Comparing Autosomal SSR and PCR-RFLP Markers to Determine Phylogenetic Relationship Based on Genetic Distances in Livestock

Year 2020, Volume: 61 Issue: 2 , 135 - 141 , 29.12.2020

Taki Karslı , Eymen Demir , Bahar Argun Karslı , Hüseyin Göktuğ Fidan , Murat Balcıoğlu

https://doi.org/10.29185/hayuretim.709504

Cited By: 1

https://izlik.org/JA45PM25JU

Abstract

Objective: Many molecular tools are available to analyse phylogenetic relationships in livestock. Nowadays, Simple Sequence Repeats and Single Nucleotide Polymorphisms are commonly used molecular techniques to determine phylogenetic relationships in livestock breeds or types. However, alternative molecular techniques may be preferred to conduct phylogenetic analysis in case of limiting conditions such as budget and time. In this context, in the present study, Simple Sequence Repeats and Polymerase Chain Reaction- Restriction Fragment Length Polymorphism techniques were compared to reveal phylogenetic relationship based on genetic distances.

Material and Methods: In this study, 11 different layer pure chicken lines represented by 30 individuals for each line were genotyped based on 11 Polymerase Chain Reaction- Restriction Fragment Length Polymorphism and 17 Simple Sequence Repeats loci to analyse phylogenetic relationship.

Results: Both techniques showed almost similar results in terms of Unweighted Pair Group Method with Arithmetic Mean dendrogram created based on genetic distances. White and brown chicken lines were separated by both Polymerase Chain Reaction- Restriction Fragment Length Polymorphism and Simple Sequence Repeats techniques in harmony with their genetic origins and breeding history.

Conclusion: It is suggested that Polymerase Chain Reaction- Restriction Fragment Length Polymorphism technique may be preferred to analyse phylogenetic relationship based on genetic distance, when the budget, time and laboratory infrastructure are limited. 

Keywords

Farm animals , UPGMA dendrogram , molecular markers

Supporting Institution

The Scientific Research Projects Coordination Unit of Akdeniz University

Project Number

2013.03.0121.001; FBA-2015-756 and FYL-2017-2912

Thanks

The data of the present study were obtained from different projects supported by the Scientific Research Projects Coordination Unit of Akdeniz University (Project Number: 2013.03.0121.001; FBA-2015-756 and FYL-2017-2912). The authors grateful to the Scientific Research Projects Coordination Unit of Akdeniz University for financial support and to Ankara Poultry Research Institute for blood samples.

Çiftlik Hayvanlarında Genetik Mesafe Temelli Filogenetik İlişkinin Belirlenmesinde Otozomal SSR ve PCR-RFLP Markerlerinin Karşılaştırılması

https://izlik.org/JA45PM25JU

Abstract

Amaç: Çiftlik hayvanlarında filogenetik ilişkinin analizi için çok sayıda moleküler araç nmaktadır. Günümüzde çiftlik hayvanı ırk ve tiplerinde filogenetik ilişkinin belirlenmesinde Basit Dizi Tekrarları ve Tek Nükleotid Polimorfizmleri en yaygın kullanılan moleküler tekniklerdir. Bununla birlikte, bütçe ve zaman gibi sınırlayıcı koşullarda filogenetik analiz yapabilmek için alternatif moleküler teknikler tercih edilebilir. Bu bağlamda, mevcut çalışmada genetik mesafe temelli filogenetik ilişkinin ortaya çıkarılmasında Basit Dizi Tekrarları ve Polimeraz Zincir ReaksiyonuRestriksiyon Parça Uzunluk Polimorfizmi teknikleri karşılaştırılmıştır.

Materyal ve Metot: Bu çalışmada filogenetik ilişki analizi için 11 farklı yumurtacı saf hattın her birinden 30’ar birey 11 PCR-RFLP ve 17 SSR lokus temelinde genotiplendirilmiştir.

Bulgular: Genetik mesafe temelinde oluşturulan UPGMA dendogramı bakımından her iki teknik benzer sonuçlar göstermiştir. Hem Polimeraz Zincir ReaksiyonuRestriksiyon Parça Uzunluk Polimorfizmi hem de Basit Dizi Tekrarları tekniği ile beyaz ve kahverengi yumurtacı hatlar genetik köken ve yetiştirilme geçmişlerine uygun olarak ayrılmıştır.

Sonuç: Bütçe, zaman ve laboratuvar alt yapısı kısıtlı olduğunda, genetik mesafe temelli filogenetik ilişkinin incelenmesinde Polimeraz Zincir Reaksiyonu- Restriksiyon Parça Uzunluk Polimorfizmi tekniğinin kullanılabileceği önerilmektedir.

Keywords

Çiftlik hayvanları , UPGMA dendogramı , moleküler markerler , filogeni

Project Number

2013.03.0121.001; FBA-2015-756 and FYL-2017-2912

References

• Al-Araimi NA, Gaafar OM, Costa V, Neira AL, Al-Atiyat RM, Beja-Pereira A. 2017. Genetic origin of goat populations in Oman revealed by mitochondrial DNA analysis. Plos One 12(12): e0190235.
• Anila H, Paolo AM, Gentian H, Consortıum E. 2010. Genetic diversity in albanian sheep breeds estimated by AFLP markers. Albanian Journal of Agricultural Sciences 9(2): 23-29.
• Balcıoğlu MS, Șahin E, Karabağ K, Karslı T, Alkan S. 2010. Determination of DNA fingerprinting of Turkish fat-tailed sheep breeds by RAPD-PCR method. Tarim Bilimleri Dergisi 16(1): 55-61.
• Elmacı C, Öner Y, Koyuncu M. Saanen Keçilerinde b-laktoglobulin Genotiplerinin PCR-RFLP Yöntemi ile Belirlenmesi. Hayvansal Üretim 49(1): 1-4.
• FAO. 2007. The state of the world's animal genetic resources for food and agriculture – in brief, edited by Dafydd Pilling & Barbara Rischkowsky. Rome.
• Ganbold O, Lee SH, Seo D, Paek WK, Manjula P, Munkhbayar M, Lee JH. 2019. Genetic diversity and the origin of Mongolian native sheep. Livestock science 220: 17-25.
• Göğer H, Demirtaş ŞE, Yurtoğullari Ş, Taşdemir AN, Şenkal UE, Boyali B. 2017. Breeding studies on pure lines at Poultry Research Institute. Tavukçuluk Araştırma Dergisi 14 (2): 30-38.
• Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S, Consortium TG. 2010. Genetic diversity in farm animals–a review. Animal genetics 4(1): 6-31.
• Hailu A, Getu A. 2015. Breed characterization: Tools and their applications. Open Access Library Journal 2(4): e1438 Kanginakudru S, Metta M, Jakati RD, Nagaraju J. 2008. Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken. BMC Evolution Biology 8(174): 1-14.
• Karslı T, Balcıoğlu MS, Demir E, Fidan HG, Aslan M, Aktan S, Kamanlı S, Karabağ K, Şahin E. 2017. Determination of polymorphisms in IGF-I and NPY candidate genes associated with egg yield in pure layers chicken lines reared in the Ankara Poultry Research Institute. Turkish Journal of Agriculture-Food Science and Technology 5(9): 1051-1056.
• Karslı T, Balcıoğlu MS. 2019. Genetic characterization and population structure of six brown layer pure lines using microsatellite markers. Asian-Australasian Journal of Animal Sciences 32(1): 49-57.
• Karslı T, Fidan HG. 2019. Assessment of genetic diversity and conservation priorities among five White Leghorn Lines based on SSR markers. Animal Science Papers & Reports, 37(3): 311-322.
• Liu YP, Wu GS, Yao YG, Miao YW, Luikart G, Baig M, Beja-Pereira A, Ding Z, Palanichamy MG, Zang Y. 2006. Multiple maternal origins of chickens: out of the Asian jungles. Molecular Phylogenetics and Evolution 38(1): 12–19.
• Meydan H, Jang CP, Yıldız MA, Weigend S. 2016. Maternal origin of Turkish and Iranian native chickens inferred from mitochondrial DNA D-loop sequences. Asian-Australasian Journal of Animal Sciences 29(11):1547-1554.
• Nagaraju J, Reddy KD, Nagaraja GM, Sethuraman BN. 2001. Comparison of multilocus RFLPs and PCR-based marker systems for genetic analysis of the silkworm, Bombyx mori. Heredity 86(5): 588-597.
• Seo DW, Hoque MR, Choi NR, Sultana H, Park HB, Heo KN, Kang BS, Lim HT, Lee SH, Lee JH. 2013. Discrimination of Korean native chicken lines using fifteen selected microsatellite markers. Asian-Australasian Journal of Animal Sciences 26(3): 316-322.
• Tamura K, Stecher G, Peterson D, Stecher G, Filipski A, Kumar S. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30(12): 2725-2729.
• Touma S, Shimabukuro H, Arakawa A, Oikawa T. 2019. Maternal lineage of Okinawa indigenous Agu pig inferred from mitochondrial DNA control region. Asian-Australasian Journal of Animal Sciences 32(4): 501-507.
• Vergara AMC, Landi V, Bermejo JVD, Martínez A, Acosta PC, Barro AP, Bigi D, Sponenberg P, Helal M, Banabazi MH, Vallejo MEC. 2019. Tracing worldwide turkey genetic diversity using D-loop sequence mitochondrial DNA analysis. Animals 9(897): 1-12.
• Xia X, Huang G, Wang Z, Sun J, Wu Z, Chen N, Lei C, Hanif Q. 2020. Mitogenome diversity and maternal origins of Guangxi cattle breeds. Animals 10(1): 1-19.
• Yeh FC, Yang RC, Boyle TBJ, Ye ZH, Mao JX. 1997. POPGENE, the user friendly shareware for population genetic analysis. Molecular Biology and Biotechnology Center. University of Alberta, Edmonton.
• Zeder MA. 2008. Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact. Proceedings of the national Academy of Sciences 105(33): 11597-11604.
• Zhu YB, Basang WD, Pingcuo ZD, Cidan YJ, Luo S, Luosang DZ, Dawa YL. 2019. Genetic diversity and population structure of seven Tibet Yak ecotype populations using microsatellite markers. Pakistan Journal of Zoology 51(5): 1979-1982.