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Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand
Anticipating the evolutionary responses of long-lived organisms, such as trees, to environmental changes, requires the assessment of genetic variation of adaptive traits in natural populations. To this end, high-density markers are needed to calculate genomic relatedness between individuals allowing...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6053538/ https://www.ncbi.nlm.nih.gov/pubmed/30057586 http://dx.doi.org/10.3389/fpls.2018.00996 |
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author | Lesur, Isabelle Alexandre, Hermine Boury, Christophe Chancerel, Emilie Plomion, Christophe Kremer, Antoine |
author_facet | Lesur, Isabelle Alexandre, Hermine Boury, Christophe Chancerel, Emilie Plomion, Christophe Kremer, Antoine |
author_sort | Lesur, Isabelle |
collection | PubMed |
description | Anticipating the evolutionary responses of long-lived organisms, such as trees, to environmental changes, requires the assessment of genetic variation of adaptive traits in natural populations. To this end, high-density markers are needed to calculate genomic relatedness between individuals allowing to estimate the genetic variance of traits in wild populations. We designed a targeted capture-based, next-generation sequencing assay based on the highly heterozygous pedunculate oak (Quercus robur) reference genome, for the sequencing of 3 Mb of genic and intergenic regions. Using a mixed stand of 293 Q. robur and Q. petraea genotypes we successfully captured over 97% of the target sequences, corresponding to 0.39% of the oak genome, with sufficient depth (97×) for the detection of about 190,000 SNPs evenly spread over the targeted regions. We validated the technique by evaluating its reproducibility, and comparing the genomic relatedness of trees with their known pedigree relationship. We explored the use of the technique on other related species and highlighted the advantages and limitations of this approach. We found that 92.07% of target sequences in Q. suber and 70.36% of sequences in Fagus sylvatica were captured. We used this SNP resource to estimate genetic relatedness in the mixed oak stand. Mean pairwise genetic relatedness was low within each species with a few values exceeding 0.25 (half-sibs) or 0.5 (full-sibs). Finally, we applied the technique to a long-standing issue in population genetics of trees regarding the relationship between inbreeding and components of fitness. We found very weak signals for inbreeding depression for reproductive success and no signal for growth within both species. |
format | Online Article Text |
id | pubmed-6053538 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-60535382018-07-27 Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand Lesur, Isabelle Alexandre, Hermine Boury, Christophe Chancerel, Emilie Plomion, Christophe Kremer, Antoine Front Plant Sci Plant Science Anticipating the evolutionary responses of long-lived organisms, such as trees, to environmental changes, requires the assessment of genetic variation of adaptive traits in natural populations. To this end, high-density markers are needed to calculate genomic relatedness between individuals allowing to estimate the genetic variance of traits in wild populations. We designed a targeted capture-based, next-generation sequencing assay based on the highly heterozygous pedunculate oak (Quercus robur) reference genome, for the sequencing of 3 Mb of genic and intergenic regions. Using a mixed stand of 293 Q. robur and Q. petraea genotypes we successfully captured over 97% of the target sequences, corresponding to 0.39% of the oak genome, with sufficient depth (97×) for the detection of about 190,000 SNPs evenly spread over the targeted regions. We validated the technique by evaluating its reproducibility, and comparing the genomic relatedness of trees with their known pedigree relationship. We explored the use of the technique on other related species and highlighted the advantages and limitations of this approach. We found that 92.07% of target sequences in Q. suber and 70.36% of sequences in Fagus sylvatica were captured. We used this SNP resource to estimate genetic relatedness in the mixed oak stand. Mean pairwise genetic relatedness was low within each species with a few values exceeding 0.25 (half-sibs) or 0.5 (full-sibs). Finally, we applied the technique to a long-standing issue in population genetics of trees regarding the relationship between inbreeding and components of fitness. We found very weak signals for inbreeding depression for reproductive success and no signal for growth within both species. Frontiers Media S.A. 2018-07-13 /pmc/articles/PMC6053538/ /pubmed/30057586 http://dx.doi.org/10.3389/fpls.2018.00996 Text en Copyright © 2018 Lesur, Alexandre, Boury, Chancerel, Plomion and Kremer. 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 | Plant Science Lesur, Isabelle Alexandre, Hermine Boury, Christophe Chancerel, Emilie Plomion, Christophe Kremer, Antoine Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand |
title | Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand |
title_full | Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand |
title_fullStr | Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand |
title_full_unstemmed | Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand |
title_short | Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand |
title_sort | development of target sequence capture and estimation of genomic relatedness in a mixed oak stand |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6053538/ https://www.ncbi.nlm.nih.gov/pubmed/30057586 http://dx.doi.org/10.3389/fpls.2018.00996 |
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