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Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array
The estimation of linkage disequilibrium between molecular markers within a population is critical when establishing the minimum number of markers required for association studies, genomic selection, and inferring historical events influencing different populations. This work aimed to evaluate the e...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6539196/ https://www.ncbi.nlm.nih.gov/pubmed/31191613 http://dx.doi.org/10.3389/fgene.2019.00498 |
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author | Barría, Agustín Christensen, Kris A. Yoshida, Grazyella Jedlicki, Ana Leong, Jong S. Rondeau, Eric B. Lhorente, Jean P. Koop, Ben F. Davidson, William S. Yáñez, José M. |
author_facet | Barría, Agustín Christensen, Kris A. Yoshida, Grazyella Jedlicki, Ana Leong, Jong S. Rondeau, Eric B. Lhorente, Jean P. Koop, Ben F. Davidson, William S. Yáñez, José M. |
author_sort | Barría, Agustín |
collection | PubMed |
description | The estimation of linkage disequilibrium between molecular markers within a population is critical when establishing the minimum number of markers required for association studies, genomic selection, and inferring historical events influencing different populations. This work aimed to evaluate the extent and decay of linkage disequilibrium in a coho salmon breeding population using a high-density SNP array. Linkage disequilibrium was estimated between a total of 93,502 SNPs found in 64 individuals (33 dams and 31 sires) from the breeding population. The markers encompass all 30 coho salmon chromosomes and comprise 1,684.62 Mb of the genome. The average density of markers per chromosome ranged from 48.31 to 66 per 1 Mb. The minor allele frequency averaged 0.26 (with a range from 0.22 to 0.27). The overall average linkage disequilibrium among SNPs pairs measured as r(2) was 0.10. The Average r(2) value decreased with increasing physical distance, with values ranging from 0.21 to 0.07 at a distance lower than 1 kb and up to 10 Mb, respectively. An r(2) threshold of 0.2 was reached at distance of approximately 40 Kb. Chromosomes Okis05, Okis15 and Okis28 showed high levels of linkage disequilibrium (>0.20 at distances lower than 1 Mb). Average r(2) values were lower than 0.15 for all chromosomes at distances greater than 4 Mb. An effective population size of 43 was estimated for the population 10 generations ago, and 325, for 139 generations ago. Based on the effective number of chromosome segments, we suggest that at least 74,000 SNPs would be necessary for an association mapping study and genomic predictions. Therefore, the SNP panel used allowed us to capture high-resolution information in the farmed coho salmon population. Furthermore, based on the contemporary N(e), a new mate allocation strategy is suggested to increase the effective population size. |
format | Online Article Text |
id | pubmed-6539196 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-65391962019-06-12 Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array Barría, Agustín Christensen, Kris A. Yoshida, Grazyella Jedlicki, Ana Leong, Jong S. Rondeau, Eric B. Lhorente, Jean P. Koop, Ben F. Davidson, William S. Yáñez, José M. Front Genet Genetics The estimation of linkage disequilibrium between molecular markers within a population is critical when establishing the minimum number of markers required for association studies, genomic selection, and inferring historical events influencing different populations. This work aimed to evaluate the extent and decay of linkage disequilibrium in a coho salmon breeding population using a high-density SNP array. Linkage disequilibrium was estimated between a total of 93,502 SNPs found in 64 individuals (33 dams and 31 sires) from the breeding population. The markers encompass all 30 coho salmon chromosomes and comprise 1,684.62 Mb of the genome. The average density of markers per chromosome ranged from 48.31 to 66 per 1 Mb. The minor allele frequency averaged 0.26 (with a range from 0.22 to 0.27). The overall average linkage disequilibrium among SNPs pairs measured as r(2) was 0.10. The Average r(2) value decreased with increasing physical distance, with values ranging from 0.21 to 0.07 at a distance lower than 1 kb and up to 10 Mb, respectively. An r(2) threshold of 0.2 was reached at distance of approximately 40 Kb. Chromosomes Okis05, Okis15 and Okis28 showed high levels of linkage disequilibrium (>0.20 at distances lower than 1 Mb). Average r(2) values were lower than 0.15 for all chromosomes at distances greater than 4 Mb. An effective population size of 43 was estimated for the population 10 generations ago, and 325, for 139 generations ago. Based on the effective number of chromosome segments, we suggest that at least 74,000 SNPs would be necessary for an association mapping study and genomic predictions. Therefore, the SNP panel used allowed us to capture high-resolution information in the farmed coho salmon population. Furthermore, based on the contemporary N(e), a new mate allocation strategy is suggested to increase the effective population size. Frontiers Media S.A. 2019-05-22 /pmc/articles/PMC6539196/ /pubmed/31191613 http://dx.doi.org/10.3389/fgene.2019.00498 Text en Copyright © 2019 Barría, Christensen, Yoshida, Jedlicki, Leong, Rondeau, Lhorente, Koop, Davidson and Yáñez. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Barría, Agustín Christensen, Kris A. Yoshida, Grazyella Jedlicki, Ana Leong, Jong S. Rondeau, Eric B. Lhorente, Jean P. Koop, Ben F. Davidson, William S. Yáñez, José M. Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array |
title | Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array |
title_full | Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array |
title_fullStr | Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array |
title_full_unstemmed | Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array |
title_short | Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array |
title_sort | whole genome linkage disequilibrium and effective population size in a coho salmon (oncorhynchus kisutch) breeding population using a high-density snp array |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6539196/ https://www.ncbi.nlm.nih.gov/pubmed/31191613 http://dx.doi.org/10.3389/fgene.2019.00498 |
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