Overt and concealed genetic loads revealed by QTL mapping of genotype-dependent viability in the Pacific oyster Crassostrea gigas
Understanding the genetic bases of inbreeding depression, heterosis, and genetic load is integral to understanding how genetic diversity is maintained in natural populations. The Pacific oyster Crassostrea gigas, like many long-lived plants, has high fecundity and high early mortality (type-III surv...
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ftpubmed:oai:pubmedcentral.nih.gov:8664565 2023-05-15T15:58:22+02:00 Overt and concealed genetic loads revealed by QTL mapping of genotype-dependent viability in the Pacific oyster Crassostrea gigas Yin, Xiaoshen Hedgecock, Dennis 2021-10-06 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8664565/ http://www.ncbi.nlm.nih.gov/pubmed/34739049 https://doi.org/10.1093/genetics/iyab165 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8664565/ http://www.ncbi.nlm.nih.gov/pubmed/34739049 http://dx.doi.org/10.1093/genetics/iyab165 © The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. All rights reserved. For permissions, please email: journals.permissions@oup.com https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_modelThis article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) Genetics Investigation Text 2021 ftpubmed https://doi.org/10.1093/genetics/iyab165 2022-10-09T00:28:18Z Understanding the genetic bases of inbreeding depression, heterosis, and genetic load is integral to understanding how genetic diversity is maintained in natural populations. The Pacific oyster Crassostrea gigas, like many long-lived plants, has high fecundity and high early mortality (type-III survivorship), manifesting a large, overt, genetic load; the oyster harbors an even greater concealed genetic load revealed by inbreeding. Here, we map viability QTL (vQTL) in six interrelated F(2) oyster families, using high-density linkage maps of single nucleotide polymorphisms generated by genotyping-by-sequencing (GBS) methods. Altogether, we detect 70 vQTL and provisionally infer 89 causal mutations, 11 to 20 per family. Genetic mortality caused by independent (unlinked) vQTL ranges from 94.2% to 97.8% across families, consistent with previous reports. High-density maps provide better resolution of genetic mechanisms, however. Models of one causal mutation present in both identical-by-descent (IBD) homozygotes and heterozygotes fit genotype frequencies at 37 vQTL; consistent with the mutation-selection balance theory of genetic load, 20 are highly deleterious, completely recessive mutations and 17 are less deleterious, partially dominant mutations. Another 22 vQTL require pairs of recessive or partially dominant causal mutations, half showing selection against recessive mutations linked in repulsion, producing pseudo-overdominance. Only eight vQTL appear to support the overdominance theory of genetic load, with deficiencies of both IBD homozygotes, but at least four of these are likely caused by pseudo-overdominance. Evidence for epistasis is absent. A high mutation rate, random genetic drift, and pseudo-overdominance may explain both the oyster’s extremely high genetic diversity and a high genetic load maintained primarily by mutation-selection balance. Text Crassostrea gigas Pacific oyster PubMed Central (PMC) Pacific Genetics 219 4 |
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Investigation Yin, Xiaoshen Hedgecock, Dennis Overt and concealed genetic loads revealed by QTL mapping of genotype-dependent viability in the Pacific oyster Crassostrea gigas |
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Investigation |
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Understanding the genetic bases of inbreeding depression, heterosis, and genetic load is integral to understanding how genetic diversity is maintained in natural populations. The Pacific oyster Crassostrea gigas, like many long-lived plants, has high fecundity and high early mortality (type-III survivorship), manifesting a large, overt, genetic load; the oyster harbors an even greater concealed genetic load revealed by inbreeding. Here, we map viability QTL (vQTL) in six interrelated F(2) oyster families, using high-density linkage maps of single nucleotide polymorphisms generated by genotyping-by-sequencing (GBS) methods. Altogether, we detect 70 vQTL and provisionally infer 89 causal mutations, 11 to 20 per family. Genetic mortality caused by independent (unlinked) vQTL ranges from 94.2% to 97.8% across families, consistent with previous reports. High-density maps provide better resolution of genetic mechanisms, however. Models of one causal mutation present in both identical-by-descent (IBD) homozygotes and heterozygotes fit genotype frequencies at 37 vQTL; consistent with the mutation-selection balance theory of genetic load, 20 are highly deleterious, completely recessive mutations and 17 are less deleterious, partially dominant mutations. Another 22 vQTL require pairs of recessive or partially dominant causal mutations, half showing selection against recessive mutations linked in repulsion, producing pseudo-overdominance. Only eight vQTL appear to support the overdominance theory of genetic load, with deficiencies of both IBD homozygotes, but at least four of these are likely caused by pseudo-overdominance. Evidence for epistasis is absent. A high mutation rate, random genetic drift, and pseudo-overdominance may explain both the oyster’s extremely high genetic diversity and a high genetic load maintained primarily by mutation-selection balance. |
format |
Text |
author |
Yin, Xiaoshen Hedgecock, Dennis |
author_facet |
Yin, Xiaoshen Hedgecock, Dennis |
author_sort |
Yin, Xiaoshen |
title |
Overt and concealed genetic loads revealed by QTL mapping of genotype-dependent viability in the Pacific oyster Crassostrea gigas |
title_short |
Overt and concealed genetic loads revealed by QTL mapping of genotype-dependent viability in the Pacific oyster Crassostrea gigas |
title_full |
Overt and concealed genetic loads revealed by QTL mapping of genotype-dependent viability in the Pacific oyster Crassostrea gigas |
title_fullStr |
Overt and concealed genetic loads revealed by QTL mapping of genotype-dependent viability in the Pacific oyster Crassostrea gigas |
title_full_unstemmed |
Overt and concealed genetic loads revealed by QTL mapping of genotype-dependent viability in the Pacific oyster Crassostrea gigas |
title_sort |
overt and concealed genetic loads revealed by qtl mapping of genotype-dependent viability in the pacific oyster crassostrea gigas |
publisher |
Oxford University Press |
publishDate |
2021 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8664565/ http://www.ncbi.nlm.nih.gov/pubmed/34739049 https://doi.org/10.1093/genetics/iyab165 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
Genetics |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8664565/ http://www.ncbi.nlm.nih.gov/pubmed/34739049 http://dx.doi.org/10.1093/genetics/iyab165 |
op_rights |
© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. All rights reserved. For permissions, please email: journals.permissions@oup.com https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_modelThis article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) |
op_doi |
https://doi.org/10.1093/genetics/iyab165 |
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Genetics |
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219 |
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4 |
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1766394096608346112 |