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Biodiversity of 20 chicken breeds assessed by SNPs located in gene regions
Year:
2007
Source of publication :
Cytogenetic and Genome Research
Authors :
Lavi, Uri
;
.
Twito, Tal
;
.
Volume :
117
Co-Authors:
Twito, T., Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel, ARO - Volcani Center, Bet Dagan, Israel, Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
Weigend, S., Institute for Animal Breeding, Federal Agricultural Research Centre, Mariensee, Germany
Blum, S., Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
Granevitze, Z., Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
Feldman, M.W., Department of Biological Sciences, Stanford University, Stanford, CA, United States
Perl-Treves, R., Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
Lavi, U., ARO - Volcani Center, Bet Dagan, Israel
Hillel, J., Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel, Robert H. Smith Institute of Plant Sciences and Genetics, Hebrew University of Jerusalem, Rehovot 76100, Israel
Facilitators :
From page:
319
To page:
326
(
Total pages:
8
)
Abstract:
Twenty-five single nucleotide polymorphisms (SNPs) were analyzed in 20 distinct chicken breeds. The SNPs, each located in a different gene and mostly on different chromosomes, were chosen to examine the use of SNPs in or close to genes (g-SNPs), for biodiversity studies. Phylogenetic trees were constructed from these data. When bootstrap values were used as a criterion for the tree repeatability, doubling the number of SNPs from 12 to 25 improved tree repeatability more than doubling the number of individuals per population, from five to ten. Clustering results of these 20 populations, based on the software STRUCTURE, are in agreement with those previously obtained from the analysis of microsatellites. When the number of clusters was similar to the number of populations, affiliation of birds to their original populations was correct (>95%) only when at least the 22 most polymorphic SNP loci (out of 25) were included. When ten populations were clustered into five groups based on STRUCTURE, we used membership coefficient (Q) of the major cluster at each population as an indicator for clustering success level. This value was used to compare between three marker types; microsatellites, SNPs in or close to genes (g-SNPs) and SNPs in random fragments (r-SNPs). In this comparison, the same individuals were used (five to ten birds per population) and the same number of loci (14) used for each of the marker types. The average membership coefficients (Q) of the major cluster for microsatellites, g-SNPs and r-SNPs were 0.85, 0.7, and 0.64, respectively. Analysis based on microsatellites resulted in significantly higher clustering success due to their multi-allelic nature. Nevertheless, SNPs have obvious advantages, and are an efficient and cost-effective genetic tool, providing broader genome coverage and reliable estimates of genetic relatedness. Copyright © 2007 S. Karger AG.
Note:
Related Files :
animal experiment
Animals
biodiversity
breeding
Chickens
Cluster analysis
Evolution
genetic markers
Show More
Related Content
More details
DOI :
10.1159/000103194
Article number:
0
Affiliations:
Database:
Scopus
Publication Type:
article
;
.
Language:
English
Editors' remarks:
ID:
29187
Last updated date:
02/03/2022 17:27
Creation date:
17/04/2018 00:44
Scientific Publication
Biodiversity of 20 chicken breeds assessed by SNPs located in gene regions
117
Twito, T., Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel, ARO - Volcani Center, Bet Dagan, Israel, Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
Weigend, S., Institute for Animal Breeding, Federal Agricultural Research Centre, Mariensee, Germany
Blum, S., Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
Granevitze, Z., Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
Feldman, M.W., Department of Biological Sciences, Stanford University, Stanford, CA, United States
Perl-Treves, R., Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
Lavi, U., ARO - Volcani Center, Bet Dagan, Israel
Hillel, J., Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel, Robert H. Smith Institute of Plant Sciences and Genetics, Hebrew University of Jerusalem, Rehovot 76100, Israel
Biodiversity of 20 chicken breeds assessed by SNPs located in gene regions
Twenty-five single nucleotide polymorphisms (SNPs) were analyzed in 20 distinct chicken breeds. The SNPs, each located in a different gene and mostly on different chromosomes, were chosen to examine the use of SNPs in or close to genes (g-SNPs), for biodiversity studies. Phylogenetic trees were constructed from these data. When bootstrap values were used as a criterion for the tree repeatability, doubling the number of SNPs from 12 to 25 improved tree repeatability more than doubling the number of individuals per population, from five to ten. Clustering results of these 20 populations, based on the software STRUCTURE, are in agreement with those previously obtained from the analysis of microsatellites. When the number of clusters was similar to the number of populations, affiliation of birds to their original populations was correct (>95%) only when at least the 22 most polymorphic SNP loci (out of 25) were included. When ten populations were clustered into five groups based on STRUCTURE, we used membership coefficient (Q) of the major cluster at each population as an indicator for clustering success level. This value was used to compare between three marker types; microsatellites, SNPs in or close to genes (g-SNPs) and SNPs in random fragments (r-SNPs). In this comparison, the same individuals were used (five to ten birds per population) and the same number of loci (14) used for each of the marker types. The average membership coefficients (Q) of the major cluster for microsatellites, g-SNPs and r-SNPs were 0.85, 0.7, and 0.64, respectively. Analysis based on microsatellites resulted in significantly higher clustering success due to their multi-allelic nature. Nevertheless, SNPs have obvious advantages, and are an efficient and cost-effective genetic tool, providing broader genome coverage and reliable estimates of genetic relatedness. Copyright © 2007 S. Karger AG.
Scientific Publication
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