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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Online Access: | http://hdl.handle.net/11390/1110617 https://doi.org/10.1534/g3.116.028753 |
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ftunivudineiris:oai:air.uniud.it:11390/1110617 2023-07-30T04:03:28+02:00 Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies Chen, Jun Källman, Thomas Ma, Xiao Fei Zaina, Giusi Lascoux, Martin MORGANTE, Michele Chen, Jun Källman, Thoma Ma, Xiao Fei Zaina, Giusi Morgante, Michele Lascoux, Martin 2016 http://hdl.handle.net/11390/1110617 https://doi.org/10.1534/g3.116.028753 eng eng info:eu-repo/semantics/altIdentifier/wos/WOS:000379590200018 volume:6 issue:7 firstpage:1979 lastpage:1989 numberofpages:11 journal:G3 http://hdl.handle.net/11390/1110617 doi:10.1534/g3.116.028753 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-84978401120 FST allele frequencie local adaptation pooled sequencing info:eu-repo/semantics/article 2016 ftunivudineiris https://doi.org/10.1534/g3.116.028753 2023-07-18T20:14:33Z 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 FST 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 FST 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 Università degli Studi di Udine: CINECA IRIS Norway G3 Genes|Genomes|Genetics 6 7 1979 1989 |
institution |
Open Polar |
collection |
Università degli Studi di Udine: CINECA IRIS |
op_collection_id |
ftunivudineiris |
language |
English |
topic |
FST allele frequencie local adaptation pooled sequencing |
spellingShingle |
FST allele frequencie local adaptation pooled sequencing Chen, Jun Källman, Thomas Ma, Xiao Fei Zaina, Giusi Lascoux, Martin MORGANTE, Michele Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies |
topic_facet |
FST allele frequencie local adaptation pooled sequencing |
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 FST 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 FST 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. |
author2 |
Chen, Jun Källman, Thoma Ma, Xiao Fei Zaina, Giusi Morgante, Michele Lascoux, Martin |
format |
Article in Journal/Newspaper |
author |
Chen, Jun Källman, Thomas Ma, Xiao Fei Zaina, Giusi Lascoux, Martin MORGANTE, Michele |
author_facet |
Chen, Jun Källman, Thomas Ma, Xiao Fei Zaina, Giusi Lascoux, Martin MORGANTE, Michele |
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 |
publishDate |
2016 |
url |
http://hdl.handle.net/11390/1110617 https://doi.org/10.1534/g3.116.028753 |
geographic |
Norway |
geographic_facet |
Norway |
genre |
Fennoscandian |
genre_facet |
Fennoscandian |
op_relation |
info:eu-repo/semantics/altIdentifier/wos/WOS:000379590200018 volume:6 issue:7 firstpage:1979 lastpage:1989 numberofpages:11 journal:G3 http://hdl.handle.net/11390/1110617 doi:10.1534/g3.116.028753 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-84978401120 |
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_ |
1772814477429833728 |