Assessment of the population structure and genetic diversity of Denizli chicken subpopulations using SSR markers

The aim of this study was to characterise the genetic diversity, genetic relationship and population structure within local Turkish Denizli chicken subpopulations in rural areas using 19 microsatellite markers. To assess the uniqueness and relations of the Denizli subpopulations we used six local It...

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Main Authors: Demir Özdemir, Martino Cassandro
Format: Article
Language:English
Published: Taylor & Francis Group 2018-04-01
Series:Italian Journal of Animal Science
Subjects:
Online Access:http://dx.doi.org/10.1080/1828051X.2017.1384336
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spelling doaj-fa11e69932a042e9ae65c6315b4982e22020-11-25T02:07:47ZengTaylor & Francis GroupItalian Journal of Animal Science1594-40771828-051X2018-04-0117231232010.1080/1828051X.2017.13843361384336Assessment of the population structure and genetic diversity of Denizli chicken subpopulations using SSR markersDemir Özdemir0Martino Cassandro1Teknik Bilimler Meslek Yüksekokulu, University of AkdenizUniversity of PadovaThe aim of this study was to characterise the genetic diversity, genetic relationship and population structure within local Turkish Denizli chicken subpopulations in rural areas using 19 microsatellite markers. To assess the uniqueness and relations of the Denizli subpopulations we used six local Italian chicken breeds’ samples, which were genotyped in the same laboratory with the same molecular markers. In total, 105 alleles were found across 19 microsatellite loci with a mean number of 5.53 alleles per locus. Considering all subpopulations and loci, genetic differentiation based on global FST was 0.030 (p < .01). Global FIS values (0.200) indicated that non-random mating occurred in all subpopulations of Denizli fowl and all subpopulations deviated significantly (p < .01) from HWE. Over all subpopulations, the mean observed heterozygosity was 0.473, ranging from 0.399 to 0.562. Genetic differentiations between pairs of subpopulations based on the proportion of shared alleles ranged 0.140–0.297. The neighbour-net tree, based on marker estimated kinship distances, separated Denizli subpopulations and Italian breeds into two main clusters. The most likely number of different populations was estimated using the clustering procedure implemented in STRUCTURE. Structure analysis showed a clear separation of the Denizli fowl subpopulations from the Italian populations. A second step sub-clustering allowed discriminating among the six subpopulations of Denizli breed. The results of this study can be used as baseline genetic information to place breeders’ flocks in conservation programmes, controlling inbreeding and safeguarding the genetic variability of the populations.http://dx.doi.org/10.1080/1828051X.2017.1384336denizli fowlmicrosatellitepopulation structuregenetic diversitysubpopulations
collection DOAJ
language English
format Article
sources DOAJ
author Demir Özdemir
Martino Cassandro
spellingShingle Demir Özdemir
Martino Cassandro
Assessment of the population structure and genetic diversity of Denizli chicken subpopulations using SSR markers
Italian Journal of Animal Science
denizli fowl
microsatellite
population structure
genetic diversity
subpopulations
author_facet Demir Özdemir
Martino Cassandro
author_sort Demir Özdemir
title Assessment of the population structure and genetic diversity of Denizli chicken subpopulations using SSR markers
title_short Assessment of the population structure and genetic diversity of Denizli chicken subpopulations using SSR markers
title_full Assessment of the population structure and genetic diversity of Denizli chicken subpopulations using SSR markers
title_fullStr Assessment of the population structure and genetic diversity of Denizli chicken subpopulations using SSR markers
title_full_unstemmed Assessment of the population structure and genetic diversity of Denizli chicken subpopulations using SSR markers
title_sort assessment of the population structure and genetic diversity of denizli chicken subpopulations using ssr markers
publisher Taylor & Francis Group
series Italian Journal of Animal Science
issn 1594-4077
1828-051X
publishDate 2018-04-01
description The aim of this study was to characterise the genetic diversity, genetic relationship and population structure within local Turkish Denizli chicken subpopulations in rural areas using 19 microsatellite markers. To assess the uniqueness and relations of the Denizli subpopulations we used six local Italian chicken breeds’ samples, which were genotyped in the same laboratory with the same molecular markers. In total, 105 alleles were found across 19 microsatellite loci with a mean number of 5.53 alleles per locus. Considering all subpopulations and loci, genetic differentiation based on global FST was 0.030 (p < .01). Global FIS values (0.200) indicated that non-random mating occurred in all subpopulations of Denizli fowl and all subpopulations deviated significantly (p < .01) from HWE. Over all subpopulations, the mean observed heterozygosity was 0.473, ranging from 0.399 to 0.562. Genetic differentiations between pairs of subpopulations based on the proportion of shared alleles ranged 0.140–0.297. The neighbour-net tree, based on marker estimated kinship distances, separated Denizli subpopulations and Italian breeds into two main clusters. The most likely number of different populations was estimated using the clustering procedure implemented in STRUCTURE. Structure analysis showed a clear separation of the Denizli fowl subpopulations from the Italian populations. A second step sub-clustering allowed discriminating among the six subpopulations of Denizli breed. The results of this study can be used as baseline genetic information to place breeders’ flocks in conservation programmes, controlling inbreeding and safeguarding the genetic variability of the populations.
topic denizli fowl
microsatellite
population structure
genetic diversity
subpopulations
url http://dx.doi.org/10.1080/1828051X.2017.1384336
work_keys_str_mv AT demirozdemir assessmentofthepopulationstructureandgeneticdiversityofdenizlichickensubpopulationsusingssrmarkers
AT martinocassandro assessmentofthepopulationstructureandgeneticdiversityofdenizlichickensubpopulationsusingssrmarkers
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