Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies
The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclea...
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Uppsala universitet, Växtekologi och evolution
2016
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Online Access: | http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-300546 https://doi.org/10.1534/g3.116.028753 |
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ftuppsalauniv:oai:DiVA.org:uu-300546 2024-02-11T10:03:47+01:00 Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies Chen, Jun Källman, Thomas Ma, Xiao-Fei Zaina, Giusi Morgante, Michele Lascoux, Martin 2016 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-300546 https://doi.org/10.1534/g3.116.028753 eng eng Uppsala universitet, Växtekologi och evolution Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi Chinese Acad Sci, Key Lab Stress Physiol & Ecol Cold & Arid Reg, Lanzhou, Peoples R China. Univ Udine, Dept Agr Food Environm & Anim Sci, I-33100 Udine, Italy. G3 : Genes, Genomes, Genetics, 2016, 6:7, s. 1979-1989 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-300546 doi:10.1534/g3.116.028753 PMID 27172202 ISI:000379590200018 info:eu-repo/semantics/openAccess pooled sequencing F-ST allele frequencies local adaptation Genetics Genetik Article in journal info:eu-repo/semantics/article text 2016 ftuppsalauniv https://doi.org/10.1534/g3.116.028753 2024-01-17T23:33:40Z The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower F-ST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both F-ST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI. Article in Journal/Newspaper Fennoscandian Uppsala University: Publications (DiVA) Norway G3 Genes|Genomes|Genetics 6 7 1979 1989 |
institution |
Open Polar |
collection |
Uppsala University: Publications (DiVA) |
op_collection_id |
ftuppsalauniv |
language |
English |
topic |
pooled sequencing F-ST allele frequencies local adaptation Genetics Genetik |
spellingShingle |
pooled sequencing F-ST allele frequencies local adaptation Genetics Genetik Chen, Jun Källman, Thomas Ma, Xiao-Fei Zaina, Giusi Morgante, Michele Lascoux, Martin Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies |
topic_facet |
pooled sequencing F-ST allele frequencies local adaptation Genetics Genetik |
description |
The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower F-ST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both F-ST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI. |
format |
Article in Journal/Newspaper |
author |
Chen, Jun Källman, Thomas Ma, Xiao-Fei Zaina, Giusi Morgante, Michele Lascoux, Martin |
author_facet |
Chen, Jun Källman, Thomas Ma, Xiao-Fei Zaina, Giusi Morgante, Michele Lascoux, Martin |
author_sort |
Chen, Jun |
title |
Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies |
title_short |
Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies |
title_full |
Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies |
title_fullStr |
Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies |
title_full_unstemmed |
Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies |
title_sort |
identifying genetic signatures of natural selection using pooled population sequencing in picea abies |
publisher |
Uppsala universitet, Växtekologi och evolution |
publishDate |
2016 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-300546 https://doi.org/10.1534/g3.116.028753 |
geographic |
Norway |
geographic_facet |
Norway |
genre |
Fennoscandian |
genre_facet |
Fennoscandian |
op_relation |
G3 : Genes, Genomes, Genetics, 2016, 6:7, s. 1979-1989 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-300546 doi:10.1534/g3.116.028753 PMID 27172202 ISI:000379590200018 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1534/g3.116.028753 |
container_title |
G3 Genes|Genomes|Genetics |
container_volume |
6 |
container_issue |
7 |
container_start_page |
1979 |
op_container_end_page |
1989 |
_version_ |
1790600113664557056 |