Bioinformatic analyses in microsatellite-based genetic diversity of Turkish sheep breeds

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2010

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Acar, Hande

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In the present study, within and among breed genetic diversity in thirteen Turkish sheep breeds (Sakız, Karagül, Hemşin, Çine Çaparı, Norduz, Herik, Akkaraman, Dağlıç, Gökçeada, İvesi, Karayaka, Kıvırcık and Morkaraman; in total represented by 628 individuals) were analyzed based on 20 microsatellite loci. Loci were amplified by Polymerase Chain Reactions and products were electronically recorded and converted into [628 x 20] matrix representing genotypes of individuals. Reliability of the genotyping and genetic diversity analyses were done by means of various bioinformatics tools. For the analyses, various statistical methods (Fisher's Exact Test, Neighbor-Joining tree construction, Factorial Correspondence Analysis (FCA), Analysis of Molecular Variation, Structure Analysis and Delaunay Analysis) were used. Since, inputs of some software were not compatible with the outputs of other software some Java classes were written whenever necessary. Analyses revealed that among the major breeds Dağlıç, Karayaka and Morkaraman breeds are highly admixed but Kıvırcık, Akkaraman and İvesi are relatively distinct. Among the minor breeds, distinctness of Hemsin, Sakız, Çine Çaparı, Gökçeada and Karagül are more pronounced compared to all of the examined breeds. Since highly admixed individuals can be identified by Structure and FCA tests, results of the present study, which is part of a national project with the acronym TURKHAYGEN-I (www.turkhaygen.gov.tr), were found to be promising in establishing and managing relatively pure conservation flocks for the Turkish native sheep breeds which are believed to be the reservoirs of genetic variability.

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Bioinformatics.

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http://etd.lib.metu.edu.tr/upload/12612585/index.pdf
https://hdl.handle.net/11511/20240

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Graduate School of Informatics, Thesis

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Citation Formats

H. Acar, “Bioinformatic analyses in microsatellite-based genetic diversity of Turkish sheep breeds,” M.S. - Master of Science, Middle East Technical University, 2010.