Genetic Diversity of Five Local Swedish Chicken Breeds Detected by Microsatellite Markers

<div><p>This study aimed at investigating the genetic diversity, relationship and population structure of 110 local Swedish chickens derived from five breeds (Gotlandshöna, Hedemorahöna, Öländsk dvärghöna, Skånsk blommehöna, and Bohuslän- Dals svarthöna, in the rest of the paper the shorter name Svarthöna is used) using 24 microsatellite markers. In total, one hundred thirteen alleles were detected in all populations, with a mean of 4.7 alleles per locus. For the five chicken breeds, the observed and expected heterozygosity ranged from 0.225 to 0.408 and from 0.231 to 0.515, with the lowest scores for the Svarthöna and the highest scores for the Skånsk blommehöna breeds, respectively. Similarly, the average within breed molecular kinship varied from 0.496 to 0.745, showing high coancestry, with Skånsk blommehöna having the lowest and Svarthöna the highest coancestry. Furthermore, all breeds showed significant deviations from Hardy-Weinberg expectations. Across the five breeds, the global heterozygosity deficit (F_IT) was 0.545, population differentiation index (F_ST) was 0.440, and the global inbreeding of individuals within breed (F_IS) was 0.187. The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed two main clusters, with Hedemorahöna and Öländsk dvärghöna breeds in one cluster, and Gotlandshöna and Svarthöna breeds in the second cluster leaving the Skånsk blommehöna in the middle. Based on the results of the STRUCTURE analysis, the most likely number of clustering of the five breeds was at K = 4, with Hedemorahöna, Gotlandshöna and Svarthöna breeds forming their own distinct clusters, while Öländsk dvärghöna and Skånsk blommehöna breeds clustered together. Losses in the overall genetic diversity of local Swedish chickens due to breeds extinction varied from -1.46% to -6.723%. The results of the current study can be used as baseline genetic information for genetic conservation program, for instance, to control inbreeding and to implement further genetic studies in local Swedish chickens.</p></div

Map of Sweden with the geographic origin of the five breeds indicated.

<p>Map of Sweden with the geographic origin of the five breeds indicated.</p

Mean number of alleles (MNA) per locus, observed (HO) and expected (HE) heterozygosity, Hardy-Weinberg test (HW) and mean molecular kinship within breed.

<p><i>**p<0.01;</i></p><p><i>***p<0.001</i></p><p>Mean number of alleles (MNA) per locus, observed (HO) and expected (HE) heterozygosity, Hardy-Weinberg test (HW) and mean molecular kinship within breed.</p

Number of alleles (NA), polymorphism information content (PIC), observed (HO) and expected (HE) heterozygosity with standard deviation of the mean values within parenthesis and Hardy Weinberg (HW) tests.

<p><i>*p<0.05;</i></p><p><i>**p<0.01;</i></p><p><i>***p<0.001;</i></p><p><i>NS = non-significant</i></p><p>Number of alleles (NA), polymorphism information content (PIC), observed (HO) and expected (HE) heterozygosity with standard deviation of the mean values within parenthesis and Hardy Weinberg (HW) tests.</p

Neighbor-joining tree of individual chickens.

<p>Bootstrap values are shown partially. Each breed is marked with a specific color.</p

STRUCTURE Clustering of five local Swedish chicken breeds.

<p>Gotla = Gotlandshöna; Hedem = Hedemorahöna; Öland = Öländsk dvärghöna; Skånsk = Skånsk blommehöna; Svart = Svarthöna. Numbers in the parenthesis indicate the average similarity index between individuals assigned into the same cluster</p

Loss or gain (%) of the total genetic diversity of local Swedish chickens when one of the breed was removed from the population based on the method developed by Caballero and Toro [25].

<p>Loss or gain (%) of the total genetic diversity of local Swedish chickens when one of the breed was removed from the population based on the method developed by Caballero and Toro [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120580#pone.0120580.ref025" target="_blank">25</a>].</p

Additional file 2: of Evaluation of whole-genome sequencing of four Chinese crested dogs for variant detection using the ion proton system

PI chip productivity and per base quality scores. Table describing the yield and base quality of eight sequencing chips. (XLSX 40ย�kb

NeighborNet graph of genetic distances of Indonesian cattle populations.

<p>The animal pictures are from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005490#pone.0005490-Felius1" target="_blank">[8]</a> or were drawn from photographs.</p

Y-chromomal sequence variation diagnostic for indicine and Y1 and Y2 taurine haplotypes.

*<p>Corresponding to the <i>Bfa</i>I site in banteng.</p><p>Database entries and the numbering refer to sequences from taurine cattle.</p