The Identification of Novel Single Nucleotide Polymorphisms in Calpain 1 (CAPN1) Gene of Japanese Quail (Coturnix coturnix japonica)

Year 2019, , 25 - 29, 28.06.2019

Raziye Işık

https://doi.org/10.29185/hayuretim.529317

Abstract

Objective: Calpains, in particular μ-calpain, are responsible for the post mortem proteolysis processes in muscle tissue and have main influences on meat quality. The CAPN1 gene that codes for large subunit of μ-calpain is revealed as a candidate gene related with meat quality and tenderization traits for livestock. For this reason, in this study it is aimed to investigate the genetic variation of CAPN1 gene in Japanese quails.

Material and Methods: In this study, the genetic variation of CAPN1 gene was analyzed via DNA sequencing of 35 (13 males and 12 females) Japanese quails which were reared in Tekirdağ Namık Kemal University, Animal Research Unit.

Results: Some genetic variants which are found in the 4th and 5th exons are as g.103969C>T in the 4th exon region and eight novel SNPs as g.104116A>T, g.104118T>G, g.104148G>C, g.104169G>C, g.104172A>G, g.104179C>G, g.104181G>A, g.104184T>C in the 5th exon of CAPN1 gene. The novel DNA polymorphisms of CAPN1 gene in Japanese quails are reported for the first time in this study and these sequences were deposited to NCBI GenBank Database, with the accession numbers MK496828-MK496837, respectively. g.103969C>T transversion which is localized in the 4th exon region and g.104148G>C, g.104169G>C transversions and g.104172A>G, g.104181G>A, g.104184T>C transitions which are localized in the 5th exon region have not caused an amino acid change. Instead, g.104116A>T, g.104118T>G tranversions caused the change from Threonine to Serine amino acid. Similarly, C→G transversion which was observed on the 104179th position caused the amino acid change from Proline to Alanine.

Conclusion: These observed SNPs may have an effect on meat yield and tenderness in quails, so further researches are needed to demonstrate this hypothesis and these SNPs may be candidate SNPs for quails breeding.

Keywords

CAPN1 Gene, DNA sequencing, Coturnix japonica, quail

Japon Bıldırcınlarında Calpain 1 (CAPN1) Geni Tek Nükleotid Polimorfizmlerinin Tanımlanması

Abstract

Amaç: Kalpainler, özellikle μ-kalpain, kas dokusunda ölümden sonraki proteoliz işlemlerinden sorumludur ve et kalitesi üzerinde ana etkiye sahiptir. Büyük μ-kalpain alt birimi tarafından kodlanan CAPN1 geni, çiftlik hayvanlarında et kalitesi ve lezzet özellikleri ile ilgili aday gen olarak belirlenmiştir. Bu nedenle Japon bıldırcınlarında CAPN1 geni genetik varyasyonunun tanımlanması amaçlanmıştır.

Materyal ve Metot: Bu çalışmada CAPN1 geni genetik varyasyonu Tekirdağ Namık Kemal Üniversitesi Hayvan Araştırmaları Birimi'nde yetiştirilen 35 adet (13 erkek ve 12 dişi) Japon bıldırcında DNA dizi analizi yöntemi ile belirlenmiştir.

Bulgular: CAPN1 genindeki genetik varyasyonlar 4. ve 5. ekzonlarda olmak üzere; g.103969C> T varyasyonu 4. ekzon bölgesinde, ve g.104116A>T, g.104118T>G, g.104148G>C, g.104169G>C, g.104172A>G, g.104179C>G, g.104181G>A, g.104184T>C olmak üzere sekiz yeni SNP 5. ekzonda görülmüştür. Japon bıldırcınlarındaki CAPN1 genindeki yeni DNA varyasyonları ilk kez bu çalışmada bildirilmiştir ve bu diziler sırasıyla MK496828-MK496837 erişim numarasıyla NCBI GenBank veri tabanına kaydedilmiştir. 4. ekzon bölgesinde görülen 103969C> T transversiyonu ve 5. ekzon bölgesindeki g.104148G> C, g.104169G> C transversiyonları ve g.104172A> G, g.104181G> A, g.104184T> C transisyonları amino asit değişikliğine neden olmamıştır. Ancak g.104116A>T, g.104118T>G transversiyonları, Threonin'den Serin amino asidi değişimine neden olmuştur. Benzer şekilde, 104179. pozisyonda C→G transversiyonu, Prolin'den Alanin amino asidi değişimine neden olmuştur.

Sonuç: Bu çalışmada tespit edilen SNP'lerin bıldırcınlardaki et verimi ve lezzeti üzerinde bir etkisi olabileceği düşünülmektedir. Bu nedenle bu hipotezi doğrulamak için daha fazla araştırmaya ihtiyaç duyulmaktadır. Tespit edilen SNP'lerin bıldırcın ıslahında aday gen ve SNP'ler olarak kullanılabilirlikleri değerlendirilmelidir.

Keywords

CAPN1 Geni, DNA dizi analizi, Coturnix japonica, bıldırcın

References

• Barendse W. 2002. DNA markers for meat tenderness. Patent WO02064820. Bastos, pp. 1–88.
• Geesink GH, Koohmaraie M. 1999. Effect of calpastatin on degradation of myofibrillar proteins by l-calpain under postmortem conditions. Journal of Animal Science 77: 2685–2692.
• Goll, D.E., Thompson, V.F., Li, H.,Wei,W., Cong, J., 2003. The calpain system. Physiological Reviews 83: 731–801
• Hall T. 2011. BioEdit: An important software for molecular biology. GERF Bulletin of Biosciences 2(1):60-61.
• Ishiura S, Murofushi H, Suzuki K, Imahori K. 1978. Study of a calcium-activated neutral protease from chicken skeletal muscle. The Journal of Biological Chemistry 84: 225–230.
• Koohmaraie M. 1992. The role of Ca(2+)-dependent proteases (calpains) in post mortem proteolysis and meat tenderness. Biochimie 74: 239–245.
• Koohmaraie M, Geesink GH. 2006. Contribution of postmortem muscle biochemistry to the delivery of consistent meat quality with particular focus on the calpain system. Meat Science 74: 34–43.
• Geesink GH, Koohmaraie M. 1999. Postmortem Proteolysis and Calpain/Calpastatin Activity in Callipyge and Normal Lamb Biceps Femoris During Extended Postmortem Storage. Journal of Animal Science 77:1490-1501.
• Johari S, Maeda Y, Okamoto S, Hashiguchi T. 1993. Comparison of calpain and calpastatin activities in skeletal muscle of broiler and layer chickens. British Poultry Science 34: 819–824.
• Li Z, Cao B, Zhao B, Yang X, Fan MZ, Yang J. 2009. Decreased expression of calpain and calpastatin mRNA during development is highly correlated with muscle protein accumulation in neonatal pigs. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology 152: 498–503.
• Maeda Y, Kawabe K, Okamoto S, Hashiguchi T. 1991. General studies on muscle protein turnover rate and calcium activated neutral protease activity in skeletal muscle of the Japanese quail, Coturnix coturnix japonica. Journal of Animal Science and Technology 62: 813–821.
• Maeda Y, Okamoto S, Okano K, Tomita T, Hashiguchi T. 1990. The comparison of muscle protein turnover rate among the egg type, meat type and Japanese native chicken stocks. Japanese Journal of Zootechnical Science 61: 701–706.
• Negro S, Solé M, Membrillo A, Peña F, Domenech V, Verona JC, Rubí M, Valera M, Molina A. 2016. Association analysis of g.68G-A SNP in CAPN1 gene with carcass and meat quality traits in goose. 67th EAAP annual meeting Belfast.
• Palmer BR, Robert N, Kent MP. 1999. A candidate gene approach to animal quality traits. Proceedings of The New Zealand Society of Animal Production, 57: 294–296.
• Page BT, Casas E, Heaton MP, Cullen NG, Hyndman DL, Morris CA, Crawford AM, Wheeler TL, Koohmaraie M, Keele JW, Smith TPL. 2002. Evaluation of single-nucleotide polymorphisms in CAPN1 for association with meat tenderness in cattle. Journal of Animal Science 80: 3077–3085.
• Page BT, Casas E, Heaton MP, Cullen NG, Hyndman DL, Morris CA, Crawford AM, Wheeler TL, Koohmaraie M, Keele JW, Smith TPL. 2004. Association of markers in the bovine CAPN1 gene with meat tenderness in large crossbred populations that sample influential industry sires. Journal of Animal Science 82: 3474–3481.
• Rasouli Z, Zerehdaran S, Azari MA, Shargh MS. 2013. Genetic polymorphism of the CAPN1 gene is associated with meat quality traits in Japanese quail. British Poultry Science 2013. 54(2): 171–175, http://dx.doi.org/10.1080/00071668.2013.770128
• Ropka-Molik K, Eckert R, Piórkowska K. 2014. New polymorphisms in regulatory regions of porcine μ-calpain gene and their association with CAPN1 transcript abundance. Annals of Animal Science 14(3): 525–535 DOI: 10.2478/aoas-2014-0027
• Sentandreu MA, Coulis G, Ouali A. 2002. Role of muscle endopeptidases and their inhibitors in meat tenderness. Trends in Food Science and Technology 13: 400–421.
• Soria LA, Corva PM, Sica A, Schor A, Melucci LM, Willarreal EL, Mezzadra CA, Cantet RJC, Miquel MC. 2009. Effect of three single nucleotide polymorphisms in CAPN1 gene on beef tenderness (brief report). Archiv Tierzucht 52: 546–549.
• Smith T, Thomas MG, Bidner TD, Paschal JC, Franke DE. 2009. Single nucleotide polymorphisms in Brahman steers and their association with carcass and tenderness traits. Genetics and Molecular Research 8: 39–46.
• Okumura F, Shimogiri T, Shinbo Y, Yoshizawa K, Kawabe K, Mannen H, Okamoto S, Cheng HH, Maeda Y. 2005. Linkage mapping of four chicken calpain genes. Journal of Animal Science 76: 121–127.
• White SN, Casas E, Wheeler TL, Shackelford SD, Koohmaraie M, Riley DG, Chase JRCC, Johnson DD, Keele JW, Smith TPL. 2008. 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, 83: 2001–2008.
• Yang XQ, Liu H, Guo LJ, Xu Y, Liu D. 2007. The mutation site analysis on CAPN1 gene of wild boar, Min pig and Yorkshire. Yi Chuan (Hereditas (Beijing)) 29: 581–586.
• Yang XQ, Liu H, Guo LJ, Guan OZ, Xu Y, Liu D. 2008. Analysis of SNPs in partial exons and 3’UTR of CAPN1 in porcine. Yi Chuan (Hereditas (Beijing)) 30: 741–746.
• Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6, Molecular Evolutionary Genetics Analysis Version 6.0; 2013, http://www.megasoftware.net/
• Zhang ZR, Liu YP, Jiang X, Du HR, Zhu O. 2008. Study on association of single nucleotide polymorphism of CAPN1 gene with muscle fibre and carcase traits in quality chicken populations. Journal of Animal Breeding and Genetics 125: 258–264.