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

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

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

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