Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle
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Abstract. Jakaria, Ulum MF, Lestari D, Akwila S, Sihite DEWT, Priyanto R, Muladno, Sumantri C. 2020. Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle. Biodiversitas 21: 2971-2976. The present investigation aims to explore specific SNPs of Bali cattle, focusing mainly on CAST, CAPN, and SCD genes in 5'UTR. DNA of Bali cattle (25 individuals) from Breeding Centre of Bali cattle in Bali Province, Indonesia, were extracted according to the protocol of GenAID. Amplification of the CAST, CAPN, and SCD genes were designed using the Primer3 program based on reference sequences (access numbers AH014526.2, AH009246.3, and AY241932). Furthermore, the PCR product was sequenced through forward primer sequencing. The data sequence results were analyzed using the Bioedit, MEGA7, Popgen 3.2, and DnaSP6 V6 programs. The results showed that SNPs were detected at g.921C>T and g.922T>G in 5'UTR for the CAST gene between the reference of GenBank AH014526.2 and Bali cattle, but it was monomorphic within the population. The high polymorphism of SNPs was found in g.232G>T for the CAPN gene and g.134A>del for the SCD gene. However, the SNP g.246C>del SCD gene was detected as monomorphic in this region. Moreover, this result shows that low nucleotide diversities (Pi) for CAST, CAPN, and SCD genes in 5'UTR of Bali cattle were 0.00422, 0.00632, and 0.00449, respectively. This finding was important for developing marker-assisted selection (MAS) to improve the meat quality of Bali cattle.
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References
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Lu W, Wang J, Li C, Sun M, Hu R, Wang W. 2018. A novel mutation in 5’-UTR of makorin ring finger 3 gene associated with the familial precocious puberty. 50:1291–1293.
Martojo H. 2012. Indigenous Bali cattle is most suitable for sustainable small farming in Indonesia. Reprod. Domest. Anim. 47:10–14.
Mignone F, Gissi C, Liuni S, Pesole G. 2002. Untranslated regions of mRNAs. Genome Biol. 3:1-10.
Nogalski Z, Pogorzelska-Przyby?ek P, Sobczuk-Szul M, Nogalska A, Modzelewska-Kapitu?a M, Purwin C. 2018. Carcass characteristics and meat quality of bulls and steers slaughtered at two different ages. Ital. J. Anim. Sci. 17: 279–288.
Nowak D. 2011. Enzymes in tenderization of meat - the system of calpains and other systems - a review. Polish J. Food Nutr. Sci. 61:231–237.
Oh DY, Jin MH, Lee YS, Ha JJ, Kim BK, Yeo JS, Lee JY. 2013. Identification of stearoyl-CoA desaturase (SCD) gene interactions in Korean native cattle based on the multifactor-dimensionality reduction method. Asian-Australasian J. Anim. Sci. 26:1218–1228.
Öner Y, Keskin A, Üstüner H, Soysal D, Karaka? V. 2017. Genetic diversity of the 3? and 5? untranslated regions of the HSP70.1 gene between native Turkish and Holstein Friesian cattle breeds. S. Afr. J. Anim. Sci. 47:424–439.
Paramitasari KA, Sumantri C, Jakaria J. 2015. The genetic variability of prolactin and signal transducers and activators of transcription 5A (STAT5A) genes in Bali cattle. Media Peternak. 38:1–11.
Pintos D, Corva PM. 2011. Association between molecular markers for beef tenderness and growth traits in Argentinian Angus cattle. Anim. Genet. 42: 329–332.
Pratiwi N, Maskur, Priyanto R, Jakaria J. 2016. Novel SNP of calpain-1 (CAPN1) gene and its association with carcass and meat characteristics traits in Bali cattle. Trop. Anim. Sci. J. 41:109–116.
Putri R, Priyanto R, Gunawan A, Jakaria J. 2015. Association of calpastatin (CAST) gene with growth traits and carcass characteristics in Bali cattle. Media Peternak 38:145–149.
Raynaud P, Jayat-Vignoles C, Laforêt MP, Levéziel H, Amarger V. 2005. Four promoters direct expression of the calpastatin gene. Arch. Biochem. Biophys. 437:69–77.
Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sanchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol. Biol. Evol. 34:3299–3302.
Shafee T, Lowe R. 2017. Eukaryotic and Prokaryotic Gene Structure. Wiki J. Med. 4:1–5.
Shin Y, Jung H, Jung M, Yoo S, Subramaniyam S, Markkandan K. 2016. Discovery of gene sources for economic traits in Hanwoo by whole-genome resequencing. Asian Australas. J. Anim. Sci. 29:1353–1362.
Sutikno, Priyanto R, Sumantri C, Jakaria J. 2018. Polymorphism of ADIPOQ and EDG1 genes in Indonesian beef cattle. J. Indones. Trop. Anim. Agric. 43:323-332.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30: 2725–9.
Taniguchi M, Utsugi T, Oyama K, Mannen H, Kobayashi M, Tanabe Y, Ogino A, Tsuji S. 2004. Genotype of stearoyl-CoA desaturase is associated with fatty acid composition in Japanese Black cattle. Mamm. Genome 15:142–148.
Wahid F, Shehzad A, Khan T, Kim YY. 2010. MicroRNAs: Synthesis, mechanism, function, and recent clinical trials. Biochim. Biophys. Acta - Mol. Cell Res. 1803:1231–1243.
Xu Y, Shi T, Zhou Y, Liu M, Klaus S, Lan X, Lei C, Chen H. 2018. A novel PAX7 10-bp indel variant modulates promoter activity, gene expression and contributes to different phenotypes of Chinese cattle. Sci. Rep. 8:1–10.
Yeh F, Yang RC, Boyle TBJ, Ye ZA, Mao J. 1997. POPGENE, The User-friendly Shareware for Population Genetic Analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Canada.
Zulkharnaim, Jakaria, Noor RR. 2010. Identification of genetic diversity of growth hormone receptor (GHR|Alu I) gene in Bali cattle. Media Peternakan. 33:81–87.
Alwiyah A, Naraini H, Agung PP, Jakaria J. 2016. Polymorphism stearoyl-coa desaturase (SCD) gene and associaton with characteristics meat in Bali cattle. Trop. Anim. Scien. J. 41:188-195.
Araujo PR, Yoon K, Ko D, Smith AD, Qiao M, Suresh U, Burns SC, Penalva LOF. 2012. Before it gets started: Regulating translation at the 5?; UTR. Comp. Funct. Genomics 2012:1-8.
Asaf VNM, Kumar A, Rahim A, Sebastian R, Mohan V, Dewangan P, Panigrahi M. 2014. An overview on single nucleotide polymorphism studies in mastitis research. Vet. World 7:416–421.
Avilés C, Juárez M, Peña F, Domenech V, Clemente I, Molina A. 2013. Association of single nucleotide polymorphisms in CAPN1 and CAST genes with beef tenderness from Spanish commercial feedlots. Czech J. Anim. Sci. 58:479–487.
Casas E, White SN, Wheeler TL, Shackelford SD, Koohmaraie M, Riley DG, Chase CC, Johnson DD, Smith TPL. 2006. Effects of calpastatin and ?-calpain markers in beef cattle on tenderness traits. J. Anim. Sci. 84:520–525.
Corva P, Soria L, Schor A, Villarreal E, Cenci MP, Motter M, Mezzadra C, Melucci L, Miquel C, Paván E, Depetris G, Santini F, Naón JG. 2007. Association of CAPN1 and CAST gene polymorphisms with meat tenderness in Bos taurus beef cattle from Argentina. Genet. Mol. Biol. 30:1064–1069.
Duran C, Appleby N, Edwards D, Batley J. 2009. Molecular genetic markers: discovery, applications, data storage and visualisation. Curr. Bioinform. 4: 16–27.
Enriquez-Valencia CE, Pereira GL, Malheiros JM, de Vasconcelos Silva JAII, Albuquerque LG, de Oliveira HN, Chardulo LAL, Curi RA. 2017. Effect of the g.98535683A > G SNP in the CAST gene on meat traits of Nellore beef cattle (Bos indicus) and their crosses with Bos taurus. Meat Sci. 123: 64–66.
Gu W, Xu Y, Xie X, Wang T, Ko J, Zhou T. 2014. The role of RNA structure at 5? untranslated region in microRNA-mediated gene regulation. RNA 20: 1369–1375.
Hajibemani A, Sharifiyazdi H, Mirzaei A, Ghasrodashti AR. 2012. Characterization of single nucleotide polymorphism in the 5’-untranslated region (5’-UTR) of Lactoferrin gene and its association with reproductive parameters and uterine infection in dairy cattle. Vet. Res. forum an Int. Q. J. 3:37–43.
Hall T. 1999. BioEdit: a user-friendly biological sequnce alignment editor and analysis program for Windos 95/98/NT. Nucleic Acids Symposium Series 41:95–98.
Jakaria J, Noor RR. 2011. Analysis on Alu-I growth hormone (GHA|Alu-I) gene in Bali cattle. Trop. Anim. Sci. J. 36:77–82.
Kaplanova K, Dufek A, Drackova E, Simeonovova J, Subrt J, Vrtkova I, Dvorak J. 2013. The association of CAPN1, CAST, SCD, and FASN polymorphisms with beef quality traits in commercial crossbred cattle in the Czech republic. Czech J. Anim. Sci. 58:489–496.
Koohmaraie M. 1992. Role of the Neutral Proteinases in postmortem Muscle Protein Degradation and Meat Tenderness. Reciprocal Meat Conf. Proc. 45: 63–74.
Leal-Gutiérrez JD, Elzo MA, Johnson DD, Scheffler TL, Scheffler JM, Mateescu RG. 2018. Association of ?-calpain and calpastatin polymorphisms with meat tenderness in a Brahman-Angus population. Front. Genet. 9:56.
Leppek K, Das R, Barna M. 2017. Functional 5? UTR mRNA structures in eukaryotic translation regulation and how to find them. Nat. Rev. Mol. Cell Biol. 19:158–174.
Li L, Fu Q, Li X, Zhou R, Ren Y. 2014. Identification and characterization of SNP in 5’UTR of MLPH gene for goats with different coat colours. Anim. Sci. Pap. Reports 32:33–40.
Lu D, Sargolzaei M, Kelly M, Vander Voort G, Wang Z, Mandell I, Moore S, Plastow G, Miller SP. 2013. Genome-wide association analyses for carcass quality in crossbred beef cattle. BMC Genet. 14:1-10.
Lu W, Wang J, Li C, Sun M, Hu R, Wang W. 2018. A novel mutation in 5’-UTR of makorin ring finger 3 gene associated with the familial precocious puberty. 50:1291–1293.
Martojo H. 2012. Indigenous Bali cattle is most suitable for sustainable small farming in Indonesia. Reprod. Domest. Anim. 47:10–14.
Mignone F, Gissi C, Liuni S, Pesole G. 2002. Untranslated regions of mRNAs. Genome Biol. 3:1-10.
Nogalski Z, Pogorzelska-Przyby?ek P, Sobczuk-Szul M, Nogalska A, Modzelewska-Kapitu?a M, Purwin C. 2018. Carcass characteristics and meat quality of bulls and steers slaughtered at two different ages. Ital. J. Anim. Sci. 17: 279–288.
Nowak D. 2011. Enzymes in tenderization of meat - the system of calpains and other systems - a review. Polish J. Food Nutr. Sci. 61:231–237.
Oh DY, Jin MH, Lee YS, Ha JJ, Kim BK, Yeo JS, Lee JY. 2013. Identification of stearoyl-CoA desaturase (SCD) gene interactions in Korean native cattle based on the multifactor-dimensionality reduction method. Asian-Australasian J. Anim. Sci. 26:1218–1228.
Öner Y, Keskin A, Üstüner H, Soysal D, Karaka? V. 2017. Genetic diversity of the 3? and 5? untranslated regions of the HSP70.1 gene between native Turkish and Holstein Friesian cattle breeds. S. Afr. J. Anim. Sci. 47:424–439.
Paramitasari KA, Sumantri C, Jakaria J. 2015. The genetic variability of prolactin and signal transducers and activators of transcription 5A (STAT5A) genes in Bali cattle. Media Peternak. 38:1–11.
Pintos D, Corva PM. 2011. Association between molecular markers for beef tenderness and growth traits in Argentinian Angus cattle. Anim. Genet. 42: 329–332.
Pratiwi N, Maskur, Priyanto R, Jakaria J. 2016. Novel SNP of calpain-1 (CAPN1) gene and its association with carcass and meat characteristics traits in Bali cattle. Trop. Anim. Sci. J. 41:109–116.
Putri R, Priyanto R, Gunawan A, Jakaria J. 2015. Association of calpastatin (CAST) gene with growth traits and carcass characteristics in Bali cattle. Media Peternak 38:145–149.
Raynaud P, Jayat-Vignoles C, Laforêt MP, Levéziel H, Amarger V. 2005. Four promoters direct expression of the calpastatin gene. Arch. Biochem. Biophys. 437:69–77.
Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sanchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol. Biol. Evol. 34:3299–3302.
Shafee T, Lowe R. 2017. Eukaryotic and Prokaryotic Gene Structure. Wiki J. Med. 4:1–5.
Shin Y, Jung H, Jung M, Yoo S, Subramaniyam S, Markkandan K. 2016. Discovery of gene sources for economic traits in Hanwoo by whole-genome resequencing. Asian Australas. J. Anim. Sci. 29:1353–1362.
Sutikno, Priyanto R, Sumantri C, Jakaria J. 2018. Polymorphism of ADIPOQ and EDG1 genes in Indonesian beef cattle. J. Indones. Trop. Anim. Agric. 43:323-332.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30: 2725–9.
Taniguchi M, Utsugi T, Oyama K, Mannen H, Kobayashi M, Tanabe Y, Ogino A, Tsuji S. 2004. Genotype of stearoyl-CoA desaturase is associated with fatty acid composition in Japanese Black cattle. Mamm. Genome 15:142–148.
Wahid F, Shehzad A, Khan T, Kim YY. 2010. MicroRNAs: Synthesis, mechanism, function, and recent clinical trials. Biochim. Biophys. Acta - Mol. Cell Res. 1803:1231–1243.
Xu Y, Shi T, Zhou Y, Liu M, Klaus S, Lan X, Lei C, Chen H. 2018. A novel PAX7 10-bp indel variant modulates promoter activity, gene expression and contributes to different phenotypes of Chinese cattle. Sci. Rep. 8:1–10.
Yeh F, Yang RC, Boyle TBJ, Ye ZA, Mao J. 1997. POPGENE, The User-friendly Shareware for Population Genetic Analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Canada.
Zulkharnaim, Jakaria, Noor RR. 2010. Identification of genetic diversity of growth hormone receptor (GHR|Alu I) gene in Bali cattle. Media Peternakan. 33:81–87.