Data_Sheet_6_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).PDF
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...
Main Authors: | , , , , , , , |
---|---|
Format: | Dataset |
Language: | unknown |
Published: |
2020
|
Subjects: | |
Online Access: | https://doi.org/10.3389/fgene.2020.00296.s006 https://figshare.com/articles/Data_Sheet_6_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_PDF/12076869 |
id |
ftfrontimediafig:oai:figshare.com:article/12076869 |
---|---|
record_format |
openpolar |
spelling |
ftfrontimediafig:oai:figshare.com:article/12076869 2023-05-15T18:15:48+02:00 Data_Sheet_6_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).PDF Oscar Aramburu Francisco Ceballos Adrián Casanova Alan Le Moan Jakob Hemmer-Hansen Dorte Bekkevold Carmen Bouza Paulino Martínez 2020-04-03T15:08:59Z https://doi.org/10.3389/fgene.2020.00296.s006 https://figshare.com/articles/Data_Sheet_6_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_PDF/12076869 unknown doi:10.3389/fgene.2020.00296.s006 https://figshare.com/articles/Data_Sheet_6_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_PDF/12076869 CC BY 4.0 CC-BY Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy turbot SNP panels runs of homozygosity genetic diversity selective sweep Dataset 2020 ftfrontimediafig https://doi.org/10.3389/fgene.2020.00296.s006 2020-04-08T22:52:46Z 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 ... Dataset Scophthalmus maximus Turbot Frontiers: Figshare |
institution |
Open Polar |
collection |
Frontiers: Figshare |
op_collection_id |
ftfrontimediafig |
language |
unknown |
topic |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy turbot SNP panels runs of homozygosity genetic diversity selective sweep |
spellingShingle |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy turbot SNP panels runs of homozygosity genetic diversity selective sweep Oscar Aramburu Francisco Ceballos Adrián Casanova Alan Le Moan Jakob Hemmer-Hansen Dorte Bekkevold Carmen Bouza Paulino Martínez Data_Sheet_6_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).PDF |
topic_facet |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy turbot SNP panels runs of homozygosity genetic diversity selective sweep |
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 |
Dataset |
author |
Oscar Aramburu Francisco Ceballos Adrián Casanova Alan Le Moan Jakob Hemmer-Hansen Dorte Bekkevold Carmen Bouza Paulino Martínez |
author_facet |
Oscar Aramburu Francisco Ceballos Adrián Casanova Alan Le Moan Jakob Hemmer-Hansen Dorte Bekkevold Carmen Bouza Paulino Martínez |
author_sort |
Oscar Aramburu |
title |
Data_Sheet_6_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).PDF |
title_short |
Data_Sheet_6_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).PDF |
title_full |
Data_Sheet_6_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).PDF |
title_fullStr |
Data_Sheet_6_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).PDF |
title_full_unstemmed |
Data_Sheet_6_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).PDF |
title_sort |
data_sheet_6_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).pdf |
publishDate |
2020 |
url |
https://doi.org/10.3389/fgene.2020.00296.s006 https://figshare.com/articles/Data_Sheet_6_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_PDF/12076869 |
genre |
Scophthalmus maximus Turbot |
genre_facet |
Scophthalmus maximus Turbot |
op_relation |
doi:10.3389/fgene.2020.00296.s006 https://figshare.com/articles/Data_Sheet_6_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_PDF/12076869 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fgene.2020.00296.s006 |
_version_ |
1766189018588905472 |