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

Acar, Hande
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 (, 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.


Reassessment of genetic diversity in native turkish sheep breeds with large numbers of microsatellite markers and mitochondrial DNA (MTDNA)
Doğan, Şükrü Anıl; Togan, İnci Zehra; Department of Biology (2009)
In the present study, within and among breed genetic variability in seven native Turkish sheep breeds (Akkaraman, Dağlıç, Gökçeada, İvesi, Karayaka, Kıvırcık and Morkaraman) were analyzed based on 20 microsatellite loci. For the analysis, various statistical methods such as Neighbor-Net, Factorial Correspondence Analysis (FCA) and Structure were used. High level of genetic variability within the Turkish breeds was observed. Gene pools of the breeds were visualized and found that they are highly overlapping ...
Yerli koyun ırklarında bulunan genetik çeşitlilik
Soysal, İhsan M.; Togan, İnci Zehra; Ünal, Özkan Emel; Baştanlar, Koban Evren; Ergüven, Ayşe; Altunok, Vahdettin(2004)
Bu çalışmada, Türk koyun ırklarında mevcut genetik çeşitlilik 5 mikrosatelit lokusu kullanılarak incelenmiştir. Devlet üretim çiftlikleri, üniversite üretim çiftlikleri ve yerel yetiştiricilerin elinde bulunan sürülerden yerli ve melez onbir Türk ırkı (Akkaraman, Morkaraman, Kıvırcık, İvesi, Dağlıç, Karayaka, Hemşin, Norduz, Kangal, Konya Merinosu, Türkgeldi) ile bireyleri Irak'tan getirilmiş yabancı bir ırkı (Hamdani) temsil eden toplam 423 birey bu çalışmada kullanılmıştır. Bazı ır...
Genetic diversity of native and crossbreed sheep breeds in Anatolia
Koban, Evren; Togan, İnci Zehra; Department of Biology (2004)
In this study the genetic diversity in Turkish native sheep breeds was investigated based on microsatellite DNA loci. In total, 423 samples from 11 native and crossbreed Turkish sheep breeds (Akkaraman, Morkaraman, Kivircik, Ivesi, Dagliç, Karayaka, Hemsin, Norduz, Kangal, Konya Merinosu, Türkgeldi) and one Iraqi breed (Hamdani) were analyzed by sampling from breeding farms and local breeders. After excluding close relatives by Kinship analysis, the genetic variation within breeds was estimated as gene dive...
Genotyping of beta-casein, kappa-casein and beta-lactoglobulin genes in turkish native cattle breeds and efforts to delineate bcm-7 on human pbmc
Dinç, Havva; Kence, Aykut; Department of Biology (2009)
The main aim of this study is to determine genetic diversity of milk protein genes associated with milk traits, namely beta-casein, kappa-casein and betalactoglobulin, in native Turkish cattle breeds (Turkish Grey, Eastern Anatolian Red, Anatolian Black, and Southern Anatolian Red) and Turkish Holstein. Only 11% deviation from the Hardy-Weinberg equilibrium and insignificant Fis values for the populations were observed, indicating that samples are free of inbreeding. B alleles of these genes, which are posi...
MTDNA based genetic diversity of native sheep breeds and Anatolian mouflon (Ovis Gmelini Anatolica)
Demirci, Sevgin; Togan, İnci Zehra; Department of Bioinformatics (2012)
In the present study, history of domestic sheep were investigated by mitochondrial DNA (mtDNA) based haplogroups (HPG) of 628 samples and mtDNA control region (CR) sequences of 240 samples from 13 Turkish sheep breeds which were located in the hearth of the first domestication center. Also, 30 Anatolian wild sheep (Ovis gmelinii anatolica) mtDNA CR sequences were obtained to contribute to the scenarios on initial domestication stages of sheep. Haplogroup compositions of breeds were identified with SSCP meth...
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.