Estimates of Linkage Disequilibrium and Effective Population Size in Wild and Selected Populations of the Pacific Oyster Using Single‐nucleotide Polymorphism Markers
Abstract The level and extent of linkage disequilibrium ( LD ) and effective population size ( Ne ) were studied in three selected lines and a wild population of Pacific oyster, Crassostrea gigas , using 61 single‐nucleotide polymorphisms. Significant differences were detected in the average r 2 bet...
Published in: | Journal of the World Aquaculture Society |
---|---|
Main Authors: | , , , |
Other Authors: | , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Wiley
2017
|
Subjects: | |
Online Access: | http://dx.doi.org/10.1111/jwas.12393 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fjwas.12393 https://onlinelibrary.wiley.com/doi/pdf/10.1111/jwas.12393 |
id |
crwiley:10.1111/jwas.12393 |
---|---|
record_format |
openpolar |
spelling |
crwiley:10.1111/jwas.12393 2024-03-31T07:52:24+00:00 Estimates of Linkage Disequilibrium and Effective Population Size in Wild and Selected Populations of the Pacific Oyster Using Single‐nucleotide Polymorphism Markers Zhong, Xiaoxiao Li, Qi Kong, Lingfeng Yu, Hong National Natural Science Foundation of China Shandong Province 2017 http://dx.doi.org/10.1111/jwas.12393 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fjwas.12393 https://onlinelibrary.wiley.com/doi/pdf/10.1111/jwas.12393 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Journal of the World Aquaculture Society volume 48, issue 5, page 791-801 ISSN 0893-8849 1749-7345 Agronomy and Crop Science Aquatic Science journal-article 2017 crwiley https://doi.org/10.1111/jwas.12393 2024-03-05T05:50:34Z Abstract The level and extent of linkage disequilibrium ( LD ) and effective population size ( Ne ) were studied in three selected lines and a wild population of Pacific oyster, Crassostrea gigas , using 61 single‐nucleotide polymorphisms. Significant differences were detected in the average r 2 between the selected lines and wild population for both syntenic and nonsyntenic loci with LD beyond population‐specific critical values ( P <0.05). Moreover, the proportions of syntenic and nonsyntenic loci with the expected LD level in the wild population were lower than that in the selected lines. Taken together, the LD level of the selected lines was higher than that of the wild population. The extent of LD analysis showed that a short range of LD (0–0.23 cM ) was detected in the four populations, and the decay distance was lower in the wild population than in the selected lines. Ne values ranged from 47.6 to 58.5 in the selected lines and ranged from 527.9 to 709.6 with infinite upper limits in the wild population. Further variance analysis of LD demonstrated that genetic drift and epistatic selection might account for the increased LD levels in selected lines. The LD information will be valuable for further association study and marker‐assisted selection in oysters. Article in Journal/Newspaper Crassostrea gigas Pacific oyster Wiley Online Library Pacific Journal of the World Aquaculture Society 48 5 791 801 |
institution |
Open Polar |
collection |
Wiley Online Library |
op_collection_id |
crwiley |
language |
English |
topic |
Agronomy and Crop Science Aquatic Science |
spellingShingle |
Agronomy and Crop Science Aquatic Science Zhong, Xiaoxiao Li, Qi Kong, Lingfeng Yu, Hong Estimates of Linkage Disequilibrium and Effective Population Size in Wild and Selected Populations of the Pacific Oyster Using Single‐nucleotide Polymorphism Markers |
topic_facet |
Agronomy and Crop Science Aquatic Science |
description |
Abstract The level and extent of linkage disequilibrium ( LD ) and effective population size ( Ne ) were studied in three selected lines and a wild population of Pacific oyster, Crassostrea gigas , using 61 single‐nucleotide polymorphisms. Significant differences were detected in the average r 2 between the selected lines and wild population for both syntenic and nonsyntenic loci with LD beyond population‐specific critical values ( P <0.05). Moreover, the proportions of syntenic and nonsyntenic loci with the expected LD level in the wild population were lower than that in the selected lines. Taken together, the LD level of the selected lines was higher than that of the wild population. The extent of LD analysis showed that a short range of LD (0–0.23 cM ) was detected in the four populations, and the decay distance was lower in the wild population than in the selected lines. Ne values ranged from 47.6 to 58.5 in the selected lines and ranged from 527.9 to 709.6 with infinite upper limits in the wild population. Further variance analysis of LD demonstrated that genetic drift and epistatic selection might account for the increased LD levels in selected lines. The LD information will be valuable for further association study and marker‐assisted selection in oysters. |
author2 |
National Natural Science Foundation of China Shandong Province |
format |
Article in Journal/Newspaper |
author |
Zhong, Xiaoxiao Li, Qi Kong, Lingfeng Yu, Hong |
author_facet |
Zhong, Xiaoxiao Li, Qi Kong, Lingfeng Yu, Hong |
author_sort |
Zhong, Xiaoxiao |
title |
Estimates of Linkage Disequilibrium and Effective Population Size in Wild and Selected Populations of the Pacific Oyster Using Single‐nucleotide Polymorphism Markers |
title_short |
Estimates of Linkage Disequilibrium and Effective Population Size in Wild and Selected Populations of the Pacific Oyster Using Single‐nucleotide Polymorphism Markers |
title_full |
Estimates of Linkage Disequilibrium and Effective Population Size in Wild and Selected Populations of the Pacific Oyster Using Single‐nucleotide Polymorphism Markers |
title_fullStr |
Estimates of Linkage Disequilibrium and Effective Population Size in Wild and Selected Populations of the Pacific Oyster Using Single‐nucleotide Polymorphism Markers |
title_full_unstemmed |
Estimates of Linkage Disequilibrium and Effective Population Size in Wild and Selected Populations of the Pacific Oyster Using Single‐nucleotide Polymorphism Markers |
title_sort |
estimates of linkage disequilibrium and effective population size in wild and selected populations of the pacific oyster using single‐nucleotide polymorphism markers |
publisher |
Wiley |
publishDate |
2017 |
url |
http://dx.doi.org/10.1111/jwas.12393 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fjwas.12393 https://onlinelibrary.wiley.com/doi/pdf/10.1111/jwas.12393 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
Journal of the World Aquaculture Society volume 48, issue 5, page 791-801 ISSN 0893-8849 1749-7345 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1111/jwas.12393 |
container_title |
Journal of the World Aquaculture Society |
container_volume |
48 |
container_issue |
5 |
container_start_page |
791 |
op_container_end_page |
801 |
_version_ |
1795031504988930048 |