PSVIII-23 High-density SNP marker based genetic diversity and population structure study of reindeer populations
Wild reindeer populations form the basis of the traditional activities of indigenous peoples of the northern territories of Siberia, the main part of which is concentrated in two large regions: Taimyr and Northern Yakutia. Currently, there is a sharp decline in the number of wild reindeer, which lea...
Published in: | Journal of Animal Science |
---|---|
Main Authors: | , , , , , , |
Format: | Text |
Language: | English |
Published: |
Oxford University Press
2019
|
Subjects: | |
Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6898397/ https://doi.org/10.1093/jas/skz258.540 |
id |
ftpubmed:oai:pubmedcentral.nih.gov:6898397 |
---|---|
record_format |
openpolar |
spelling |
ftpubmed:oai:pubmedcentral.nih.gov:6898397 2023-05-15T18:30:30+02:00 PSVIII-23 High-density SNP marker based genetic diversity and population structure study of reindeer populations Kharzinova, Veronika R Dotsev, Arsen V Solovieva, Anastasiya Wimmers, Klaus Reyer, Henry Brem, Gottfried Zinovieva, Natalia A 2019-12 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6898397/ https://doi.org/10.1093/jas/skz258.540 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6898397/ http://dx.doi.org/10.1093/jas/skz258.540 © The Author(s) 2019. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) J Anim Sci POSTER PRESENTATIONS Text 2019 ftpubmed https://doi.org/10.1093/jas/skz258.540 2020-12-06T01:24:24Z Wild reindeer populations form the basis of the traditional activities of indigenous peoples of the northern territories of Siberia, the main part of which is concentrated in two large regions: Taimyr and Northern Yakutia. Currently, there is a sharp decline in the number of wild reindeer, which leads to a loss of the genetic diversity necessary for survival in the changing habitat conditions. To infer the population structure and genome-wide diversity of wild reindeer, the Taymyr (TAI, n = 33) and Yakut populations including Tundra Leno-Olenek (LNO, n = 20), the Island (ISL, n = 6), the Sundrun (SUN, n = 6) and the Taiga (TGA, n = 5) were genotyped with the Illumina Bovine HD BeadChip. Data set consisting of 8801 polymorphic SNP markers was used to calculate population genetic parameters in PLINK 1.9, SplitsTree 4.14.6. software, R packages “diveRsity” and “StAMMP.” We detected the similar level of observed heterozygosity across the TAI, ISL, SUN and LNO: 0.187, 0.188, 0.184, and 0.189 respectively. Meanwhile, allelic richness was slightly higher in Taimyr population compared to the Yakut groups. The lowest level of genetic diversity was recorded in the Taiga reindeer (H(o)=0.168; A(r) = 1.476). All populations showed heterozygotes deficiency (uF(IS) 95%, CI > 0) with higher uF(IS) values in TGA (0.079). MDS analysis revealed the high level of genetic similarity of TAI, ISL and LNO and placed SUN in close proximity to them. The first and the second MDS components (2.36% and 2.15% of the genetic variability) clearly divided the Taiga reindeer, the genetic apartness of which was also confirmed by the results of the Neighbour-Net tree analysis. Information obtained here, might be helpful for further effective use and maintenance of the reindeer populations as well as for overcoming the negative effects of decreasing their number. The study was supported by Russian Science Foundation within Pr. no. 16-16-10068. Text taiga Taimyr Taymyr Tundra Yakut Yakutia Siberia PubMed Central (PMC) Sundrun ENVELOPE(152.546,152.546,70.773,70.773) Journal of Animal Science 97 Supplement_3 265 266 |
institution |
Open Polar |
collection |
PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
POSTER PRESENTATIONS |
spellingShingle |
POSTER PRESENTATIONS Kharzinova, Veronika R Dotsev, Arsen V Solovieva, Anastasiya Wimmers, Klaus Reyer, Henry Brem, Gottfried Zinovieva, Natalia A PSVIII-23 High-density SNP marker based genetic diversity and population structure study of reindeer populations |
topic_facet |
POSTER PRESENTATIONS |
description |
Wild reindeer populations form the basis of the traditional activities of indigenous peoples of the northern territories of Siberia, the main part of which is concentrated in two large regions: Taimyr and Northern Yakutia. Currently, there is a sharp decline in the number of wild reindeer, which leads to a loss of the genetic diversity necessary for survival in the changing habitat conditions. To infer the population structure and genome-wide diversity of wild reindeer, the Taymyr (TAI, n = 33) and Yakut populations including Tundra Leno-Olenek (LNO, n = 20), the Island (ISL, n = 6), the Sundrun (SUN, n = 6) and the Taiga (TGA, n = 5) were genotyped with the Illumina Bovine HD BeadChip. Data set consisting of 8801 polymorphic SNP markers was used to calculate population genetic parameters in PLINK 1.9, SplitsTree 4.14.6. software, R packages “diveRsity” and “StAMMP.” We detected the similar level of observed heterozygosity across the TAI, ISL, SUN and LNO: 0.187, 0.188, 0.184, and 0.189 respectively. Meanwhile, allelic richness was slightly higher in Taimyr population compared to the Yakut groups. The lowest level of genetic diversity was recorded in the Taiga reindeer (H(o)=0.168; A(r) = 1.476). All populations showed heterozygotes deficiency (uF(IS) 95%, CI > 0) with higher uF(IS) values in TGA (0.079). MDS analysis revealed the high level of genetic similarity of TAI, ISL and LNO and placed SUN in close proximity to them. The first and the second MDS components (2.36% and 2.15% of the genetic variability) clearly divided the Taiga reindeer, the genetic apartness of which was also confirmed by the results of the Neighbour-Net tree analysis. Information obtained here, might be helpful for further effective use and maintenance of the reindeer populations as well as for overcoming the negative effects of decreasing their number. The study was supported by Russian Science Foundation within Pr. no. 16-16-10068. |
format |
Text |
author |
Kharzinova, Veronika R Dotsev, Arsen V Solovieva, Anastasiya Wimmers, Klaus Reyer, Henry Brem, Gottfried Zinovieva, Natalia A |
author_facet |
Kharzinova, Veronika R Dotsev, Arsen V Solovieva, Anastasiya Wimmers, Klaus Reyer, Henry Brem, Gottfried Zinovieva, Natalia A |
author_sort |
Kharzinova, Veronika R |
title |
PSVIII-23 High-density SNP marker based genetic diversity and population structure study of reindeer populations |
title_short |
PSVIII-23 High-density SNP marker based genetic diversity and population structure study of reindeer populations |
title_full |
PSVIII-23 High-density SNP marker based genetic diversity and population structure study of reindeer populations |
title_fullStr |
PSVIII-23 High-density SNP marker based genetic diversity and population structure study of reindeer populations |
title_full_unstemmed |
PSVIII-23 High-density SNP marker based genetic diversity and population structure study of reindeer populations |
title_sort |
psviii-23 high-density snp marker based genetic diversity and population structure study of reindeer populations |
publisher |
Oxford University Press |
publishDate |
2019 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6898397/ https://doi.org/10.1093/jas/skz258.540 |
long_lat |
ENVELOPE(152.546,152.546,70.773,70.773) |
geographic |
Sundrun |
geographic_facet |
Sundrun |
genre |
taiga Taimyr Taymyr Tundra Yakut Yakutia Siberia |
genre_facet |
taiga Taimyr Taymyr Tundra Yakut Yakutia Siberia |
op_source |
J Anim Sci |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6898397/ http://dx.doi.org/10.1093/jas/skz258.540 |
op_rights |
© The Author(s) 2019. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) |
op_doi |
https://doi.org/10.1093/jas/skz258.540 |
container_title |
Journal of Animal Science |
container_volume |
97 |
container_issue |
Supplement_3 |
container_start_page |
265 |
op_container_end_page |
266 |
_version_ |
1766214007357702144 |