Research Article
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Three Previously Unseen Genotypes Detected in IGFBP - 3 Gene in Buffalo Breed

Year 2023, Volume: 12 Issue: 1, 35 - 40, 22.06.2023
https://doi.org/10.31196/huvfd.1245427

Abstract

Anatolian water buffalo breed is Turkey’s sole water buffalo breed, and their numbers steadily increased with the national “Water Buffalo Breeding by Breeders Project”. This study aimed to investigate of the gene region polymorphisms (Intron-2, Exon-2/Intron-3, Exon-3) of the meat-yield-related Insulin-like Growth Factor Binding Protein-3 (IGFBP-3) gene in Anatolian water buffaloes by TaqI, HaeIII, and MspI restriction endonucleases. The phenol/chloroform method was used for DNA isolation from 151 blood samples, and extracted DNAs were amplified by touchdown PCR using specific primers. Amplified PCR products were digested with restriction endonucleases (REs) and separated in 3% agarose gel electrophoresis (AGE), then genotypes were determined. Results revealed two genotypes [AA (98.68%) and AC (1.32%)] and two alleles [A (0.99) and C (0.01)] for the Exon-2 to Intron-3 region from HaeIII digestion. TaqI digestion of the Intron-2 region revealed three genotypes [AA (7.94%), AB (3.97%), and BB (88.10%)] and two alleles [A (0.10) and B (0.90)]. MspI digestion of the Exon-3 region revealed only the AA genotype and A allele, thus revealing monomorphism. Overall, HaeIII digestion revealed insignificant polymorphism (P>0.05), and TaqI digestion revealed significant polymorphism (P<0.001) for their respective regions. Gene polymorphisms of these regions were investigated for the first time in Anatolian water buffaloes. Additionally, three novel genotypes for the IGFBP-3 gene (one from HaeIII and two from TaqI) were determined for the first time. The novel B allele from TaqI digestion was observed to have a substantial frequency.

Supporting Institution

Scientific Research Project Fund of Sivas Cumhuriyet University

Project Number

V-051

Thanks

We would like to thank Prof. Dr. Haki KARA for their support in this study

References

  • Ali BA, El-Hanafy AA, Salem HH, 2009: Genetic biodiversity studies on IGFBP-3 gene in Egyptian sheep breeds. Biotechnol Anim Husb, 25 (1-2), 101-109.
  • Choudhary V, Kumar P, Bhattacharya TK, Bhushan B, Sharma A, Shukla A, 2007: DNA polymorphism of insulin-like growth factor-binding protein-3 gene and its association with birth weight and body weight in cattle. J Anim Breed Genet, 124, 29-34.
  • Don RH, Cox PT, Wainwright BJ, Baker K, Mattick JS, 1991: ‘Touchdown’ PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res, 19, 4008.
  • EL-Hanafy AA, Salem HH, 2009: PCR-RFLP of IGFBP3 gene in some Egyptian sheep breeds. American-Eurasian J Agric & Environ Sci, 5 (1), 82-85.
  • Fadhıl M, Aytekin İ, Zülkadir U, 2020: Polymorphism in Anatolian Black and Holstein Friesian cattle breeds. Selcuk J Agr Food Sci, 34 (2), 137-140.
  • FAO, 2005: Buffalo Production and Research. Edited by Antonio Borghese. REU technical Series 67. ftp://ftp.fao.org/docrep/fao/010/ah847e/ah847e.pdf. Accessed 16 July 2019.
  • FAO, 2015: The Second Report on the State of the World’s Animal Genetic Resources for Food and Agriculture, edited by B.D. Scherf and D. Pilling. FAO Commission on Genetic Resources for Food and Agriculture Assessments. Rome. http://www.fao.org/3/a-i4787e/index.html. Accessed 16 July 2019.
  • Hays J, 2014: Water Buffaloes. Facts and details, Asian and Asians-International and Economic Issues http://factsanddetails.com/asian/cat62/sub408/entry-2830.html. Accessed 16 March 2019.
  • GDAR, 2011: Domestic animal genetics resources in Turkey. Republic of Turkey, Ministry of Food Agriculture and Livestock, General Directorate of Agricultural Research and Policy, Ankara, Türkiye.
  • Kumar P, Choudhary V, Padma B, Shukla A, Misra A, Bhattacharya TK, Bhushan B, Sharma A, 2004: Buffalo Insulin-like growth factor binding protein-3 (IGFBP-3) gene polymorphism and its comparison with cattle. Buffalo J, 2, 183-192.
  • Kumar P, Choudhary V, Kumar KG, Bhattacharya TK, Bhushan B, Sharma A, Mishra A, 2006: Nucleotide sequencing and DNA polymorphism studies on IGFBP-3 gene in sheep and its comparison with cattle and buffalo. Small Rum Res, 64, 285-292.
  • Lan XY, Pan CY, Chen H, Lei CZ, Liu SQ, Zhang YB, Min LJ, Yu J, Li JY, Zhao M, Hu SR, 2007: The HaeIII and XspI PCR-RFLPs detecting polymorphisms at the goat IGFBP-3 locus. Small Rum Res, 73, 283-286.
  • Lan XY, Pan CY, Zhang CL, Hu SR, Liu SQ, Zhang YB, Lei CZ, Chen H, 2009: Relationships between polymorphisms of IGFBP-3 gene and Cashmere traits in Cashmere goats. J App Anim Res, 35 (1), 29-32.
  • Maciulla JH, Zhang HM. DeNise SK, 1997: A novel polymorphism in the bovine insulin-like growth factor binding protein-3 (IGPBP3) gene. Anim Genet, 28, 375.
  • Michelizzi VN, Dodson MV, Pan Z, Amaral MEJ, Michal JJ, McLean DJ, Womack JE, Jiang Z, 2010: Water buffalo genome science comes of age. Int J Biol Sci, 6 (4), 333-349.
  • Othman OE, Alam SS, El-Aziem SHA, 2014: Single nucleotide polymorphism in Egyptian cattle insulin-like growth factor binding protein-3 gene. JGEB, 12, 143-147.
  • Othman OE, Abou-Eisha A, El-Din AE, 2018: Study on genetic polymorphism of IGFBP-3 gene in Egyptian buffalo. ARRB, 29 (3), 1-7.
  • Padma B, Kumar P, Choudhary V, Dhara SK, Mishra A, Bhattachary TK, Bhushan B, Sharma A, 2004: Nucleotide sequencing and PCR-RFLP of Insulin-like Growth Factor Binding Protein-3 gene in riverine buffalo (Bubalus bubalis). Asian Austral J Anim, 17, 910-913.
  • Ramesha KP, Rao A, Basavaraju M, Geetha GR, Kataktalware MA, Jeyakumar S, 2015: Genetic variability of bovine GHR, IGF-1 and IGFBP-3 genes in Indian cattle and buffalo. S Afr J Anim Sci, 45 (5), 485-493.
  • Rehman MS, Mushtaq M, Hassan F, Rehman Z, Mushahid M, Shokrollahi B, 2022: Comparative genomic characterization of insulin-like growth factor binding proteins in cattle and buffalo. BioMed Res Int, 2022, 5893825.
  • Saleh AA, Rashad AMA, Hassanine NNAM, Sharaby MA, Zhao Y, 2019: Comparative analysis of IGFBP-3 gene sequence in Egyptian sheep, cattle, and buffalo. BMC Res Notes, 12, 623.
  • Saleh AA, Hammouf MH, Dabour NA, Hafez EEE, Sharaby MA, 2022: Genetic variability in GH and IGFBP-3 genes and their association with growth performance in Egyptian sheep. Appl Vet Res, 1(3): e2022012.
  • Sambrook J, Fritsch EF, Maniatis T, 1989: Molecular cloning: A laboratory manual. 2nd ed., Cold Spring Harbor Laboratory Pres. Cold Spring Harbor.
  • Shimasaki S, Ling N, 1991: Identification and molecular characterization of insulin-like growth factor binding proteins (IGFBP-1, -2, -3, -4, -5 and -6). Progress in Growth Factor Research, 3, 243-266.
  • TurkStat, 2022a: Animal Production Statistics, December 2021. In: TurkStat News Bulletin. Number: 45593, Data:09.02.2022. https://data.tuik.gov.tr/Bulten/Index?p=Hayvansal-Uretim-Istatistikleri-Aralik-2021-45593. Accessed 01 May 2022.
  • TurkStat, 2022b: Red Meat Production Statistics, 2020-2021. TurkStat News Bulletin. Number: 45671, Data: 06.05.2022. https://data.tuik.gov.tr/Bulten/Index?p=Kirmizi-Et-Uretim-Istatistikleri-2020-2021-45671. Accessed 01 Jun 2022.

Mandalarda IGFBP-3 Geninde Daha Önce Görülmemiş Üç Genotip Tespit Edildi

Year 2023, Volume: 12 Issue: 1, 35 - 40, 22.06.2023
https://doi.org/10.31196/huvfd.1245427

Abstract

Anadolu su mandası Türkiye’de yetiştirilen tek manda ırkıdır ve sayıları ülke genelinde “Halk Elinde Manda Yetiştiriciliği Projesi” ile artmıştır. Bu çalışmanın amacı, Anadolu Mandalarında et verimi ile ilgili olan insülin benzeri büyüme faktörü bağlayıcı protein - 3 (IGFBP-3) geninin Taq I, Hae III ve Msp I restriksiyon enzimi (RE) ile gen polimorfizmlerinin (İntron 2, Exon 2 / İntron 3, Exon 3) araştırılmasıdır. Toplam 151 kan örneğinden Fenol/Kloroform yöntemi kullanılarak DNA izolasyonu yapılmıştır ve elde edilen DNA örnekleri spesifik primerler kullanılarak Touchdown PZR ile çoğaltılmıştır. Yükseltgenen PZR ürünleri restriksiyon enzimleri ile kesilmiş, %3 agaroz jel elektroforez yönteminde ayrıştırılmış ve genotipler belirlenmiştir. Sonuç olarak, Hae III RE’nde (Exon 2 – İntron 3) AA (%98.68) ve AC (%1.32) 2 genotip ve A (0.99) ve C (0.01) 2 allel tespit edilmiştir. Taq I RE’nde (İntron 2) AA (%7.94), AB (%3.97) ve BB (%88.10) 3 genotip ve A (0.10) ve B (0.90) 2 allel ve Msp I RE’nde (Exon 3) ise sadece AA genotipi ve A alleli tespit edilmiştir. IGFBP-3 geninde Msp I enzimi monomorfik (P>0.05), Hae III enzimi polimorfik fakat önemsiz (P>0.05) bulunurken Taq 1 enzimi yönünden hem polimorfik hem de önemlilik tespit edilmiştir (P<0.001). IGFBP-3 gen bölgelerinin polimorfizmleri Anadolu mandalarında ilk kez araştırılmıştır. Ayrıca IGFBP-3 geninde diğer manda ırklarında yapılan çalışmalardan farklı olarak ilk kez üç yeni genotip (Taq I enzim kesimi sonucunda iki, Hae III enzim kesimi sonucunda bir) tespit edilmiştir. Ayrıca Taq I enzim işlemi sonucu yeni tespit edilen B allelinin frekansı diğer alleline göre çok yüksek bulunmuştur.

Project Number

V-051

References

  • Ali BA, El-Hanafy AA, Salem HH, 2009: Genetic biodiversity studies on IGFBP-3 gene in Egyptian sheep breeds. Biotechnol Anim Husb, 25 (1-2), 101-109.
  • Choudhary V, Kumar P, Bhattacharya TK, Bhushan B, Sharma A, Shukla A, 2007: DNA polymorphism of insulin-like growth factor-binding protein-3 gene and its association with birth weight and body weight in cattle. J Anim Breed Genet, 124, 29-34.
  • Don RH, Cox PT, Wainwright BJ, Baker K, Mattick JS, 1991: ‘Touchdown’ PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res, 19, 4008.
  • EL-Hanafy AA, Salem HH, 2009: PCR-RFLP of IGFBP3 gene in some Egyptian sheep breeds. American-Eurasian J Agric & Environ Sci, 5 (1), 82-85.
  • Fadhıl M, Aytekin İ, Zülkadir U, 2020: Polymorphism in Anatolian Black and Holstein Friesian cattle breeds. Selcuk J Agr Food Sci, 34 (2), 137-140.
  • FAO, 2005: Buffalo Production and Research. Edited by Antonio Borghese. REU technical Series 67. ftp://ftp.fao.org/docrep/fao/010/ah847e/ah847e.pdf. Accessed 16 July 2019.
  • FAO, 2015: The Second Report on the State of the World’s Animal Genetic Resources for Food and Agriculture, edited by B.D. Scherf and D. Pilling. FAO Commission on Genetic Resources for Food and Agriculture Assessments. Rome. http://www.fao.org/3/a-i4787e/index.html. Accessed 16 July 2019.
  • Hays J, 2014: Water Buffaloes. Facts and details, Asian and Asians-International and Economic Issues http://factsanddetails.com/asian/cat62/sub408/entry-2830.html. Accessed 16 March 2019.
  • GDAR, 2011: Domestic animal genetics resources in Turkey. Republic of Turkey, Ministry of Food Agriculture and Livestock, General Directorate of Agricultural Research and Policy, Ankara, Türkiye.
  • Kumar P, Choudhary V, Padma B, Shukla A, Misra A, Bhattacharya TK, Bhushan B, Sharma A, 2004: Buffalo Insulin-like growth factor binding protein-3 (IGFBP-3) gene polymorphism and its comparison with cattle. Buffalo J, 2, 183-192.
  • Kumar P, Choudhary V, Kumar KG, Bhattacharya TK, Bhushan B, Sharma A, Mishra A, 2006: Nucleotide sequencing and DNA polymorphism studies on IGFBP-3 gene in sheep and its comparison with cattle and buffalo. Small Rum Res, 64, 285-292.
  • Lan XY, Pan CY, Chen H, Lei CZ, Liu SQ, Zhang YB, Min LJ, Yu J, Li JY, Zhao M, Hu SR, 2007: The HaeIII and XspI PCR-RFLPs detecting polymorphisms at the goat IGFBP-3 locus. Small Rum Res, 73, 283-286.
  • Lan XY, Pan CY, Zhang CL, Hu SR, Liu SQ, Zhang YB, Lei CZ, Chen H, 2009: Relationships between polymorphisms of IGFBP-3 gene and Cashmere traits in Cashmere goats. J App Anim Res, 35 (1), 29-32.
  • Maciulla JH, Zhang HM. DeNise SK, 1997: A novel polymorphism in the bovine insulin-like growth factor binding protein-3 (IGPBP3) gene. Anim Genet, 28, 375.
  • Michelizzi VN, Dodson MV, Pan Z, Amaral MEJ, Michal JJ, McLean DJ, Womack JE, Jiang Z, 2010: Water buffalo genome science comes of age. Int J Biol Sci, 6 (4), 333-349.
  • Othman OE, Alam SS, El-Aziem SHA, 2014: Single nucleotide polymorphism in Egyptian cattle insulin-like growth factor binding protein-3 gene. JGEB, 12, 143-147.
  • Othman OE, Abou-Eisha A, El-Din AE, 2018: Study on genetic polymorphism of IGFBP-3 gene in Egyptian buffalo. ARRB, 29 (3), 1-7.
  • Padma B, Kumar P, Choudhary V, Dhara SK, Mishra A, Bhattachary TK, Bhushan B, Sharma A, 2004: Nucleotide sequencing and PCR-RFLP of Insulin-like Growth Factor Binding Protein-3 gene in riverine buffalo (Bubalus bubalis). Asian Austral J Anim, 17, 910-913.
  • Ramesha KP, Rao A, Basavaraju M, Geetha GR, Kataktalware MA, Jeyakumar S, 2015: Genetic variability of bovine GHR, IGF-1 and IGFBP-3 genes in Indian cattle and buffalo. S Afr J Anim Sci, 45 (5), 485-493.
  • Rehman MS, Mushtaq M, Hassan F, Rehman Z, Mushahid M, Shokrollahi B, 2022: Comparative genomic characterization of insulin-like growth factor binding proteins in cattle and buffalo. BioMed Res Int, 2022, 5893825.
  • Saleh AA, Rashad AMA, Hassanine NNAM, Sharaby MA, Zhao Y, 2019: Comparative analysis of IGFBP-3 gene sequence in Egyptian sheep, cattle, and buffalo. BMC Res Notes, 12, 623.
  • Saleh AA, Hammouf MH, Dabour NA, Hafez EEE, Sharaby MA, 2022: Genetic variability in GH and IGFBP-3 genes and their association with growth performance in Egyptian sheep. Appl Vet Res, 1(3): e2022012.
  • Sambrook J, Fritsch EF, Maniatis T, 1989: Molecular cloning: A laboratory manual. 2nd ed., Cold Spring Harbor Laboratory Pres. Cold Spring Harbor.
  • Shimasaki S, Ling N, 1991: Identification and molecular characterization of insulin-like growth factor binding proteins (IGFBP-1, -2, -3, -4, -5 and -6). Progress in Growth Factor Research, 3, 243-266.
  • TurkStat, 2022a: Animal Production Statistics, December 2021. In: TurkStat News Bulletin. Number: 45593, Data:09.02.2022. https://data.tuik.gov.tr/Bulten/Index?p=Hayvansal-Uretim-Istatistikleri-Aralik-2021-45593. Accessed 01 May 2022.
  • TurkStat, 2022b: Red Meat Production Statistics, 2020-2021. TurkStat News Bulletin. Number: 45671, Data: 06.05.2022. https://data.tuik.gov.tr/Bulten/Index?p=Kirmizi-Et-Uretim-Istatistikleri-2020-2021-45671. Accessed 01 Jun 2022.
There are 26 citations in total.

Details

Primary Language English
Subjects Veterinary Surgery, Animal Science, Genetics and Biostatistics
Journal Section Research
Authors

Yusuf Özşensoy 0000-0002-2605-2410

İnanc Baral 0000-0001-7272-3724

Project Number V-051
Early Pub Date June 22, 2023
Publication Date June 22, 2023
Submission Date January 31, 2023
Acceptance Date April 4, 2023
Published in Issue Year 2023 Volume: 12 Issue: 1

Cite

APA Özşensoy, Y., & Baral, İ. (2023). Three Previously Unseen Genotypes Detected in IGFBP - 3 Gene in Buffalo Breed. Harran Üniversitesi Veteriner Fakültesi Dergisi, 12(1), 35-40. https://doi.org/10.31196/huvfd.1245427
AMA Özşensoy Y, Baral İ. Three Previously Unseen Genotypes Detected in IGFBP - 3 Gene in Buffalo Breed. Harran Univ Vet Fak Derg. June 2023;12(1):35-40. doi:10.31196/huvfd.1245427
Chicago Özşensoy, Yusuf, and İnanc Baral. “Three Previously Unseen Genotypes Detected in IGFBP - 3 Gene in Buffalo Breed”. Harran Üniversitesi Veteriner Fakültesi Dergisi 12, no. 1 (June 2023): 35-40. https://doi.org/10.31196/huvfd.1245427.
EndNote Özşensoy Y, Baral İ (June 1, 2023) Three Previously Unseen Genotypes Detected in IGFBP - 3 Gene in Buffalo Breed. Harran Üniversitesi Veteriner Fakültesi Dergisi 12 1 35–40.
IEEE Y. Özşensoy and İ. Baral, “Three Previously Unseen Genotypes Detected in IGFBP - 3 Gene in Buffalo Breed”, Harran Univ Vet Fak Derg, vol. 12, no. 1, pp. 35–40, 2023, doi: 10.31196/huvfd.1245427.
ISNAD Özşensoy, Yusuf - Baral, İnanc. “Three Previously Unseen Genotypes Detected in IGFBP - 3 Gene in Buffalo Breed”. Harran Üniversitesi Veteriner Fakültesi Dergisi 12/1 (June 2023), 35-40. https://doi.org/10.31196/huvfd.1245427.
JAMA Özşensoy Y, Baral İ. Three Previously Unseen Genotypes Detected in IGFBP - 3 Gene in Buffalo Breed. Harran Univ Vet Fak Derg. 2023;12:35–40.
MLA Özşensoy, Yusuf and İnanc Baral. “Three Previously Unseen Genotypes Detected in IGFBP - 3 Gene in Buffalo Breed”. Harran Üniversitesi Veteriner Fakültesi Dergisi, vol. 12, no. 1, 2023, pp. 35-40, doi:10.31196/huvfd.1245427.
Vancouver Özşensoy Y, Baral İ. Three Previously Unseen Genotypes Detected in IGFBP - 3 Gene in Buffalo Breed. Harran Univ Vet Fak Derg. 2023;12(1):35-40.