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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Frontiers Media S.A.
2020-04-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2020.00296/full |
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| author | Oscar Aramburu Oscar Aramburu Francisco Ceballos Adrián Casanova Adrián Casanova Alan Le Moan Jakob Hemmer-Hansen Dorte Bekkevold Carmen Bouza Carmen Bouza Paulino Martínez Paulino Martínez |
| author_facet | Oscar Aramburu Oscar Aramburu Francisco Ceballos Adrián Casanova Adrián Casanova Alan Le Moan Jakob Hemmer-Hansen Dorte Bekkevold Carmen Bouza Carmen Bouza Paulino Martínez Paulino Martínez |
| author_sort | Oscar Aramburu |
| collection | DOAJ |
| 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 (FROH) 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 of the domestic broodstock, 7 in the wild population and one in both populations; one (broodstock) and two (wild) of those were found in significant regions retained under more restrictive ZHp criteria in the broodstock and the wild population, respectively. Genome mining and functional enrichment within regions associated with selective sweeps disclosed relevant genes and pathways related to aquaculture target traits, including growth and immune-related pathways, metabolism and response to hypoxia, which showcases how this genome atlas of genetic diversity can be a valuable resource to look for candidate genes related to natural or artificial selection in turbot populations. |
| first_indexed | 2024-12-10T06:36:18Z |
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| id | doaj.art-375c58b307674e519dd5809bb1621718 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-10T06:36:18Z |
| publishDate | 2020-04-01 |
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| series | Frontiers in Genetics |
| spelling | doaj.art-375c58b307674e519dd5809bb16217182022-12-22T01:58:54ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-04-011110.3389/fgene.2020.00296471343Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot (Scophthalmus maximus)Oscar Aramburu0Oscar Aramburu1Francisco Ceballos2Adrián Casanova3Adrián Casanova4Alan Le Moan5Jakob Hemmer-Hansen6Dorte Bekkevold7Carmen Bouza8Carmen Bouza9Paulino Martínez10Paulino Martínez11Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, SpainInstituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, SpainSydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Johannesburg, South AfricaDepartment of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, SpainInstituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, SpainNational Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, DenmarkNational Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, DenmarkNational Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, DenmarkDepartment of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, SpainInstituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, SpainDepartment of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, SpainInstituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, SpainMassive 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 (FROH) 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 of the domestic broodstock, 7 in the wild population and one in both populations; one (broodstock) and two (wild) of those were found in significant regions retained under more restrictive ZHp criteria in the broodstock and the wild population, respectively. Genome mining and functional enrichment within regions associated with selective sweeps disclosed relevant genes and pathways related to aquaculture target traits, including growth and immune-related pathways, metabolism and response to hypoxia, which showcases how this genome atlas of genetic diversity can be a valuable resource to look for candidate genes related to natural or artificial selection in turbot populations.https://www.frontiersin.org/article/10.3389/fgene.2020.00296/fullturbotSNP panelsruns of homozygositygenetic diversityselective sweep |
| spellingShingle | Oscar Aramburu Oscar Aramburu Francisco Ceballos Adrián Casanova Adrián Casanova Alan Le Moan Jakob Hemmer-Hansen Dorte Bekkevold Carmen Bouza Carmen Bouza Paulino Martínez Paulino Martínez 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) Frontiers in Genetics turbot SNP panels runs of homozygosity genetic diversity selective sweep |
| 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_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_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_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 |
| topic | turbot SNP panels runs of homozygosity genetic diversity selective sweep |
| url | https://www.frontiersin.org/article/10.3389/fgene.2020.00296/full |
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