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Patterns of Nucleotide Diversity at Photoperiod Related Genes in Norway Spruce [Picea abies (L.) Karst.]

The ability of plants to track seasonal changes is largely dependent on genes assigned to the photoperiod pathway, and variation in those genes is thereby important for adaptation to local day length conditions. Extensive physiological data in several temperate conifer species suggest that populatio...

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Autores principales: Källman, Thomas, De Mita, Stéphane, Larsson, Hanna, Gyllenstrand, Niclas, Heuertz, Myriam, Parducci, Laura, Suyama, Yoshihisa, Lagercrantz, Ulf, Lascoux, Martin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014479/
https://www.ncbi.nlm.nih.gov/pubmed/24810273
http://dx.doi.org/10.1371/journal.pone.0095306
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author Källman, Thomas
De Mita, Stéphane
Larsson, Hanna
Gyllenstrand, Niclas
Heuertz, Myriam
Parducci, Laura
Suyama, Yoshihisa
Lagercrantz, Ulf
Lascoux, Martin
author_facet Källman, Thomas
De Mita, Stéphane
Larsson, Hanna
Gyllenstrand, Niclas
Heuertz, Myriam
Parducci, Laura
Suyama, Yoshihisa
Lagercrantz, Ulf
Lascoux, Martin
author_sort Källman, Thomas
collection PubMed
description The ability of plants to track seasonal changes is largely dependent on genes assigned to the photoperiod pathway, and variation in those genes is thereby important for adaptation to local day length conditions. Extensive physiological data in several temperate conifer species suggest that populations are adapted to local light conditions, but data on the genes underlying this adaptation are more limited. Here we present nucleotide diversity data from 19 genes putatively involved in photoperiodic response in Norway spruce (Picea abies). Based on similarity to model plants the genes were grouped into three categories according to their presumed position in the photoperiod pathway: photoreceptors, circadian clock genes, and downstream targets. An HKA (Hudson, Kreitman and Aquade) test showed a significant excess of diversity at photoreceptor genes, but no departure from neutrality at circadian genes and downstream targets. Departures from neutrality were also tested with Tajima's D and Fay and Wu's H statistics under three demographic scenarios: the standard neutral model, a population expansion model, and a more complex population split model. Only one gene, the circadian clock gene PaPRR3 with a highly positive Tajima's D value, deviates significantly from all tested demographic scenarios. As the PaPRR3 gene harbours multiple non-synonymous variants it appears as an excellent candidate gene for control of photoperiod response in Norway spruce.
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spelling pubmed-40144792014-05-14 Patterns of Nucleotide Diversity at Photoperiod Related Genes in Norway Spruce [Picea abies (L.) Karst.] Källman, Thomas De Mita, Stéphane Larsson, Hanna Gyllenstrand, Niclas Heuertz, Myriam Parducci, Laura Suyama, Yoshihisa Lagercrantz, Ulf Lascoux, Martin PLoS One Research Article The ability of plants to track seasonal changes is largely dependent on genes assigned to the photoperiod pathway, and variation in those genes is thereby important for adaptation to local day length conditions. Extensive physiological data in several temperate conifer species suggest that populations are adapted to local light conditions, but data on the genes underlying this adaptation are more limited. Here we present nucleotide diversity data from 19 genes putatively involved in photoperiodic response in Norway spruce (Picea abies). Based on similarity to model plants the genes were grouped into three categories according to their presumed position in the photoperiod pathway: photoreceptors, circadian clock genes, and downstream targets. An HKA (Hudson, Kreitman and Aquade) test showed a significant excess of diversity at photoreceptor genes, but no departure from neutrality at circadian genes and downstream targets. Departures from neutrality were also tested with Tajima's D and Fay and Wu's H statistics under three demographic scenarios: the standard neutral model, a population expansion model, and a more complex population split model. Only one gene, the circadian clock gene PaPRR3 with a highly positive Tajima's D value, deviates significantly from all tested demographic scenarios. As the PaPRR3 gene harbours multiple non-synonymous variants it appears as an excellent candidate gene for control of photoperiod response in Norway spruce. Public Library of Science 2014-05-08 /pmc/articles/PMC4014479/ /pubmed/24810273 http://dx.doi.org/10.1371/journal.pone.0095306 Text en © 2014 Källman et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Källman, Thomas
De Mita, Stéphane
Larsson, Hanna
Gyllenstrand, Niclas
Heuertz, Myriam
Parducci, Laura
Suyama, Yoshihisa
Lagercrantz, Ulf
Lascoux, Martin
Patterns of Nucleotide Diversity at Photoperiod Related Genes in Norway Spruce [Picea abies (L.) Karst.]
title Patterns of Nucleotide Diversity at Photoperiod Related Genes in Norway Spruce [Picea abies (L.) Karst.]
title_full Patterns of Nucleotide Diversity at Photoperiod Related Genes in Norway Spruce [Picea abies (L.) Karst.]
title_fullStr Patterns of Nucleotide Diversity at Photoperiod Related Genes in Norway Spruce [Picea abies (L.) Karst.]
title_full_unstemmed Patterns of Nucleotide Diversity at Photoperiod Related Genes in Norway Spruce [Picea abies (L.) Karst.]
title_short Patterns of Nucleotide Diversity at Photoperiod Related Genes in Norway Spruce [Picea abies (L.) Karst.]
title_sort patterns of nucleotide diversity at photoperiod related genes in norway spruce [picea abies (l.) karst.]
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014479/
https://www.ncbi.nlm.nih.gov/pubmed/24810273
http://dx.doi.org/10.1371/journal.pone.0095306
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