Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot (Scophthalmus maximus)
Massive genotyping of single nucleotide polymorphisms (SNP) has opened opportunities for analyzing the way in which selection shapes genomes. Artificial or natural selection usually leaves genomic signatures associated with selective sweeps around the responsible locus. Strong selective sweeps are m...
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Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169425/ http://www.ncbi.nlm.nih.gov/pubmed/32346384 https://doi.org/10.3389/fgene.2020.00296 |
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ftpubmed:oai:pubmedcentral.nih.gov:7169425 2023-05-15T18:15:46+02:00 Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot (Scophthalmus maximus) Aramburu, Oscar Ceballos, Francisco Casanova, Adrián Le Moan, Alan Hemmer-Hansen, Jakob Bekkevold, Dorte Bouza, Carmen Martínez, Paulino 2020-04-03 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169425/ http://www.ncbi.nlm.nih.gov/pubmed/32346384 https://doi.org/10.3389/fgene.2020.00296 en eng Frontiers Media S.A. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169425/ http://www.ncbi.nlm.nih.gov/pubmed/32346384 http://dx.doi.org/10.3389/fgene.2020.00296 Copyright © 2020 Aramburu, Ceballos, Casanova, Le Moan, Hemmer-Hansen, Bekkevold, Bouza and Martínez. 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. CC-BY Genetics Text 2020 ftpubmed https://doi.org/10.3389/fgene.2020.00296 2020-05-03T00:29:34Z Massive genotyping of single nucleotide polymorphisms (SNP) has opened opportunities for analyzing the way in which selection shapes genomes. Artificial or natural selection usually leaves genomic signatures associated with selective sweeps around the responsible locus. Strong selective sweeps are most often identified either by lower genetic diversity than the genomic average and/or islands of runs of homozygosity (ROHi). Here, we conducted an analysis of selective sweeps in turbot (Scophthalmus maximus) using two SNP datasets from a Northeastern Atlantic population (36 individuals) and a domestic broodstock (46 individuals). Twenty-six families (∼ 40 offspring per family) from this broodstock and three SNP datasets applying differing filtering criteria were used to adjust ROH calling parameters. The best-fitted genomic inbreeding estimate (F(ROH)) was obtained by the sum of ROH longer than 1 Mb, called using a 21,615 SNP panel, a sliding window of 37 SNPs and one heterozygous SNP per window allowed. These parameters were used to obtain the ROHi distribution in the domestic and wild populations (49 and 0 ROHi, respectively). Regions with higher and lower genetic diversity within each population were obtained using sliding windows of 37 SNPs. Furthermore, those regions were mapped in the turbot genome against previously reported genetic markers associated with QTL (Quantitative Trait Loci) and outlier loci for domestic or natural selection to identify putative selective sweeps. Out of the 319 and 278 windows surpassing the suggestive pooled heterozygosity thresholds (ZHp) in the wild and domestic population, respectively, 78 and 54 were retained under more restrictive ZHp criteria. A total of 116 suggestive windows (representing 19 genomic regions) were linked to either QTL for production traits, or outliers for divergent or balancing selection. Twenty-four of them (representing 3 genomic regions) were retained under stricter ZHp thresholds. Eleven QTL/outlier markers were exclusively found in suggestive regions ... Text Scophthalmus maximus Turbot PubMed Central (PMC) Frontiers in Genetics 11 |
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Genetics |
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Genetics Aramburu, Oscar Ceballos, Francisco Casanova, Adrián Le Moan, Alan Hemmer-Hansen, Jakob Bekkevold, Dorte Bouza, Carmen Martínez, Paulino Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot (Scophthalmus maximus) |
topic_facet |
Genetics |
description |
Massive genotyping of single nucleotide polymorphisms (SNP) has opened opportunities for analyzing the way in which selection shapes genomes. Artificial or natural selection usually leaves genomic signatures associated with selective sweeps around the responsible locus. Strong selective sweeps are most often identified either by lower genetic diversity than the genomic average and/or islands of runs of homozygosity (ROHi). Here, we conducted an analysis of selective sweeps in turbot (Scophthalmus maximus) using two SNP datasets from a Northeastern Atlantic population (36 individuals) and a domestic broodstock (46 individuals). Twenty-six families (∼ 40 offspring per family) from this broodstock and three SNP datasets applying differing filtering criteria were used to adjust ROH calling parameters. The best-fitted genomic inbreeding estimate (F(ROH)) was obtained by the sum of ROH longer than 1 Mb, called using a 21,615 SNP panel, a sliding window of 37 SNPs and one heterozygous SNP per window allowed. These parameters were used to obtain the ROHi distribution in the domestic and wild populations (49 and 0 ROHi, respectively). Regions with higher and lower genetic diversity within each population were obtained using sliding windows of 37 SNPs. Furthermore, those regions were mapped in the turbot genome against previously reported genetic markers associated with QTL (Quantitative Trait Loci) and outlier loci for domestic or natural selection to identify putative selective sweeps. Out of the 319 and 278 windows surpassing the suggestive pooled heterozygosity thresholds (ZHp) in the wild and domestic population, respectively, 78 and 54 were retained under more restrictive ZHp criteria. A total of 116 suggestive windows (representing 19 genomic regions) were linked to either QTL for production traits, or outliers for divergent or balancing selection. Twenty-four of them (representing 3 genomic regions) were retained under stricter ZHp thresholds. Eleven QTL/outlier markers were exclusively found in suggestive regions ... |
format |
Text |
author |
Aramburu, Oscar Ceballos, Francisco Casanova, Adrián Le Moan, Alan Hemmer-Hansen, Jakob Bekkevold, Dorte Bouza, Carmen Martínez, Paulino |
author_facet |
Aramburu, Oscar Ceballos, Francisco Casanova, Adrián Le Moan, Alan Hemmer-Hansen, Jakob Bekkevold, Dorte Bouza, Carmen Martínez, Paulino |
author_sort |
Aramburu, Oscar |
title |
Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot (Scophthalmus maximus) |
title_short |
Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot (Scophthalmus maximus) |
title_full |
Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot (Scophthalmus maximus) |
title_fullStr |
Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot (Scophthalmus maximus) |
title_full_unstemmed |
Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot (Scophthalmus maximus) |
title_sort |
genomic signatures after five generations of intensive selective breeding: runs of homozygosity and genetic diversity in representative domestic and wild populations of turbot (scophthalmus maximus) |
publisher |
Frontiers Media S.A. |
publishDate |
2020 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169425/ http://www.ncbi.nlm.nih.gov/pubmed/32346384 https://doi.org/10.3389/fgene.2020.00296 |
genre |
Scophthalmus maximus Turbot |
genre_facet |
Scophthalmus maximus Turbot |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169425/ http://www.ncbi.nlm.nih.gov/pubmed/32346384 http://dx.doi.org/10.3389/fgene.2020.00296 |
op_rights |
Copyright © 2020 Aramburu, Ceballos, Casanova, Le Moan, Hemmer-Hansen, Bekkevold, Bouza and Martínez. 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. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fgene.2020.00296 |
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Frontiers in Genetics |
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11 |
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1766188992576880640 |