative genetics, Pearson Education Ltd, Harlow, England; 1996.
  • 13. Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 1980;32(3):314-331.
  • 14. Crow JF, Kimura M. Properties of a finite population. An introduction to population genetics theory. Caldwell, New Jersey: The Blackburn Press; 1970. p. 319-365.
  • 15. Nei M, Roychoudhury A. Sampling variances of heterozygosity and genetic distance. Genetics 1974;76(2):379-390.
  • 16. Ardicli S, Dincel D, Samli H, Balci F. Effects of polymorphisms at LEP, CAST, CAPN1, GHR, FABP4 and DGAT1 genes on fattening performance and carcass traits in Simmental bulls. Archives Animal Breeding 2017;60(2):61-70.
  • 17. Li X, Ekerljung M, Lundström K, Lundén A. Association of polymorphisms at DGAT1, leptin, SCD1, CAPN1 and CAST genes with color, marbling and water holding capacity in meat from beef cattle populations in Sweden. Meat Science 2013;94(2):153-158.
  • 18. Ardicli S, Ustüner H, Arslan Ö, Kandazoğlu O. Variability of CAPN1 g. 5709 C> G and MYF5 g. 1911 A> G Polymorphisms in Beef Cattle Imported from Brazil to Turkey. Lalahan Hayvancılık Araştırma Enstitüsü Dergisi 2019;59(2):72-78.
  • 19. Curi RA, Chardulo LAL, Giusti J, Silveira AC, Martins CL, de Oliveira HN. Assessment of GH1, CAPN1 and CAST polymorphisms as markers of carcass and meat traits in Bos indicus and Bos taurus–Bos indicus cross beef cattle. Meat Science 2010;86(4):915-920.
  • 20. Kök S, Atalay S, Eken HS, Savasci M. The genetic characterization of Turkish grey cattle with regard to UoG Cast, CAPN1 316 and CAPN1 4751 markers. Pakistan Journal of Zoology 2017;49(1):281-287.
  • 21. Allais S, Journaux L, Levéziel H, et al. Effects of polymorphisms in the calpastatin and µ-calpain genes on meat tenderness in 3 French beef breeds. Journal of Animal Science 2011;89(1):1-11.
  • 22. Ardicli S, Samli H, Dincel D, Soyudal B, Balci F. Individual and combined effects of CAPN1, CAST, LEP and GHR gene polymorphisms on carcass characteristics and meat quality in Holstein bulls. Archives Animal Breeding 2017;60(3):303-313.
  • 23. Ardicli S, Samli H, Vatansever B, Soyudal B, Dincel D, Balci F. Comprehensive assessment of candidate genes associated with fattening performance in Holstein–Friesian bulls. Archives Animal Breeding 2019;62(1):9-32.
  • 24. Miquel MC, Villarreal E, Mezzadra C, et al. The association of CAPN1 316 marker genotypes with growth and meat quality traits of steers finished on pasture. Genetics and Molecular Biology 2009;32(3):491-496.
  • 25. Bonilla C, Rubio M, Sifuentes A, et al. Association of CAPN1 316, CAPN1 4751 and TG5 markers with bovine meat quality traits in Mexico. Genetics and Molecular Research 2010;9(4):2395-2405.
  • 26. Gill JL, Bishop SC, McCorquodale C, Williams JL, 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. Genetics Selection Evolution 2009;41(1):1-12.
  • 27. Van Eenennaam A, Li J, Thallman R, et al. Validation of commercial DNA tests for quantitative beef quality traits. Journal of Animal Science 2007;85(4):891-900.
  • 28. Bracamonte MP, Rincón AMS, Rivas EGC, Medhin AT, Gonzalez JCM. Polymorphism in Calpain gene of registered Brahman cattle from Mexico. Latin American Archives of Animal Production 2007;15(1):33-38.
  • 29. Carvalho TDd, Siqueira F, Torres Júnior RAdA, et al. Association of polymorphisms in the leptin and thyroglobulin genes with meat quality and carcass traits in beef cattle. Revista Brasileira de Zootecnia 2012;41(10):2162-2168.
  • 30. Menezes MPC, Martinez AM, Ribeiro MN, Pimenta Filho EC, Bermejo JVD. Genetic characterization of Brazilian native breeds of goats using 27 markers microsatellites. Revista Brasileira de Zootecnia 2006;35:1336-1341.
  • 31. Trakovická A, Moravčíková N, Kasarda R. Genetic polymorphisms of leptin and leptin receptor genes in relation with production and reproduction traits in cattle. Acta Biochimica Polonica 2013;60(4): 783-787.
  • 32. Machado MA, Azevedo ALS, Teodoro RL, et al. Genome wide scan for quantitative trait loci affecting tick resistance in cattle (Bos taurus× Bos indicus). BMC Genomics 2010;11(1):1-11.
  • 33. Konopiński MK. Shannon diversity index: a call to replace the original Shannon’s formula with unbiased estimator in the population genetics studies. PeerJ 2020;8:e9391.
There are 33 citations in total.

Details

Primary Language Turkish
Subjects Veterinary Surgery
Journal Section Research Articles
Authors

Sena Ardıclı 0000-0003-2758-5945

Özden Çobanoğlu 0000-0001-9633-634X

Publication Date July 26, 2022
Acceptance Date June 21, 2022
Published in Issue Year 2022 Volume: 41 Issue: 1

Cite

APA Ardıclı, S., & Çobanoğlu, Ö. (2022). Boz ve Yerli Kara Irkı Sığırlarda Kalpain 1 p.Ala316Gly Genotiplerine Ait Genetik Varyasyonun Değerlendirilmesi. Journal of Research in Veterinary Medicine, 41(1), 55-61. https://doi.org/10.30782/jrvm.1090467
AMA Ardıclı S, Çobanoğlu Ö. Boz ve Yerli Kara Irkı Sığırlarda Kalpain 1 p.Ala316Gly Genotiplerine Ait Genetik Varyasyonun Değerlendirilmesi. J Res Vet Med. July 2022;41(1):55-61. doi:10.30782/jrvm.1090467
Chicago Ardıclı, Sena, and Özden Çobanoğlu. “Boz Ve Yerli Kara Irkı Sığırlarda Kalpain 1 p.Ala316Gly Genotiplerine Ait Genetik Varyasyonun Değerlendirilmesi”. Journal of Research in Veterinary Medicine 41, no. 1 (July 2022): 55-61. https://doi.org/10.30782/jrvm.1090467.
EndNote Ardıclı S, Çobanoğlu Ö (July 1, 2022) Boz ve Yerli Kara Irkı Sığırlarda Kalpain 1 p.Ala316Gly Genotiplerine Ait Genetik Varyasyonun Değerlendirilmesi. Journal of Research in Veterinary Medicine 41 1 55–61.
IEEE S. Ardıclı and Ö. Çobanoğlu, “Boz ve Yerli Kara Irkı Sığırlarda Kalpain 1 p.Ala316Gly Genotiplerine Ait Genetik Varyasyonun Değerlendirilmesi”, J Res Vet Med, vol. 41, no. 1, pp. 55–61, 2022, doi: 10.30782/jrvm.1090467.
ISNAD Ardıclı, Sena - Çobanoğlu, Özden. “Boz Ve Yerli Kara Irkı Sığırlarda Kalpain 1 p.Ala316Gly Genotiplerine Ait Genetik Varyasyonun Değerlendirilmesi”. Journal of Research in Veterinary Medicine 41/1 (July 2022), 55-61. https://doi.org/10.30782/jrvm.1090467.
JAMA Ardıclı S, Çobanoğlu Ö. Boz ve Yerli Kara Irkı Sığırlarda Kalpain 1 p.Ala316Gly Genotiplerine Ait Genetik Varyasyonun Değerlendirilmesi. J Res Vet Med. 2022;41:55–61.
MLA Ardıclı, Sena and Özden Çobanoğlu. “Boz Ve Yerli Kara Irkı Sığırlarda Kalpain 1 p.Ala316Gly Genotiplerine Ait Genetik Varyasyonun Değerlendirilmesi”. Journal of Research in Veterinary Medicine, vol. 41, no. 1, 2022, pp. 55-61, doi:10.30782/jrvm.1090467.
Vancouver Ardıclı S, Çobanoğlu Ö. Boz ve Yerli Kara Irkı Sığırlarda Kalpain 1 p.Ala316Gly Genotiplerine Ait Genetik Varyasyonun Değerlendirilmesi. J Res Vet Med. 2022;41(1):55-61.