Araştırma Makalesi
Bazı Türkiye yerli koyun populasyonlarında HSP90AA1 gen bölgesindeki polimorfizlerin AS-PZR ile belirlenmesi
Öz
Isı şok proteinleri (HSPs) canlı hücreleri aşırı ortam sıcaklıklarının olumsuz etkilerinden koruyan moleküler şaperonlardır. Bu çalışmada, İvesi (IVS), Güney Karaman (GKR) ve Karakaş (KRK) olarak bilinen üç farklı Türkiye yerli koyun populasyonunda HSP90AA1 genindeki genetik polimorfizmler Allel-Spesifik Polimeraz Zincir Reaksiyonu (AS-PZR) yöntemiyle incelenmiştir. İki allel (C ve G) ve üç genotipin (CC, CG ve GG) belirlendiği çalışmada, HSP90AA1 geni bütün populasyonlarda polimorfizm göstermiştir. Bütün populasyonlarda G allel frekansı C allel frekansından yüksek bulunmuştur. En düşük (0.100) ve en yüksek (0.246) CC frekansı sırasıyla KRK ve IVS populasyonlarında belirlenirken, GG genotip frekansı 0.250 (GKR) ile 0.600 (KRK) aralığında değişmiştir. IVS ırkında HSP90AA1 geni bakımından Hardy-Weinberg dengesinden (HWE) olan sapma önemli (p<0.001) bulunmuştur. Genetik mesafe temelli filogenetik ağaç, HSP90AA1 polimorfizmi bakımından GKR populasyonunun IVS ve KRK populasyonlarından genetik olarak farklı olduğunu ortaya koymuştur. Gelecekte küresel ısınma ve iklim değişikliğinin olumsuz etkileri daha da tehlikeli olacağından HSP90AA1 genindeki bu varyasyonların korunması gerekmektedir. Ayrıca, bu genetik varyasyonlar çiftçilerin Türkiye yerli koyun populasyonlarında ısı stresine karşı yapılacakları kapsamlı seleksiyon çalışmalarında kullanılabilecektir.
Anahtar Kelimeler
Kaynakça
- Ameur, A.A., Yılmaz, O., Nezih, A., Cemal, I., & Gaouar, S.B.S. (2020). Assessment of genetic diversity of Turkish and Algerian native sheep breeds. Acta Agriculturae Slovenica, 115, 5-14.
- Biçer, O., Keskin, M., Gül, S., Gündüz, Z., Oflaz, N.Z., & Behrem, S. (2019). Comparison of yield characteristics of brown and black headed Awassi sheep. Mustafa Kemal University Journal of Agricultural Sciences, 24, 58-61.
- Çelikeloğlu, K., Erdoğan, M., Hacan, Ö., Koçak, S., Bozkurt, Z., & Tekerli, M. (2018). Investigation of possible polymorphisms in BMPR1B, BMP15 and GDF9 genes in Pırlak sheep. Kocatepe Veterinary Journal, 11, 356-362. https://doi.org/10.30607/kvj.428999
- Demir, E., Bilginer, U., Balcioglu, M.S., & Karsli, T. (2021). Direct and indirect contributions of molecular genetics to farm animal welfare: A review. Animal Health Research Reviews, 22, 177-186. https://doi.org/10.1017/S1466252321000104
- Demir, E., Ceccobelli, S., Bilginer, U., Pasquini, M., Attard, G., & Karsli, T. (2022). Conservation and selection of genes related to environmental adaptation in native small ruminant breeds: A review. Ruminants, 2, 255-270. https://doi.org/10.3390/ruminants2020017
- Karsli, B.A., Demir, E., Fidan, H.G., & Karsli, T. (2020). Assessment of genetic diversity and differentiation among four indigenous Turkish sheep breeds using microsatellites. Archives Animal Breeding, 63, 165-172. https://doi.org/10.5194/aab-63-165-2020
- Koyun, H., Kiraz, S., Karaca, S., Koncagül, S., Yılmaz, A., Karakuş, K., Yeşilova, A.B., & Aygün, T. (2021). Single nucleotide polymorphisms of GDF9 gene/exon 2 region and their associations with milk yield and milk content traits in Karakaş and Norduz sheep breeds. Turkish Journal of Veterinary & Animal Sciences, 45, 881-889. https://doi.org/10.3906/vet-2010-26
- Kirikci, K., Cam, M.A., & Mercan, L. (2020). Genetic diversity and relationship among indigenous Turkish Karayaka sheep subpopulations. Archives Animal Breeding, 63, 269-275. https://doi.org/10.5194/aab-63-269-2020
- Kumar, R., Gupta, I.D., Verma, A., Singh, S.V., Verma, N., Vineeth, M.R., Magotra, A., & Das, R. (2016). Novel SNP identification in exon 3 of HSP90AA1 gene and their association with heat tolerance traits in Karan Fries (Bos taurus× Bos indicus) cows under tropical climatic condition. Tropical Animal Health and Production, 48, 735-740. https://doi.org/10.1007/s11250-016-1016-7
- Kumar, S., Nei, M., Dudley, J., & Tamura, K. (2008). MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics, 9, 299-306. https://doi.org/10.1093/bib/bbn017
- Marcos-Carcavilla, A., Mutikainen, M., González, C., Calvo, J.H., Kantanen, J., Sanz, A., Marzanov, N.S., Pérez-Guzmán, M.D., & Serrano, M. (2010). A SNP in the HSP90AA1 gene 5′ flanking region is associated with the adaptation to differential thermal conditions in the ovine species. Cell Stress and Chaperones, 15, 67-81. https://doi.org/10.1007/s12192-009-0123-z
- Miller, S., Dykes, D., & Polesky, H. (1988). A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Research, 16, 1215-1215.
- Nei, M. (1972). Genetic distance between populations. The American Naturalist, 106 (949), 283-292. https://doi.org/10.1086/282771
- Oner, Y., Calvo, J.H., Serrano, M., & Elmaci, C. (2012). Polymorphisms at the 5′ flanking region of the HSP90AA1 gene in native Turkish sheep breeds. Livestock Science, 150, 381-385. https://doi.org/10.1016/j.livsci.2012.07.028
- Ozmen, O., Kul, S., & Gok, T. (2020). Determination of genetic diversity of the Akkaraman sheep breed from Turkey. Small Ruminant Research, 182, 37-45. https://doi.org/10.1016/j.smallrumres.2019.10.009
- Papadopoulou, A., Ragkos, A., Theodoridis, A., Skordos, D., Parissi, Z., & Abraham, E. (2020). Evaluation of the contribution of pastures on the economic sustainability of small ruminant farms in a typical Greek area. Agronomy, 11, 1-16. https://doi.org/10.3390/agronomy11010063
- Peakall, R., & Smouse, P.E. (2012). GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformics, 6, 2537-2539.
- Perini, F., Cendron, F., Rovelli, G., Castellini, C., Cassandro, M., & Lasagna, E. (2020). Emerging genetic tools to investigate molecular pathways related to heat stress in chickens: A review. Animals, 11, 1-19. https://doi.org/10.3390/ani11010046
- Pinotti, L., Manoni, M., Ferrari, L., Tretola, M., Cazzola, R., & Givens, I. (2021). The contribution of dietary magnesium in farm animals and human nutrition. Nutrients, 13, 1-15. https://doi.org/10.3390/nu13020509
- Rovelli, G., Ceccobelli, S., Perini, F., Demir, E., Mastrangelo, S., Conte, G., Abeni, F., Marletta, D., Ciampolini, R., Cassandro, M., Bernabucci, U., & Lasagna, E. (2020). The genetics of phenotypic plasticity in livestock in the era of climate change: A review. Italian Journal of Animal Science, 19, 997-1014. https://doi.org/10.1080/1828051X.2020.1809540
- Salces-Ortiz, J., González, C., Martínez, M., Mayoral, T., Calvo, J.H., & Serrano, M. M. (2015). Looking for adaptive footprints in the HSP90AA1 ovine gene. BMC Evolutionary Biology, 15, 1-24. https://doi.org/10.1186/s12862-015-0280-x
- Sejian, V., Bhatta, R., Gaughan, J.B., Dunshea, F.R., & Lacetera, N. (2018). Adaptation of animals to heat stress. Animal, 12, 431-444. https://doi.org/10.1017/S1751731118001945
- Singh, K.M., Singh, S., Ganguly, I., Nachiappan, R.K., Ganguly, A., Venkataramanan, R., Chopra, A., & Narula, H.K. (2017). Association of heat stress protein 90 and 70 gene polymorphism with adaptability traits in Indian sheep (Ovis aries). Cell Stress and Chaperones, 22, 675-684. https://doi.org/10.1007/s12192-017-0770-4
- Taşkın, T., & Kandemir, Ç. (2022). Current situation and future of sheep breeds: Aegean region. Journal of Agriculture Faculty of Ege University, 59, 485-498. https://doi.org/10.20289/zfdergi.1058959
- Yeh, F.C., Yang, R.C., Boyle, T.J., Ye, Z., Xiyan, J.M., & Yang, R. (2000). POPGENE 32, Microsoft Windows-based freeware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton.
- Yilmaz, O., Cemal, I., & Karaca, O. (2014). Genetic diversity in nine native Turkish sheep breeds based on microsatellite analysis. Animal Genetics, 45, 604-608. https://doi.org/10.1111/age.12173
- Yurdagül, K.G., Atay, S., Bilginer, Ü., Karslı, T., & Demir, E. (2023). Genetic variations in HSP90AA1 gene region in Pirlak sheep breed. Journal of Animal Production, 64 (1): 12-16. https://doi.org/10.29185/hayuretim.1268591
Determination of polymorphisms in the HSP90AA1 gene region in some Turkish sheep populations by AS-PCR
Öz
Heat shock proteins (HSPs) are molecular chaperones protecting living cells from the negative effects of extreme ambient temperatures. In this study, genetic polymorphisms of the HSP90AA1 gene were monitored via Allele-Specific Polymerase Chain Reaction (AS-PCR) in three native Turkish sheep populations namely İvesi (IVS), Güney Karaman (GKR), and Karakaş (KRK). The HSP90AA1 was polymorphic in all populations yielding two alleles (C and G) and three genotypes (CC, CG, and GG). The G allele frequency was higher than the C allele frequency in all populations. The lowest (0.100) and highest (0.246) CC frequency was observed in KRK and IVS, respectively, while the GG genotype frequency varied between 0.250 (GKR) and 0.600 (KRK). Significant deviation (p<0.001) from Hardy-Weinberg Equilibrium (HWE) was detected in the IVS breed in terms of the HSP90AA1 gene. The genetic distance-based phylogenetic tree indicated that GKR was genetically different from IVS and KRK populations in terms of the HSP90AA1 polymorphism. These variations regarding the HSP90AA1 gene should be conserved, since the negative effects of global warming and climate change are expected to be more hazardous in the future. Besides, these genetic variations may be utilized by the farmers to design comprehensive selection strategies against heat stress in native Turkish sheep populations.
Anahtar Kelimeler
Kaynakça
- Ameur, A.A., Yılmaz, O., Nezih, A., Cemal, I., & Gaouar, S.B.S. (2020). Assessment of genetic diversity of Turkish and Algerian native sheep breeds. Acta Agriculturae Slovenica, 115, 5-14.
- Biçer, O., Keskin, M., Gül, S., Gündüz, Z., Oflaz, N.Z., & Behrem, S. (2019). Comparison of yield characteristics of brown and black headed Awassi sheep. Mustafa Kemal University Journal of Agricultural Sciences, 24, 58-61.
- Çelikeloğlu, K., Erdoğan, M., Hacan, Ö., Koçak, S., Bozkurt, Z., & Tekerli, M. (2018). Investigation of possible polymorphisms in BMPR1B, BMP15 and GDF9 genes in Pırlak sheep. Kocatepe Veterinary Journal, 11, 356-362. https://doi.org/10.30607/kvj.428999
- Demir, E., Bilginer, U., Balcioglu, M.S., & Karsli, T. (2021). Direct and indirect contributions of molecular genetics to farm animal welfare: A review. Animal Health Research Reviews, 22, 177-186. https://doi.org/10.1017/S1466252321000104
- Demir, E., Ceccobelli, S., Bilginer, U., Pasquini, M., Attard, G., & Karsli, T. (2022). Conservation and selection of genes related to environmental adaptation in native small ruminant breeds: A review. Ruminants, 2, 255-270. https://doi.org/10.3390/ruminants2020017
- Karsli, B.A., Demir, E., Fidan, H.G., & Karsli, T. (2020). Assessment of genetic diversity and differentiation among four indigenous Turkish sheep breeds using microsatellites. Archives Animal Breeding, 63, 165-172. https://doi.org/10.5194/aab-63-165-2020
- Koyun, H., Kiraz, S., Karaca, S., Koncagül, S., Yılmaz, A., Karakuş, K., Yeşilova, A.B., & Aygün, T. (2021). Single nucleotide polymorphisms of GDF9 gene/exon 2 region and their associations with milk yield and milk content traits in Karakaş and Norduz sheep breeds. Turkish Journal of Veterinary & Animal Sciences, 45, 881-889. https://doi.org/10.3906/vet-2010-26
- Kirikci, K., Cam, M.A., & Mercan, L. (2020). Genetic diversity and relationship among indigenous Turkish Karayaka sheep subpopulations. Archives Animal Breeding, 63, 269-275. https://doi.org/10.5194/aab-63-269-2020
- Kumar, R., Gupta, I.D., Verma, A., Singh, S.V., Verma, N., Vineeth, M.R., Magotra, A., & Das, R. (2016). Novel SNP identification in exon 3 of HSP90AA1 gene and their association with heat tolerance traits in Karan Fries (Bos taurus× Bos indicus) cows under tropical climatic condition. Tropical Animal Health and Production, 48, 735-740. https://doi.org/10.1007/s11250-016-1016-7
- Kumar, S., Nei, M., Dudley, J., & Tamura, K. (2008). MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics, 9, 299-306. https://doi.org/10.1093/bib/bbn017
- Marcos-Carcavilla, A., Mutikainen, M., González, C., Calvo, J.H., Kantanen, J., Sanz, A., Marzanov, N.S., Pérez-Guzmán, M.D., & Serrano, M. (2010). A SNP in the HSP90AA1 gene 5′ flanking region is associated with the adaptation to differential thermal conditions in the ovine species. Cell Stress and Chaperones, 15, 67-81. https://doi.org/10.1007/s12192-009-0123-z
- Miller, S., Dykes, D., & Polesky, H. (1988). A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Research, 16, 1215-1215.
- Nei, M. (1972). Genetic distance between populations. The American Naturalist, 106 (949), 283-292. https://doi.org/10.1086/282771
- Oner, Y., Calvo, J.H., Serrano, M., & Elmaci, C. (2012). Polymorphisms at the 5′ flanking region of the HSP90AA1 gene in native Turkish sheep breeds. Livestock Science, 150, 381-385. https://doi.org/10.1016/j.livsci.2012.07.028
- Ozmen, O., Kul, S., & Gok, T. (2020). Determination of genetic diversity of the Akkaraman sheep breed from Turkey. Small Ruminant Research, 182, 37-45. https://doi.org/10.1016/j.smallrumres.2019.10.009
- Papadopoulou, A., Ragkos, A., Theodoridis, A., Skordos, D., Parissi, Z., & Abraham, E. (2020). Evaluation of the contribution of pastures on the economic sustainability of small ruminant farms in a typical Greek area. Agronomy, 11, 1-16. https://doi.org/10.3390/agronomy11010063
- Peakall, R., & Smouse, P.E. (2012). GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformics, 6, 2537-2539.
- Perini, F., Cendron, F., Rovelli, G., Castellini, C., Cassandro, M., & Lasagna, E. (2020). Emerging genetic tools to investigate molecular pathways related to heat stress in chickens: A review. Animals, 11, 1-19. https://doi.org/10.3390/ani11010046
- Pinotti, L., Manoni, M., Ferrari, L., Tretola, M., Cazzola, R., & Givens, I. (2021). The contribution of dietary magnesium in farm animals and human nutrition. Nutrients, 13, 1-15. https://doi.org/10.3390/nu13020509
- Rovelli, G., Ceccobelli, S., Perini, F., Demir, E., Mastrangelo, S., Conte, G., Abeni, F., Marletta, D., Ciampolini, R., Cassandro, M., Bernabucci, U., & Lasagna, E. (2020). The genetics of phenotypic plasticity in livestock in the era of climate change: A review. Italian Journal of Animal Science, 19, 997-1014. https://doi.org/10.1080/1828051X.2020.1809540
- Salces-Ortiz, J., González, C., Martínez, M., Mayoral, T., Calvo, J.H., & Serrano, M. M. (2015). Looking for adaptive footprints in the HSP90AA1 ovine gene. BMC Evolutionary Biology, 15, 1-24. https://doi.org/10.1186/s12862-015-0280-x
- Sejian, V., Bhatta, R., Gaughan, J.B., Dunshea, F.R., & Lacetera, N. (2018). Adaptation of animals to heat stress. Animal, 12, 431-444. https://doi.org/10.1017/S1751731118001945
- Singh, K.M., Singh, S., Ganguly, I., Nachiappan, R.K., Ganguly, A., Venkataramanan, R., Chopra, A., & Narula, H.K. (2017). Association of heat stress protein 90 and 70 gene polymorphism with adaptability traits in Indian sheep (Ovis aries). Cell Stress and Chaperones, 22, 675-684. https://doi.org/10.1007/s12192-017-0770-4
- Taşkın, T., & Kandemir, Ç. (2022). Current situation and future of sheep breeds: Aegean region. Journal of Agriculture Faculty of Ege University, 59, 485-498. https://doi.org/10.20289/zfdergi.1058959
- Yeh, F.C., Yang, R.C., Boyle, T.J., Ye, Z., Xiyan, J.M., & Yang, R. (2000). POPGENE 32, Microsoft Windows-based freeware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton.
- Yilmaz, O., Cemal, I., & Karaca, O. (2014). Genetic diversity in nine native Turkish sheep breeds based on microsatellite analysis. Animal Genetics, 45, 604-608. https://doi.org/10.1111/age.12173
- Yurdagül, K.G., Atay, S., Bilginer, Ü., Karslı, T., & Demir, E. (2023). Genetic variations in HSP90AA1 gene region in Pirlak sheep breed. Journal of Animal Production, 64 (1): 12-16. https://doi.org/10.29185/hayuretim.1268591
Toplam 27 adet kaynakça vardır.
Ayrıntılar
| Birincil Dil | İngilizce |
|---|---|
| Konular | Hayvansal Üretim (Diğer) |
| Bölüm | Araştırma Makalesi |
| Yazarlar | |
| Erken Görünüm Tarihi | 14 Mart 2024 |
| Yayımlanma Tarihi | 8 Nisan 2024 |
| Gönderilme Tarihi | 28 Ağustos 2023 |
| Kabul Tarihi | 18 Ekim 2023 |
| Yayımlandığı Sayı | Yıl 2024 Cilt: 29 Sayı: 1 |
