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31 results on '"Kujala, Sonja T"'

1. Genetic Effects

Author

Kärkkäinen, Katri, Kujala, Sonja T., Garcia-Gil, Rosario, Steffenrem, Arne, Sonesson, Johan, Hoikkala, Liina, Mäkinen, Harri, Valkonen, Sauli, Tomé, Margarida, Series Editor, Seifert, Thomas, Series Editor, Kurttila, Mikko, Series Editor, Rautio, Pasi, editor, Routa, Johanna, editor, Huuskonen, Saija, editor, Holmström, Emma, editor, Cedergren, Jonas, editor, and Kuehne, Christian, editor

Published
2025
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2. Trade-offs and Trait Integration in Tree Phenotypes: Consequences for the Sustainable Use of Genetic Resources

Author

Conferencia de Rectores de las Universidades Españolas, Consejo Superior de Colegios de Ingenieros de Minas (España), European Commission, Université de Bordeaux, Agencia Estatal de Investigación (España), Climent Maldonado, José María [0000-0002-0815-2645], Alía Miranda, Ricardo [0000-0002-9426-0967], Kärkkäinen, Katri [0000-0002-3799-3013], Bastien, Catherine [0000-0002-9391-6637], Benito-Garzón, M. [0000-0002-3436-123X], Bouffier, L. [0000-0001-7493-5077], de Dato, Giovanbattista [0000-0003-0289-1727], Delzon, Sylvain [0000-0003-3442-1711], Dowkiw, Arnaud [0000-0003-0477-1091], Elvira Recuenco, Margarita [0000-0001-6749-3346], Grivet, Delphine [0000-0001-8168-4456], González-Martínez, Santiago C. [0000-0002-4534-3766], Hayatgheibi, Haleh [0009-0000-8867-9369], Kujala, Sonja T. [0000-0003-0949-6156], Leplé, J. C. [0000-0003-4125-0738], Martin-Sanz, Ruth C. [0000-0002-0980-2283], de Miguel, Marina [0000-0001-6398-2660], Monteverdi, M. Cristina [0000-0003-1786-4713], Mutke, Sven [0000-0002-6365-7128], Plomion, Christophe [0000-0002-3176-2767], Ramírez Valiente, José Alberto [0000-0002-5951-2938], Sánchez, Leopoldo [0000-0002-8285-0441], Solé-Medina, Aida [0000-0001-6681-2747], Soularue, Jean Paul [0000-0001-7631-950X], Steffenrem, Arne [0000-0001-7116-9151], Teani, Angela [0000-0002-3279-1500], Westin, Johan [0000-0003-1033-1826], Whittet, Richard [0000-0002-5481-227X], Wu, Harry [0000-0002-7072-4704], Zas Arregui, Rafael [0000-0001-6563-2461], Cavers, Stephen [0000-0003-2139-9236], Climent Maldonado, José María, Alía Miranda, Ricardo, Kärkkäinen, Katri, Bastien, Catherine, Benito-Garzón, M., Bouffier, L., de Dato, Giovanbattista, Delzon, Sylvain, Dowkiw, Arnaud, Elvira Recuenco, Margarita, Grivet, Delphine, González-Martínez, Santiago C., Hayatgheibi, Haleh, Kujala, Sonja T., Leplé, J. C., Martin-Sanz, Ruth C., de Miguel, Marina, Monteverdi, M. Cristina, Mutke, Sven, Plomion, Christophe, Ramírez Valiente, José Alberto, Sánchez, Leopoldo, Solé-Medina, Aida, Soularue, Jean Paul, Steffenrem, Arne, Teani, Angela, Westin, Johan, Whittet, Richard, Wu, Harry, Zas Arregui, Rafael, Cavers, Stephen, Conferencia de Rectores de las Universidades Españolas, Consejo Superior de Colegios de Ingenieros de Minas (España), European Commission, Université de Bordeaux, Agencia Estatal de Investigación (España), Climent Maldonado, José María [0000-0002-0815-2645], Alía Miranda, Ricardo [0000-0002-9426-0967], Kärkkäinen, Katri [0000-0002-3799-3013], Bastien, Catherine [0000-0002-9391-6637], Benito-Garzón, M. [0000-0002-3436-123X], Bouffier, L. [0000-0001-7493-5077], de Dato, Giovanbattista [0000-0003-0289-1727], Delzon, Sylvain [0000-0003-3442-1711], Dowkiw, Arnaud [0000-0003-0477-1091], Elvira Recuenco, Margarita [0000-0001-6749-3346], Grivet, Delphine [0000-0001-8168-4456], González-Martínez, Santiago C. [0000-0002-4534-3766], Hayatgheibi, Haleh [0009-0000-8867-9369], Kujala, Sonja T. [0000-0003-0949-6156], Leplé, J. C. [0000-0003-4125-0738], Martin-Sanz, Ruth C. [0000-0002-0980-2283], de Miguel, Marina [0000-0001-6398-2660], Monteverdi, M. Cristina [0000-0003-1786-4713], Mutke, Sven [0000-0002-6365-7128], Plomion, Christophe [0000-0002-3176-2767], Ramírez Valiente, José Alberto [0000-0002-5951-2938], Sánchez, Leopoldo [0000-0002-8285-0441], Solé-Medina, Aida [0000-0001-6681-2747], Soularue, Jean Paul [0000-0001-7631-950X], Steffenrem, Arne [0000-0001-7116-9151], Teani, Angela [0000-0002-3279-1500], Westin, Johan [0000-0003-1033-1826], Whittet, Richard [0000-0002-5481-227X], Wu, Harry [0000-0002-7072-4704], Zas Arregui, Rafael [0000-0001-6563-2461], Cavers, Stephen [0000-0003-2139-9236], Climent Maldonado, José María, Alía Miranda, Ricardo, Kärkkäinen, Katri, Bastien, Catherine, Benito-Garzón, M., Bouffier, L., de Dato, Giovanbattista, Delzon, Sylvain, Dowkiw, Arnaud, Elvira Recuenco, Margarita, Grivet, Delphine, González-Martínez, Santiago C., Hayatgheibi, Haleh, Kujala, Sonja T., Leplé, J. C., Martin-Sanz, Ruth C., de Miguel, Marina, Monteverdi, M. Cristina, Mutke, Sven, Plomion, Christophe, Ramírez Valiente, José Alberto, Sánchez, Leopoldo, Solé-Medina, Aida, Soularue, Jean Paul, Steffenrem, Arne, Teani, Angela, Westin, Johan, Whittet, Richard, Wu, Harry, Zas Arregui, Rafael, and Cavers, Stephen

Abstract

Purpose of Review: In this review, we synthesise current knowledge on trade-offs among traits in key fitness dimensions and identify major research gaps with the intention of laying the groundwork for a rapid advance in tree breeding for multiple objectives as a key contribution to the sustainability of planted forests in the future. Recent Findings: Trade-offs among growth, reproduction, defence, stress tolerance and product quality predicted theoretically have been reported experimentally in many breeding programmes. Among these trade-offs, the genetic linkage between resistance against biotic threats and growth (or other relevant traits) is particularly critical for the current and future management of forest genetic resources. Maintaining tree growth and wood quality in the novel environments of the future requires the assessment of genetic correlations of target traits with phenology, closely linked to survival to temperature extremes. Improving our current knowledge on the genetic trade-offs of drought tolerance as a breeding objective in forest trees obligates a more precise definition of both the specific traits and the experimental conditions. Published evidence suggests that common target traits in breeding programmes may trade-off with reproductive success and fire-adaptation, and the simultaneous improvement of growth and wood quality traits still remains as a constraint in traditional tree breeding. Summary: Changing environments combined with pests and diseases are challenging plantation forestry worldwide, which implies an urgent need to develop new improvement strategies to build the resilience of forestry for our future environments. It is essential to have a better understanding of how traits interact, especially those important for production, climate and biotic threat resilience, but much of the information is still missing. Since many key trade-offs are affected by the environment, we need new studies under novel environments to forecast levels

Published
2024

6. The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

Author

Martínez-Sancho, Elisabet, Slámová, Lenka, Morganti, Sandro, Grefen, Claudio, Carvalho, Barbara, Dauphin, Benjamin, Rellstab, Christian, Gugerli, Felix, Opgenoorth, Lars, Heer, Katrin, Knutzen, Florian, von Arx, Georg, Valladares, Fernando, Cavers, Stephen, Fady, Bruno, Alía, Ricardo, Aravanopoulos, Filippos, Avanzi, Camilla, Bagnoli, Francesca, Barbas, Evangelos, Bastien, Catherine, Benavides, Raquel, Bernier, Frédéric, Bodineau, Guillaume, Bastias, Cristina C., Charpentier, Jean-Paul, Climent, José M., Corréard, Marianne, Courdier, Florence, Danusevicius, Darius, Farsakoglou, Anna-Maria, del Barrio, José M. García, Gilg, Olivier, González-Martínez, Santiago C., Gray, Alan, Hartleitner, Christoph, Hurel, Agathe, Jouineau, Arnaud, Kärkkäinen, Katri, Kujala, Sonja T., Labriola, Mariaceleste, Lascoux, Martin, Lefebvre, Marlène, Lejeune, Vincent, Le-Provost, Grégoire, Liesebach, Mirko, Malliarou, Ermioni, Mariotte, Nicolas, Matesanz, Silvia, Michotey, Célia, Milesi, Pascal, Myking, Tor, Notivol, Eduardo, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Pringarbe, Mehdi, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez-Valiente, José A., Ramskogler, Kurt, Robledo-Arnuncio, Juan J., Savolainen, Outi, Schueler, Silvio, Semerikov, Vladimir, Spanu, Ilaria, Thévenet, Jean, Mette Tollefsrud, Mari, Turion, Norbert, Veisse, Dominique, Vendramin, Giovanni Giuseppe, Villar, Marc, Westin, Johan, and Fonti, Patrick

Published
2020
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7. Author Correction: The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

Author

Martínez-Sancho, Elisabet, Slámová, Lenka, Morganti, Sandro, Grefen, Claudio, Carvalho, Barbara, Dauphin, Benjamin, Rellstab, Christian, Gugerli, Felix, Opgenoorth, Lars, Heer, Katrin, Knutzen, Florian, von Arx, Georg, Valladares, Fernando, Cavers, Stephen, Fady, Bruno, Alía, Ricardo, Aravanopoulos, Filippos, Avanzi, Camilla, Bagnoli, Francesca, Barbas, Evangelos, Bastien, Catherine, Benavides, Raquel, Bernier, Frédéric, Bodineau, Guillaume, Bastias, Cristina C., Charpentier, Jean-Paul, Climent, José M., Corréard, Marianne, Courdier, Florence, Danusevicius, Darius, Farsakoglou, Anna-Maria, García del Barrio, José M., Gilg, Olivier, González-Martínez, Santiago C., Gray, Alan, Hartleitner, Christoph, Hurel, Agathe, Jouineau, Arnaud, Kärkkäinen, Katri, Kujala, Sonja T., Labriola, Mariaceleste, Lascoux, Martin, Lefebvre, Marlène, Lejeune, Vincent, Le-Provost, Grégoire, Liesebach, Mirko, Malliarou, Ermioni, Mariotte, Nicolas, Matesanz, Silvia, Michotey, Célia, Milesi, Pascal, Myking, Tor, Notivol, Eduardo, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Pringarbe, Mehdi, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez-Valiente, José A., Ramskogler, Kurt, Robledo-Arnuncio, Juan J., Savolainen, Outi, Schueler, Silvio, Semerikov, Vladimir, Spanu, Ilaria, Thévenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Veisse, Dominique, Vendramin, Giovanni Giuseppe, Villar, Marc, Westin, Johan, and Fonti, Patrick

Published
2020
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8. Within- and between-population comparisons suggest independently acting selection maintaining parallel clines in Scots pine (Pinus sylvestris).

Author

Kujala, Sonja T, Avia, Komlan, Kumpula, Timo A, Kärkkäinen, Hanni, Heikkinen, Juha, Kärkkäinen, Katri, and Savolainen, Outi

Subjects
*SCOTS pine, *CLIMATE change adaptation, *GENETIC correlations, *GENETIC variation
Abstract

Parallel clines in traits related to adaptation in a species can be due to independent selection on a pair of traits, or due to selection in one trait resulting in a parallel cline in a correlated trait. To distinguish between the mechanisms giving rise to parallel adaptive population divergence of multiple traits along an environmental gradient we need to study variation, correlations, and selective forces within individual populations along the gradient. In many tree species, budset timing (BST) forms a latitudinal cline, and parallel clinal variation is also found in other seedling traits, such as first-year height (FYH) and fall frost injury (FFI). In this study, we set up a common garden experiment with open pollinated progeny from natural populations of Scots pine (Pinus sylvestris), with one large sample from single population (500 families) and smaller samples from across a latitudinal gradient. BST, FYH and induced FFI were first measured in a greenhouse. The seedlings were then planted in the field, where survival and height were measured at the age of 9 years as fitness proxies. We compared between- and within-population variation and genetic correlations of these three seedling traits, and estimated selection gradients at the family level in our main population, taking into account the potential effects of seed weight. Between-population genetic correlations between seedling traits were high (0.76–0.95). Within-population genetic correlations in the main population were lower (0.14–0.35), as in other populations (0.10–0.39). Within population, extensive adaptive variation persists in the seedling traits, in line with rather weak selection gradients, yet maintaining the clines. Although our sampling does not cover the whole cline equally, the results suggest that the individual clines in these traits are maintained by largely independently acting selection, which results in fewer constraints in adaptation under changing climate. [ABSTRACT FROM AUTHOR]

Published
2024
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9. Between but not within species variation in the distribution of fitness effects

Author

James, Jennifer, Kastally, Chedly, Budde, Katharina B., González-Martínez, Santiago C., Milesi, Pascal, Pyhäjärvi, Tanja, Alizoti, Paraskevi, Alía, Ricardo, Ambrosio, Olivier, Aravanopoulos, Filippos A., von Arx, Georg, Audrey, Albet, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia, Bagnoli, Francesca, Bajc, Marko, Ballesteros, Eduardo, Barbas, Evangelos, del Barrio, José M. García, Bastias, Cristina C., Bastien, Catherine, Beffa, Giorgia, Benavides, Raquel, Benoit, Vanina, Bernier, Frédéric, Bignalet, Henri, Bodineau, Guillaume, Bouic, Damien, Brodbeck, Sabine, Brunetto, William, Buchovska, Jurata, Buret, Corinne, Buy, Melanie, Cabanillas-Saldaña, Ana M., Carvalho, Bárbara, Cavers, Stephen, Del Caño, Fernando, Cervantes, Sandra, Cheval, Nicolas, Climent, José M., Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Dauphin, Benjamin, Denou, Jean-Luc, Dokhelar, Bernard, Ducousso, Alexis, Fady, Bruno, Faivre-Rampant, Patricia, Farsakoglou, Anna-Maria, Fonti, Patrick, Ganopoulos, Ioannis, Gilg, Olivier, De Girardi, Nicolas, Graf, René, Gray, Alan, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Heer, Katrin, Hollenbach, Enja, Hurel, Agathe, Issenhuth, Bernard, Jean, Florence, Jorge, Véronique, Jouineau, Arnaud, Kappner, Jan-Philipp, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T., Kumpula, Timo A., Kärkkäinen, Katri, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Le-Provost, Gregoire, Lejeune, Vincent, Lesur-Kupin, Isabelle, Levillain, Joseph, Liesebach, Mirko, López-Quiroga, David, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Mas, Antonio, Matesanz, Silvia, Meier, Benjamin, Meischner, Helge, Michotey, Célia, Morganti, Sandro, Myking, Tor, Nievergelt, Daniel, Eskild Nilsen, Anne, Notivol, Eduardo, Ojeda, Dario I., Olsson, Sanna, Opgenoorth, Lars, Ostreng, Geir, Pakull, Birte, Perry, Annika, Pinosio, Sara, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Raffin, Annie, Ramírez-Valiente, José A., Rellstab, Christian, Remi, Dourthe, Reutimann, Oliver, Richter, Sebastian, Robledo-Arnuncio, Juan J., Rogier, Odile, Sancho, Elisabet Martínez, Savolainen, Outi, Scalabrin, Simone, Schneck, Volker, Schueler, Silvio, Scotti, Ivan, Segundo, Sergio San, Semerikov, Vladimir, Slámová, Lenka, Spanu, Ilaria, Sønstebø, Jørn Henrik, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Valladares, Fernando, Vendramin, Giovanni G., Villar, Marc, Westergren, Marjana, Westin, Johan, Lascoux, Martin, James, Jennifer, Kastally, Chedly, Budde, Katharina B., González-Martínez, Santiago C., Milesi, Pascal, Pyhäjärvi, Tanja, Alizoti, Paraskevi, Alía, Ricardo, Ambrosio, Olivier, Aravanopoulos, Filippos A., von Arx, Georg, Audrey, Albet, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia, Bagnoli, Francesca, Bajc, Marko, Ballesteros, Eduardo, Barbas, Evangelos, del Barrio, José M. García, Bastias, Cristina C., Bastien, Catherine, Beffa, Giorgia, Benavides, Raquel, Benoit, Vanina, Bernier, Frédéric, Bignalet, Henri, Bodineau, Guillaume, Bouic, Damien, Brodbeck, Sabine, Brunetto, William, Buchovska, Jurata, Buret, Corinne, Buy, Melanie, Cabanillas-Saldaña, Ana M., Carvalho, Bárbara, Cavers, Stephen, Del Caño, Fernando, Cervantes, Sandra, Cheval, Nicolas, Climent, José M., Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Dauphin, Benjamin, Denou, Jean-Luc, Dokhelar, Bernard, Ducousso, Alexis, Fady, Bruno, Faivre-Rampant, Patricia, Farsakoglou, Anna-Maria, Fonti, Patrick, Ganopoulos, Ioannis, Gilg, Olivier, De Girardi, Nicolas, Graf, René, Gray, Alan, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Heer, Katrin, Hollenbach, Enja, Hurel, Agathe, Issenhuth, Bernard, Jean, Florence, Jorge, Véronique, Jouineau, Arnaud, Kappner, Jan-Philipp, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T., Kumpula, Timo A., Kärkkäinen, Katri, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Le-Provost, Gregoire, Lejeune, Vincent, Lesur-Kupin, Isabelle, Levillain, Joseph, Liesebach, Mirko, López-Quiroga, David, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Mas, Antonio, Matesanz, Silvia, Meier, Benjamin, Meischner, Helge, Michotey, Célia, Morganti, Sandro, Myking, Tor, Nievergelt, Daniel, Eskild Nilsen, Anne, Notivol, Eduardo, Ojeda, Dario I., Olsson, Sanna, Opgenoorth, Lars, Ostreng, Geir, Pakull, Birte, Perry, Annika, Pinosio, Sara, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Raffin, Annie, Ramírez-Valiente, José A., Rellstab, Christian, Remi, Dourthe, Reutimann, Oliver, Richter, Sebastian, Robledo-Arnuncio, Juan J., Rogier, Odile, Sancho, Elisabet Martínez, Savolainen, Outi, Scalabrin, Simone, Schneck, Volker, Schueler, Silvio, Scotti, Ivan, Segundo, Sergio San, Semerikov, Vladimir, Slámová, Lenka, Spanu, Ilaria, Sønstebø, Jørn Henrik, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Valladares, Fernando, Vendramin, Giovanni G., Villar, Marc, Westergren, Marjana, Westin, Johan, and Lascoux, Martin

Abstract

New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is therefore of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, i.e., whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterised the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence and genetic background. We find statistical support for there being variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and that evolutionarily recent events, such as demographic changes and local adaptation, have little impact.

Published
2023

10. Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research

Author

Kastally, Chedly, Niskanen, Alina K., Perry, Annika, Kujala, Sonja T., Avia, Komlan, Cervantes, Sandra, Haapanen, Matti, Kesalahti, Robert, Kumpula, Timo A., Mattila, Tiina M., Ojeda, Dario, I, Tyrmi, Jaakko S., Wachowiak, Witold, Cavers, Stephen, Karkkainen, Katri, Savolainen, Outi, Pyhajarvi, Tanja, Kastally, Chedly, Niskanen, Alina K., Perry, Annika, Kujala, Sonja T., Avia, Komlan, Cervantes, Sandra, Haapanen, Matti, Kesalahti, Robert, Kumpula, Timo A., Mattila, Tiina M., Ojeda, Dario, I, Tyrmi, Jaakko S., Wachowiak, Witold, Cavers, Stephen, Karkkainen, Katri, Savolainen, Outi, and Pyhajarvi, Tanja

Abstract

Pinus sylvestris (Scots pine) is the most widespread coniferous tree in the boreal forests of Eurasia, with major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies, genetic mapping and genomic selection. We present a new 50K single-nucleotide polymorphism (SNP) genotyping array for Scots pine research, breeding and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array and identified 47 712 high-quality SNPs for the final array (called 'PiSy50k'). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue-specific expression patterns and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.9%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the level of Mendelian error was negligible. In addition, array genotypes successfully discriminate between Scots pine populations of Finnish and Scottish origins. The PiSy50k SNP array will be a valuable tool for a wide variety of future genetic studies and forestry applications.

Published
2022
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11. Author Correction: The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

Author

Martínez-Sancho, Elisabet [0000-0003-4413-6818], Slámová, Lenka [0000-0001-8978-0688], Carvalho, Bárbara [0000-0002-4129-2746], Dauphin, Benjamin [0000-0003-0982-4252], Rellstab, Christian [0000-0002-0221-5975], Gugerli, Felix [0000-0003-3878-1845], Opgenoorth, Lars [0000-0003-0737-047X], Heer, Katrin [0000-0002-1036-599X], Knutzen, Florian [0000-0001-9172-4802], von Arx, Georg [0000-0002-8566-4599], Cavers, Stephen [0000-0003-2139-9236], Fady, Bruno [0000-0003-2379-7617], Alía Miranda, Ricardo [0000-0002-9426-0967], Aravanopoulos, Filippos A. [0000-0001-7194-2642], Avanzi, Camilla [0000-0003-1632-5304], Bagnoli, Francesca [0000-0001-6909-0006], Barbas, Evangelos [0000-0002-5760-605X], Bastien, Catherine [0000-0002-9391-6637], Benavides, Raquel [0000-0003-2328-5371], Bernier, Frédéric [0000-0003-4945-7215], Bastias, Cristina C. [0000-0002-2479-2001], Charpentier, Jean-Paul [0000-0002-6029-0498], Climent Maldonado, José María [0000-0002-0815-2645], Danusevicius, Darius [0000-0002-1196-9293], Farsakoglou, Anna Maria [0000-0002-1906-2813], García Del Barrio, José Manuel [0000-0001-7267-6286], Gilg, Olivier [0000-0002-9083-4492], González-Martínez, S. C. [0000-0002-4534-3766], Hurel, Agathe [0000-0002-4853-9123], Kärkkäinen, Katri [0000-0002-3799-3013], Kujala, Sonja T. [0000-0003-0949-6156], Labriola, Mariaceleste [0000-0002-7622-1921], Lascoux, Martin [0000-0003-1699-9042], Lefebvre, Marlène [0000-0002-0929-5744], Le Provost, G. [0000-0003-1561-266X], Liesebach, M. [0000-0001-8840-5026], Malliarou, Ermioni [0000-0003-4478-9173], Matesanz, Silvia [0000-0003-0060-6136], Michotey, Célia [0000-0003-1877-1703], Myking, T. [0000-0002-8207-4542], Notivol, Eduardo [0000-0003-4272-4536], Pakull, Birte [0000-0003-0921-6732], Piotti, Andrea [0000-0002-3324-5325], Plomion, Christophe [0000-0002-3176-2767], Pyhäjärvi, Tanja [0000-0001-6958-5172], Raffin, Annie [0000-0003-2459-4264], Ramírez Valiente, José Alberto [0000-0002-5951-2938], Robledo-Arnuncio, Juan José [0000-0002-3909-8928], Schueler, S.[0000-0003-0155-5692], Semerikov, Vladimir [0000-0002-2942-8794], Spanu, Ilaria [0000-0002-5682-133X], Mette Tollefsrud, Mari [0000-0002-5939-7845], Vendramin, G. G. [0000-0001-9921-7872], Fonti, Patrick [0000-0002-7070-3292], Martínez-Sancho, Elisabet, Slámová, Lenka, Morganti, Sandro, Grefen, Claudio, Carvalho, Bárbara, Dauphin, Benjamin, Rellstab, Christian, Gugerli, Felix, Opgenoorth, Lars, Heer, Katrin, Knutzen, Florian, von Arx, Georg, Valladares Ros, Fernando, Cavers, Stephen, Fady, Bruno, Alía Miranda, Ricardo, Aravanopoulos, Filippos A., Avanzi, Camilla, Bagnoli, Francesca, Barbas, Evangelos, Bastien, Catherine, Benavides, Raquel, Bernier, Frédéric, Bodineau, Guillaume, Bastias, Cristina C., Charpentier, Jean-Paul, Climent Maldonado, José María, Corréard, Marianne, Courdier, Florence, Danusevicius, Darius, Farsakoglou, Anna Maria, García Del Barrio, José Manuel, Gilg, Olivier, González-Martínez, Santiago C., Gray, Alan, Hartleitner, Christoph, Hurel, Agathe, Jouineau, Arnaud, Kärkkäinen, Katri, Kujala, Sonja T., Labriola, Mariaceleste, Lascoux, Martin, Lefebvre, Marlène, Lejeune, Vincent, Le Provost, G., Liesebach, M., Malliarou, Ermioni, Mariotte, Nicolas, Matesanz, Silvia, Michotey, Célia, Milesi, Pascal, Myking, T., Notivol, Eduardo, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Pringarbe, Mehdi, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez Valiente, José Alberto, Ramskogler, Kurt, Robledo-Arnuncio, Juan José, Savolainen, Outi, Schueler, S., Semerikov, Vladimir, Spanu, Ilaria, Thévenet, Jean, Mette Tollefsrud, Mari, Turion, Norbert, Veisse, Dominique, Vendramin, G. G., Villar, Marc, Westin, Johan, Fonti, Patrick, Martínez-Sancho, Elisabet [0000-0003-4413-6818], Slámová, Lenka [0000-0001-8978-0688], Carvalho, Bárbara [0000-0002-4129-2746], Dauphin, Benjamin [0000-0003-0982-4252], Rellstab, Christian [0000-0002-0221-5975], Gugerli, Felix [0000-0003-3878-1845], Opgenoorth, Lars [0000-0003-0737-047X], Heer, Katrin [0000-0002-1036-599X], Knutzen, Florian [0000-0001-9172-4802], von Arx, Georg [0000-0002-8566-4599], Cavers, Stephen [0000-0003-2139-9236], Fady, Bruno [0000-0003-2379-7617], Alía Miranda, Ricardo [0000-0002-9426-0967], Aravanopoulos, Filippos A. [0000-0001-7194-2642], Avanzi, Camilla [0000-0003-1632-5304], Bagnoli, Francesca [0000-0001-6909-0006], Barbas, Evangelos [0000-0002-5760-605X], Bastien, Catherine [0000-0002-9391-6637], Benavides, Raquel [0000-0003-2328-5371], Bernier, Frédéric [0000-0003-4945-7215], Bastias, Cristina C. [0000-0002-2479-2001], Charpentier, Jean-Paul [0000-0002-6029-0498], Climent Maldonado, José María [0000-0002-0815-2645], Danusevicius, Darius [0000-0002-1196-9293], Farsakoglou, Anna Maria [0000-0002-1906-2813], García Del Barrio, José Manuel [0000-0001-7267-6286], Gilg, Olivier [0000-0002-9083-4492], González-Martínez, S. C. [0000-0002-4534-3766], Hurel, Agathe [0000-0002-4853-9123], Kärkkäinen, Katri [0000-0002-3799-3013], Kujala, Sonja T. [0000-0003-0949-6156], Labriola, Mariaceleste [0000-0002-7622-1921], Lascoux, Martin [0000-0003-1699-9042], Lefebvre, Marlène [0000-0002-0929-5744], Le Provost, G. [0000-0003-1561-266X], Liesebach, M. [0000-0001-8840-5026], Malliarou, Ermioni [0000-0003-4478-9173], Matesanz, Silvia [0000-0003-0060-6136], Michotey, Célia [0000-0003-1877-1703], Myking, T. [0000-0002-8207-4542], Notivol, Eduardo [0000-0003-4272-4536], Pakull, Birte [0000-0003-0921-6732], Piotti, Andrea [0000-0002-3324-5325], Plomion, Christophe [0000-0002-3176-2767], Pyhäjärvi, Tanja [0000-0001-6958-5172], Raffin, Annie [0000-0003-2459-4264], Ramírez Valiente, José Alberto [0000-0002-5951-2938], Robledo-Arnuncio, Juan José [0000-0002-3909-8928], Schueler, S.[0000-0003-0155-5692], Semerikov, Vladimir [0000-0002-2942-8794], Spanu, Ilaria [0000-0002-5682-133X], Mette Tollefsrud, Mari [0000-0002-5939-7845], Vendramin, G. G. [0000-0001-9921-7872], Fonti, Patrick [0000-0002-7070-3292], Martínez-Sancho, Elisabet, Slámová, Lenka, Morganti, Sandro, Grefen, Claudio, Carvalho, Bárbara, Dauphin, Benjamin, Rellstab, Christian, Gugerli, Felix, Opgenoorth, Lars, Heer, Katrin, Knutzen, Florian, von Arx, Georg, Valladares Ros, Fernando, Cavers, Stephen, Fady, Bruno, Alía Miranda, Ricardo, Aravanopoulos, Filippos A., Avanzi, Camilla, Bagnoli, Francesca, Barbas, Evangelos, Bastien, Catherine, Benavides, Raquel, Bernier, Frédéric, Bodineau, Guillaume, Bastias, Cristina C., Charpentier, Jean-Paul, Climent Maldonado, José María, Corréard, Marianne, Courdier, Florence, Danusevicius, Darius, Farsakoglou, Anna Maria, García Del Barrio, José Manuel, Gilg, Olivier, González-Martínez, Santiago C., Gray, Alan, Hartleitner, Christoph, Hurel, Agathe, Jouineau, Arnaud, Kärkkäinen, Katri, Kujala, Sonja T., Labriola, Mariaceleste, Lascoux, Martin, Lefebvre, Marlène, Lejeune, Vincent, Le Provost, G., Liesebach, M., Malliarou, Ermioni, Mariotte, Nicolas, Matesanz, Silvia, Michotey, Célia, Milesi, Pascal, Myking, T., Notivol, Eduardo, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Pringarbe, Mehdi, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez Valiente, José Alberto, Ramskogler, Kurt, Robledo-Arnuncio, Juan José, Savolainen, Outi, Schueler, S., Semerikov, Vladimir, Spanu, Ilaria, Thévenet, Jean, Mette Tollefsrud, Mari, Turion, Norbert, Veisse, Dominique, Vendramin, G. G., Villar, Marc, Westin, Johan, and Fonti, Patrick

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

12. The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

Author

European Commission, Martínez-Sancho, Elisabet [0000-0003-4413-6818], Slámová, Lenka [0000-0001-8978-0688], Carvalho, Bárbara [0000-0002-4129-2746], Dauphin, Benjamin [0000-0003-0982-4252], Rellstab, Christian [0000-0002-0221-5975], Gugerli, Felix [0000-0003-3878-1845], Opgenoorth, Lars [0000-0003-0737-047X], Heer, Katrin [0000-0002-1036-599X], Knutzen, Florian [0000-0001-9172-4802], von Arx, Georg [0000-0002-8566-4599], Cavers, Stephen [0000-0003-2139-9236], Fady, Bruno [0000-0003-2379-7617], Alía Miranda, Ricardo [0000-0002-9426-0967], Aravanopoulos, Filippos A. [0000-0001-7194-2642], Avanzi, Camilla [0000-0003-1632-5304], Bagnoli, Francesca [0000-0001-6909-0006], Barbas, Evangelos [0000-0002-5760-605X], Bastien, Catherine [0000-0002-9391-6637], Benavides, Raquel [0000-0003-2328-5371], Bernier, Frédéric [0000-0003-4945-7215], Bastias, Cristina C. [0000-0002-2479-2001], Charpentier, Jean-Paul [0000-0002-6029-0498], Climent Maldonado, José María [0000-0002-0815-2645], Danusevicius, Darius [0000-0002-1196-9293], Farsakoglou, Anna Maria [0000-0002-1906-2813], García Del Barrio, José Manuel [0000-0001-7267-6286], Gilg, Olivier [0000-0002-9083-4492], González-Martínez, S. C. [0000-0002-4534-3766], Hurel, Agathe [0000-0002-4853-9123], Kärkkäinen, Katri [0000-0002-3799-3013], Kujala, Sonja T. [0000-0003-0949-6156], Labriola, Mariaceleste [0000-0002-7622-1921], Lascoux, Martin [0000-0003-1699-9042], Lefebvre, Marlène [0000-0002-0929-5744], Le Provost, G. [0000-0003-1561-266X], Liesebach, M. [0000-0001-8840-5026], Malliarou, Ermioni [0000-0003-4478-9173], Matesanz, Silvia [0000-0003-0060-6136], Michotey, Célia [0000-0003-1877-1703], Myking, T. [0000-0002-8207-4542], Notivol, Eduardo [0000-0003-4272-4536], Pakull, Birte [0000-0003-0921-6732], Piotti, Andrea [0000-0002-3324-5325], Plomion, Christophe [0000-0002-3176-2767], Pyhäjärvi, Tanja [0000-0001-6958-5172], Raffin, Annie [0000-0003-2459-4264], Ramírez Valiente, José Alberto [0000-0002-5951-2938], Robledo-Arnuncio, Juan José [0000-0002-3909-8928], Schueler, S.[0000-0003-0155-5692], Semerikov, Vladimir [0000-0002-2942-8794], Spanu, Ilaria [0000-0002-5682-133X], Mette Tollefsrud, Mari [0000-0002-5939-7845], Vendramin, G. G. [0000-0001-9921-7872], Fonti, Patrick [0000-0002-7070-3292], Martínez-Sancho, Elisabet, Slámová, Lenka, Morganti, Sandro, Grefen, Claudio, Carvalho, Bárbara, Dauphin, Benjamin, Rellstab, Christian, Gugerli, Felix, Opgenoorth, Lars, Heer, Katrin, Knutzen, Florian, von Arx, Georg, Valladares Ros, Fernando, Cavers, Stephen, Fady, Bruno, Alía Miranda, Ricardo, Aravanopoulos, Filippos A., Avanzi, Camilla, Bagnoli, Francesca, Barbas, Evangelos, Bastien, Catherine, Benavides, Raquel, Bernier, Frédéric, Bodineau, Guillaume, Bastias, Cristina C., Charpentier, Jean-Paul, Climent Maldonado, José María, Corréard, Marianne, Courdier, Florence, Danusevicius, Darius, Farsakoglou, Anna Maria, García Del Barrio, José Manuel, Gilg, Olivier, González-Martínez, Santiago C., Gray, Alan, Hartleitner, Christoph, Hurel, Agathe, Jouineau, Arnaud, Kärkkäinen, Katri, Kujala, Sonja T., Labriola, Mariaceleste, Lascoux, Martin, Lefebvre, Marlène, Lejeune, Vincent, Le Provost, G., Liesebach, M., Malliarou, Ermioni, Mariotte, Nicolas, Matesanz, Silvia, Michotey, Célia, Milesi, Pascal, Myking, T., Notivol, Eduardo, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Pringarbe, Mehdi, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez Valiente, José Alberto, Ramskogler, Kurt, Robledo-Arnuncio, Juan José, Savolainen, Outi, Schueler, S., Semerikov, Vladimir, Spanu, Ilaria, Thévenet, Jean, Mette Tollefsrud, Mari, Turion, Norbert, Veisse, Dominique, Vendramin, G. G., Villar, Marc, Westin, Johan, Fonti, Patrick, European Commission, Martínez-Sancho, Elisabet [0000-0003-4413-6818], Slámová, Lenka [0000-0001-8978-0688], Carvalho, Bárbara [0000-0002-4129-2746], Dauphin, Benjamin [0000-0003-0982-4252], Rellstab, Christian [0000-0002-0221-5975], Gugerli, Felix [0000-0003-3878-1845], Opgenoorth, Lars [0000-0003-0737-047X], Heer, Katrin [0000-0002-1036-599X], Knutzen, Florian [0000-0001-9172-4802], von Arx, Georg [0000-0002-8566-4599], Cavers, Stephen [0000-0003-2139-9236], Fady, Bruno [0000-0003-2379-7617], Alía Miranda, Ricardo [0000-0002-9426-0967], Aravanopoulos, Filippos A. [0000-0001-7194-2642], Avanzi, Camilla [0000-0003-1632-5304], Bagnoli, Francesca [0000-0001-6909-0006], Barbas, Evangelos [0000-0002-5760-605X], Bastien, Catherine [0000-0002-9391-6637], Benavides, Raquel [0000-0003-2328-5371], Bernier, Frédéric [0000-0003-4945-7215], Bastias, Cristina C. [0000-0002-2479-2001], Charpentier, Jean-Paul [0000-0002-6029-0498], Climent Maldonado, José María [0000-0002-0815-2645], Danusevicius, Darius [0000-0002-1196-9293], Farsakoglou, Anna Maria [0000-0002-1906-2813], García Del Barrio, José Manuel [0000-0001-7267-6286], Gilg, Olivier [0000-0002-9083-4492], González-Martínez, S. C. [0000-0002-4534-3766], Hurel, Agathe [0000-0002-4853-9123], Kärkkäinen, Katri [0000-0002-3799-3013], Kujala, Sonja T. [0000-0003-0949-6156], Labriola, Mariaceleste [0000-0002-7622-1921], Lascoux, Martin [0000-0003-1699-9042], Lefebvre, Marlène [0000-0002-0929-5744], Le Provost, G. [0000-0003-1561-266X], Liesebach, M. [0000-0001-8840-5026], Malliarou, Ermioni [0000-0003-4478-9173], Matesanz, Silvia [0000-0003-0060-6136], Michotey, Célia [0000-0003-1877-1703], Myking, T. [0000-0002-8207-4542], Notivol, Eduardo [0000-0003-4272-4536], Pakull, Birte [0000-0003-0921-6732], Piotti, Andrea [0000-0002-3324-5325], Plomion, Christophe [0000-0002-3176-2767], Pyhäjärvi, Tanja [0000-0001-6958-5172], Raffin, Annie [0000-0003-2459-4264], Ramírez Valiente, José Alberto [0000-0002-5951-2938], Robledo-Arnuncio, Juan José [0000-0002-3909-8928], Schueler, S.[0000-0003-0155-5692], Semerikov, Vladimir [0000-0002-2942-8794], Spanu, Ilaria [0000-0002-5682-133X], Mette Tollefsrud, Mari [0000-0002-5939-7845], Vendramin, G. G. [0000-0001-9921-7872], Fonti, Patrick [0000-0002-7070-3292], Martínez-Sancho, Elisabet, Slámová, Lenka, Morganti, Sandro, Grefen, Claudio, Carvalho, Bárbara, Dauphin, Benjamin, Rellstab, Christian, Gugerli, Felix, Opgenoorth, Lars, Heer, Katrin, Knutzen, Florian, von Arx, Georg, Valladares Ros, Fernando, Cavers, Stephen, Fady, Bruno, Alía Miranda, Ricardo, Aravanopoulos, Filippos A., Avanzi, Camilla, Bagnoli, Francesca, Barbas, Evangelos, Bastien, Catherine, Benavides, Raquel, Bernier, Frédéric, Bodineau, Guillaume, Bastias, Cristina C., Charpentier, Jean-Paul, Climent Maldonado, José María, Corréard, Marianne, Courdier, Florence, Danusevicius, Darius, Farsakoglou, Anna Maria, García Del Barrio, José Manuel, Gilg, Olivier, González-Martínez, Santiago C., Gray, Alan, Hartleitner, Christoph, Hurel, Agathe, Jouineau, Arnaud, Kärkkäinen, Katri, Kujala, Sonja T., Labriola, Mariaceleste, Lascoux, Martin, Lefebvre, Marlène, Lejeune, Vincent, Le Provost, G., Liesebach, M., Malliarou, Ermioni, Mariotte, Nicolas, Matesanz, Silvia, Michotey, Célia, Milesi, Pascal, Myking, T., Notivol, Eduardo, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Pringarbe, Mehdi, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez Valiente, José Alberto, Ramskogler, Kurt, Robledo-Arnuncio, Juan José, Savolainen, Outi, Schueler, S., Semerikov, Vladimir, Spanu, Ilaria, Thévenet, Jean, Mette Tollefsrud, Mari, Turion, Norbert, Veisse, Dominique, Vendramin, G. G., Villar, Marc, Westin, Johan, and Fonti, Patrick

Abstract

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios.

Published
2020

13. Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research

Author

Kastally, Chedly, primary, Niskanen, Alina K., additional, Perry, Annika, additional, Kujala, Sonja T., additional, Avia, Komlan, additional, Cervantes, Sandra, additional, Haapanen, Matti, additional, Kesälahti, Robert, additional, Kumpula, Timo A., additional, Mattila, Tiina M., additional, Ojeda, Dario I., additional, Tyrmi, Jaakko S., additional, Wachowiak, Witold, additional, Cavers, Stephen, additional, Kärkkäinen, Katri, additional, Savolainen, Outi, additional, and Pyhäjärvi, Tanja, additional

Published
2022
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14. 275 years of forestry meets genomics inPinus sylvestris

Author

Pyhäjärvi, Tanja, Kujala, Sonja T, and Savolainen, Outi

Subjects
0106 biological sciences, 0301 basic medicine, Linkage disequilibrium, lcsh:Evolution, Genomics, adaptation, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, DNA sequencing, 03 medical and health sciences, genomics, lcsh:QH359-425, Genetics, Inbreeding depression, Genome size, genomic prediction, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, Genetic diversity, Pinus sylvestris, Forestry, 15. Life on land, 030104 developmental biology, allele frequency spectrum, breeding, Special Issue Review and Syntheses, General Agricultural and Biological Sciences, linkage disequilibrium, inbreeding depression, Reference genome
Abstract

Pinus sylvestris has a long history of basic and applied research that is relevant for both forestry and evolutionary studies. Its patterns of adaptive variation and role in forest economic and ecological systems have been studied extensively for nearly 275 years, detailed demography for a 100 years and mating system more than 50 years. However, its reference genome sequence is not yet available and genomic studies have been lagging compared to, for example, Pinus taeda and Picea abies, two other economically important conifers. Despite the lack of reference genome, many modern genomic methods are applicable for a more detailed look at its biological characteristics. For example, RNA‐seq has revealed a complex transcriptional landscape and targeted DNA sequencing displays an excess of rare variants and geographically homogenously distributed molecular genetic diversity. Current DNA and RNA resources can be used as a reference for gene expression studies, SNP discovery, and further targeted sequencing. In the future, specific consequences of the large genome size, such as functional effects of regulatory open chromatin regions and transposable elements, should be investigated more carefully. For forest breeding and long‐term management purposes, genomic data can help in assessing the genetic basis of inbreeding depression and the application of genomic tools for genomic prediction and relatedness estimates. Given the challenges of breeding (long generation time, no easy vegetative propagation) and the economic importance, application of genomic tools has a potential to have a considerable impact. Here, we explore how genomic characteristics of P. sylvestris, such as rare alleles and the low extent of linkage disequilibrium, impact the applicability and power of the tools.

Published
2019
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15. The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species

Author

Opgenoorth, Lars, Dauphin, Benjamin, Benavides, Raquel, Heer, Katrin, Alizoti, Paraskevi, Martínez-Sancho, Elisabet, Alía, Ricardo, Ambrosio, Olivier, Audrey, Albet, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia, Bagnoli, Francesca, Barbas, Evangelos, Bastias, Cristina C, Bastien, Catherine, Ballesteros, Eduardo, Beffa, Giorgia, Bernier, Frédéric, Bignalet, Henri, Bodineau, Guillaume, Bouic, Damien, Brodbeck, Sabine, Brunetto, William, Buchovska, Jurata, Buy, Melanie, Cabanillas-Saldaña, Ana M, Carvalho, Bárbara, Cheval, Nicolas, Climent, José M, Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Del Caño, Fernando, Denou, Jean-Luc, Di Gerardi, Nicolas, Dokhelar, Bernard, Ducousso, Alexis, Nilsen, Anne Eskild, Farsakoglou, Anna-Maria, Fonti, Patrick, Ganopoulos, Ioannis, García Del Barrio, José M, Gilg, Olivier, González-Martínez, Santiago C, Graf, René, Gray, Alan, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Hollenbach, Enja, Hurel, Agathe, Issehut, Bernard, Jean, Florence, Jorge, Veronique, Jouineau, Arnaud, Kappner, Jan-Philipp, Kärkkäinen, Katri, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T, Kumpula, Timo A, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Lascoux, Martin, Lejeune, Vincent, Le-Provost, Gregoire, Levillain, Joseph, Liesebach, Mirko, López-Quiroga, David, Meier, Benjamin, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Mas, Antonio, Matesanz, Silvia, Meischner, Helge, Michotey, Célia, Milesi, Pascal, Morganti, Sandro, Nievergelt, Daniel, Notivol, Eduardo, Østreng, Geir, Pakull, Birte, Perry, Annika, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez-Valiente, José A, Rellstab, Christian, Remi, Dourthe, Richter, Sebastian, Robledo-Arnuncio, Juan J, San Segundo, Sergio, Savolainen, Outi, Schueler, Silvio, Schneck, Volker, Scotti, Ivan, Semerikov, Vladimir, Slámová, Lenka, Sønstebø, Jørn Henrik, Spanu, Ilaria, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Vendramin, Giovanni Giuseppe, Villar, Marc, von Arx, Georg, Westin, Johan, Fady, Bruno, Myking, Tor, Valladares, Fernando, Aravanopoulos, Filippos A, Cavers, Stephen, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Philipps Universität Marburg = Philipps University of Marburg, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Aristotle University of Thessaloniki, Department of Forest Ecology and Genetics, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité expérimentale Forêt Pierroton (UEFP), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office national des forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique et Biomasse Forestières ORléans (GBFOR), Vytautas Magnus University - Vytauto Didziojo Universitetas (VDU), Unité de Recherche Génomique Info (URGI), Gobierno de Aragon, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unité Expérimentale Entomologie et Forêt Méditerranéenne (UEFM), Bavarian Office for Forest Seeding and Planting, Partenaires INRAE, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Norsk institutt for bioøkonomi=Norwegian Institute of Bioeconomy Research (NIBIO), UK Centre for Ecology & Hydrology, Natural Environment Research Council (NERC), LIECO GmbH & Co KG, Natural Resources Institute Finland (LUKE), University of Oulu, Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, SILVA (SILVA), AgroParisTech-Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Thunen Institute of Forest Ecosystems, Thünen Institute, Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Universidad Rey Juan Carlos [Madrid] (URJC), Austrian Research Centre for Forests (BFW), Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences (UB RAS), Skogforsk - Swedish Forestry Research Institute, Swiss Secretariat for Education, Research and Innovation (SERI) 6.0032, European Project: 676876,H2020,H2020-SFS-2015-2,GenTree(2016), Philipps Universität Marburg, Museo Nacional de Ciencias Naturales (CSIC), Consiglio Nazionale delle Ricerche (CNR), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centro de Investigacion Y Tecnologia Agroalimentaria de Aragon, Norwegian Institute of Bioeconomy Research (NIBIO), and Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA)

Subjects
crown size, fruit number, Skogsvetenskap, bark thickness, AcademicSubjects/SCI02254, DBH, Forest Science, soil depth, forking index, Botany, Pinus sylvestris, Botanik, Forests, Data Note, stem straightness, Ecology and Environment, Trees, regeneration, branch angle, Fagus, AcademicSubjects/SCI00960, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Picea, height
Abstract

Background: Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information. Findings: The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species’ geographic ranges and reflecting local environmental gradients. Conclusion: The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data collection available.

Published
2021
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18. Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research

Author

Kastally, Chedly, primary, Niskanen, Alina K., additional, Perry, Annika, additional, Kujala, Sonja T., additional, Avia, Komlan, additional, Cervantes, Sandra, additional, Haapanen, Matti, additional, Kesälahti, Robert, additional, Kumpula, Timo A., additional, Mattila, Tiina M., additional, Ojeda, Dario I., additional, Tyrmi, Jaakko S., additional, Wachowiak, Witold, additional, Cavers, Stephen, additional, Kärkkäinen, Katri, additional, Savolainen, Outi, additional, and Pyhäjärvi, Tanja, additional

Published
2021
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19. Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research

Author

Kastally, Chedly, Niskanen, Alina K., Perry, Annika, Kujala, Sonja T., Avia, Komlan, Cervantes, Sandra, Haapanen, Matti, Kesälahti, Robert, Kumpula, Timo A., Mattila, Tiina M., Ojeda, Dario I., Tyrmi, Jaakko S., Wachowiak, Witold, Cavers, Stephen, Kärkkäinen, Katri, Savolainen, Outi, Pyhäjärvi, Tanja, Kastally, Chedly, Niskanen, Alina K., Perry, Annika, Kujala, Sonja T., Avia, Komlan, Cervantes, Sandra, Haapanen, Matti, Kesälahti, Robert, Kumpula, Timo A., Mattila, Tiina M., Ojeda, Dario I., Tyrmi, Jaakko S., Wachowiak, Witold, Cavers, Stephen, Kärkkäinen, Katri, Savolainen, Outi, and Pyhäjärvi, Tanja

Abstract

Pinus sylvestris (Scots pine) is the most widespread coniferous tree in the boreal forests of Eurasia, with major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies, genetic mapping and genomic selection. We present a new 50K single-nucleotide polymorphism (SNP) genotyping array for Scots pine research, breeding and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array and identified 47 712 high-quality SNPs for the final array (called ‘PiSy50k’). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue-specific expression patterns and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.9%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the level of Mendelian error was negligible. In addition, array genotypes successfully discriminate between Scots pine populations of Finnish and Scottish origins. The PiSy50k SNP array will be a valuable tool for a wide variety of future genetic studies and forestry applications.

Published
2021

20. The GenTree Leaf Collection: inter‐ and intraspecific leaf variation in seven forest tree species in Europe

Author

Benavides, Raquel, Carvalho, Bárbara, Bastias, Cristina C., López‐Quiroga, David, Mas, Antonio, Cavers, Stephen, Gray, Alan, Albet, Audrey, Alía, Ricardo, Ambrosio, Olivier, Aravanopoulos, Filippos, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia V., Bagnoli, Francesca, Ballesteros, Eduardo, Barbas, Evangelos, Bastien, Catherine, Bernier, Frédéric, Bignalet, Henry, Bouic, Damien, Brunetto, William, Buchovska, Jurata, Cabanillas‐Saldaña, Ana M., Cheval, Nicolas, Climent, José M., Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Dauphin, Benjamin, Del Caño, Fernando, Denou, Jean‐Luc, Dokhelar, Bernard, Dourthe, Rémi, Farsakoglou, Anna‐Maria, Fera, Andreas, Fonti, Patrick, Ganopoulos, Ioannis, García del Barrio, José M., Gilg, Olivier, González‐Martínez, Santiago C., Graf, René, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Heer, Katrin, Hollenbach, Enja, Hurel, Agathe, Issehuth, Bernard, Jean, Florence, Jorge, Veronique, Jouineau, Arnaud, Kappner, Jan‐Philipp, Kärkkäinen, Katri, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T., Kumpula, Timo, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Lascoux, Martin, Le Provost, Gregoire, Liesebach, Mirko, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Martínez‐Sancho, Elisabet, Matesanz, Silvia, Meischner, Helge, Michotey, Célia, Milesi, Pascal, Morganti, Sandro, Myking, Tor, Nilsen, Anne E., Notivol, Eduardo, Opgenoorth, Lars, Østreng, Geir, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez‐Valiente, José A., Rellstab, Christian, Richter, Sebastian, Robledo‐Arnuncio, Juan J., San Segundo, Sergio, Savolainen, Outi, Schneck, Volker, Schueler, Silvio, Scotti, Ivan, Semerikov, Vladimir, Henrik Sønstebø, Jørn, Spanu, Ilaria, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Vendramin, Giovanni Giuseppe, Villar, Marc, Westin, Johan, Fady, Bruno, Valladares, Fernando, Benavides, Raquel, Carvalho, Bárbara, Bastias, Cristina C., López‐Quiroga, David, Mas, Antonio, Cavers, Stephen, Gray, Alan, Albet, Audrey, Alía, Ricardo, Ambrosio, Olivier, Aravanopoulos, Filippos, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia V., Bagnoli, Francesca, Ballesteros, Eduardo, Barbas, Evangelos, Bastien, Catherine, Bernier, Frédéric, Bignalet, Henry, Bouic, Damien, Brunetto, William, Buchovska, Jurata, Cabanillas‐Saldaña, Ana M., Cheval, Nicolas, Climent, José M., Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Dauphin, Benjamin, Del Caño, Fernando, Denou, Jean‐Luc, Dokhelar, Bernard, Dourthe, Rémi, Farsakoglou, Anna‐Maria, Fera, Andreas, Fonti, Patrick, Ganopoulos, Ioannis, García del Barrio, José M., Gilg, Olivier, González‐Martínez, Santiago C., Graf, René, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Heer, Katrin, Hollenbach, Enja, Hurel, Agathe, Issehuth, Bernard, Jean, Florence, Jorge, Veronique, Jouineau, Arnaud, Kappner, Jan‐Philipp, Kärkkäinen, Katri, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T., Kumpula, Timo, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Lascoux, Martin, Le Provost, Gregoire, Liesebach, Mirko, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Martínez‐Sancho, Elisabet, Matesanz, Silvia, Meischner, Helge, Michotey, Célia, Milesi, Pascal, Morganti, Sandro, Myking, Tor, Nilsen, Anne E., Notivol, Eduardo, Opgenoorth, Lars, Østreng, Geir, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez‐Valiente, José A., Rellstab, Christian, Richter, Sebastian, Robledo‐Arnuncio, Juan J., San Segundo, Sergio, Savolainen, Outi, Schneck, Volker, Schueler, Silvio, Scotti, Ivan, Semerikov, Vladimir, Henrik Sønstebø, Jørn, Spanu, Ilaria, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Vendramin, Giovanni Giuseppe, Villar, Marc, Westin, Johan, Fady, Bruno, and Valladares, Fernando

Abstract

Motivation: Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait assessment are embedded in the GenTree project (EU‐Horizon 2020), which aims at characterizing the genetic and phenotypic variability of forest tree species to optimize the management and sustainable use of forest genetic resources. Our dataset captures substantial intra‐ and interspecific leaf phenotypic variability, and provides valuable information for studying the relationship between ecosystem functioning and trait variability of individuals, and the response and resilience of species to environmental changes. Main types of variable contained: We chose morphological and chemical characters linked to trade‐offs between acquisition and conservation of resources and water use, namely specific leaf area, leaf size, carbon and nitrogen content and their ratio, and the isotopic signature of stable isotope 13C and 15N in leaves. Spatial location and grain: We surveyed between 18 and 22 populations per species, 141 in total, across Europe. Time period: Leaf sampling took place between 2016 and 2017. Major taxa and level of measurement: We sampled at least 25 individuals in each population, 3,569 trees in total, and measured traits in 35,755 leaves from seven European tree species, i.e. the conifers Picea abies, Pinus pinaster and Pinus sylvestris, and the broadleaves Betula pendula, Fagus sylvatica, Populus nigra and Quercus petraea. Software format: The data files are in ASCII text, tab delimited, not compressed.

Published
2021

21. Selection patterns on early-life phenotypic traits in Pinus sylvestris are associated with precipitation and temperature along a climatic gradient in Europe

Author

European Commission, Academy of Finland, Natural Resources Institute Finland, Ramírez-Valiente, José Alberto, Solé-Medina, Aida, Pyhäjärvi, Tanja, Savolainen, Outi, Cervantes, Sandra, Kesälahti, Robert, Kujala, Sonja T., Kumpula, Timo, Heer, Katrin, Opgenoorth, Lars, Siebertz, Jan, Danusevicius, Darius, Notivol, Eduardo, Benavides, Raquel, Robledo Arnuncio, Juan José, European Commission, Academy of Finland, Natural Resources Institute Finland, Ramírez-Valiente, José Alberto, Solé-Medina, Aida, Pyhäjärvi, Tanja, Savolainen, Outi, Cervantes, Sandra, Kesälahti, Robert, Kujala, Sonja T., Kumpula, Timo, Heer, Katrin, Opgenoorth, Lars, Siebertz, Jan, Danusevicius, Darius, Notivol, Eduardo, Benavides, Raquel, and Robledo Arnuncio, Juan José

Abstract

Understanding the dynamics of selection is key to predicting the response of tree species to new environmental conditions in the current context of climate change. However, selection patterns acting on early recruitment stages and their climatic drivers remain largely unknown in most tree species, despite being a critical period of their life cycle. We measured phenotypic selection on Pinus sylvestris seed mass, emergence time and early growth rate over 2 yr in four common garden experiments established along the latitudinal gradient of the species in Europe. Significant phenotypic plasticity and among-population genetic variation were found for all measured phenotypic traits. Heat and drought negatively affected fitness in the southern sites, but heavy rainfalls also decreased early survival in middle latitudes. Climate-driven directional selection was found for higher seed mass and earlier emergence time, while the form of selection on seedling growth rates differed among sites and populations. Evidence of adaptive and maladaptive phenotypic plasticity was found for emergence time and early growth rate, respectively. Seed mass, emergence time and early growth rate have an adaptive role in the early stages of P. sylvestris and climate strongly influences the patterns of selection on these fitness-related traits.

Published
2021

22. The GenTree Leaf Collection: Inter‐ and intraspecific leaf variation in seven forest tree species in Europe

Author

Benavides, Raquel, primary, Carvalho, Bárbara, additional, Bastias, Cristina C., additional, López‐Quiroga, David, additional, Mas, Antonio, additional, Cavers, Stephen, additional, Gray, Alan, additional, Albet, Audrey, additional, Alía, Ricardo, additional, Ambrosio, Olivier, additional, Aravanopoulos, Filippos, additional, Auñón, Francisco, additional, Avanzi, Camilla, additional, Avramidou, Evangelia V., additional, Bagnoli, Francesca, additional, Ballesteros, Eduardo, additional, Barbas, Evangelos, additional, Bastien, Catherine, additional, Bernier, Frédéric, additional, Bignalet, Henry, additional, Bouic, Damien, additional, Brunetto, William, additional, Buchovska, Jurata, additional, Cabanillas‐Saldaña, Ana M., additional, Cheval, Nicolas, additional, Climent, José M., additional, Correard, Marianne, additional, Cremer, Eva, additional, Danusevičius, Darius, additional, Dauphin, Benjamin, additional, Del Caño, Fernando, additional, Denou, Jean‐Luc, additional, Dokhelar, Bernard, additional, Dourthe, Rémi, additional, Farsakoglou, Anna‐Maria, additional, Fera, Andreas, additional, Fonti, Patrick, additional, Ganopoulos, Ioannis, additional, García del Barrio, José M., additional, Gilg, Olivier, additional, González‐Martínez, Santiago C., additional, Graf, René, additional, Grivet, Delphine, additional, Gugerli, Felix, additional, Hartleitner, Christoph, additional, Heer, Katrin, additional, Hollenbach, Enja, additional, Hurel, Agathe, additional, Issehuth, Bernard, additional, Jean, Florence, additional, Jorge, Veronique, additional, Jouineau, Arnaud, additional, Kappner, Jan‐Philipp, additional, Kärkkäinen, Katri, additional, Kesälahti, Robert, additional, Knutzen, Florian, additional, Kujala, Sonja T., additional, Kumpula, Timo, additional, Labriola, Mariaceleste, additional, Lalanne, Celine, additional, Lambertz, Johannes, additional, Lascoux, Martin, additional, Le Provost, Gregoire, additional, Liesebach, Mirko, additional, Malliarou, Ermioni, additional, Marchon, Jérémy, additional, Mariotte, Nicolas, additional, Martínez‐Sancho, Elisabet, additional, Matesanz, Silvia, additional, Meischner, Helge, additional, Michotey, Célia, additional, Milesi, Pascal, additional, Morganti, Sandro, additional, Myking, Tor, additional, Nilsen, Anne E., additional, Notivol, Eduardo, additional, Opgenoorth, Lars, additional, Østreng, Geir, additional, Pakull, Birte, additional, Piotti, Andrea, additional, Plomion, Christophe, additional, Poinot, Nicolas, additional, Pringarbe, Mehdi, additional, Puzos, Luc, additional, Pyhäjärvi, Tanja, additional, Raffin, Annie, additional, Ramírez‐Valiente, José A., additional, Rellstab, Christian, additional, Richter, Sebastian, additional, Robledo‐Arnuncio, Juan J., additional, San Segundo, Sergio, additional, Savolainen, Outi, additional, Schneck, Volker, additional, Schueler, Silvio, additional, Scotti, Ivan, additional, Semerikov, Vladimir, additional, Henrik Sønstebø, Jørn, additional, Spanu, Ilaria, additional, Thevenet, Jean, additional, Tollefsrud, Mari Mette, additional, Turion, Norbert, additional, Vendramin, Giovanni Giuseppe, additional, Villar, Marc, additional, Westin, Johan, additional, Fady, Bruno, additional, and Valladares, Fernando, additional

Published
2021
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24. Selection patterns on early‐life phenotypic traits in Pinus sylvestris are associated with precipitation and temperature along a climatic gradient in Europe

Author

Ramírez‐Valiente, José Alberto, primary, Solé‐Medina, Aida, additional, Pyhäjärvi, Tanja, additional, Savolainen, Outi, additional, Cervantes, Sandra, additional, Kesälahti, Robert, additional, Kujala, Sonja T., additional, Kumpula, Timo, additional, Heer, Katrin, additional, Opgenoorth, Lars, additional, Siebertz, Jan, additional, Danusevicius, Darius, additional, Notivol, Eduardo, additional, Benavides, Raquel, additional, and Robledo‐Arnuncio, Juan José, additional

Published
2020
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25. The effects of natural and artificial selection on seedling traits in Scots pine (Pinus sylvestris)

Author

Kujala, Sonja T., Kumpula, Timo, Hayatgheibi, Haleh, Avia, Komlan, Knurr, Tino, Kärkkäinen, Katri, Savolainen, Outi, Santé de la vigne et qualité du vin (SVQV), Université de Strasbourg (UNISTRA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2020

28. Novel polymorphic nuclear microsatellite markers for Pinus sylvestris L

Author

Kujala, Sonja T. [0000-0003-0949-6156], Sebastiani, F., Pinzauti, F., Kujala, Sonja T., González-Martínez, Santiago C., Vendramin, G. G., Kujala, Sonja T. [0000-0003-0949-6156], Sebastiani, F., Pinzauti, F., Kujala, Sonja T., González-Martínez, Santiago C., and Vendramin, G. G.

Abstract

Scots pine (Pinus sylvestris L.) is one of the most widespread forest trees in the world, ranging from southern Mediterranean mountains to eastern Siberia. Ten polymorphic microsatellite loci were isolated from Scots pine cDNA sequences and were screened for variability in three natural populations. High levels of genetic variability were observed with effective number of alleles per locus ranging from 1.0 to 4.6 and average expected heterozygosity per population of 0.79. With only two exceptions, Hardy-Weinberg expectations were confirmed. All loci were in linkage equilibrium and there was little evidence for confounding null alleles. These new markers will be used to resolve population structure and gene flow patterns in this major Eurasian forest tree. © 2011 Springer Science+Business Media B.V.

Published
2012

29. 275 years of forestry meets genomics in Pinus sylvestris.

Author

Pyhäjärvi, Tanja, Kujala, Sonja T, and Savolainen, Outi

Subjects
SCOTS pine, FORESTS & forestry, GENOMICS, GENE expression, LINKAGE disequilibrium, CONIFERS, LOBLOLLY pine
Abstract

Pinus sylvestris has a long history of basic and applied research that is relevant for both forestry and evolutionary studies. Its patterns of adaptive variation and role in forest economic and ecological systems have been studied extensively for nearly 275 years, detailed demography for a 100 years and mating system more than 50 years. However, its reference genome sequence is not yet available and genomic studies have been lagging compared to, for example, Pinus taeda and Picea abies, two other economically important conifers. Despite the lack of reference genome, many modern genomic methods are applicable for a more detailed look at its biological characteristics. For example, RNA‐seq has revealed a complex transcriptional landscape and targeted DNA sequencing displays an excess of rare variants and geographically homogenously distributed molecular genetic diversity. Current DNA and RNA resources can be used as a reference for gene expression studies, SNP discovery, and further targeted sequencing. In the future, specific consequences of the large genome size, such as functional effects of regulatory open chromatin regions and transposable elements, should be investigated more carefully. For forest breeding and long‐term management purposes, genomic data can help in assessing the genetic basis of inbreeding depression and the application of genomic tools for genomic prediction and relatedness estimates. Given the challenges of breeding (long generation time, no easy vegetative propagation) and the economic importance, application of genomic tools has a potential to have a considerable impact. Here, we explore how genomic characteristics of P. sylvestris, such as rare alleles and the low extent of linkage disequilibrium, impact the applicability and power of the tools. [ABSTRACT FROM AUTHOR]

Published
2020
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31. Optimising Exome Captures in Species With Large Genomes Using Species‐Specific Repetitive DNA Blocker.

Author

Kesälahti, Robert, Kumpula, Timo A., Cervantes, Sandra, Kujala, Sonja T., Mattila, Tiina M., Tyrmi, Jaakko S., Niskanen, Alina K., Rastas, Pasi, Savolainen, Outi, and Pyhäjärvi, Tanja

Subjects
*TANDEM repeats, *SCOTS pine, *DNA sequencing, *GENOMES, *DNA
Abstract

ABSTRACT Large and highly repetitive genomes are common. However, research interests usually lie within the non‐repetitive parts of the genome, as they are more likely functional, and can be used to answer questions related to adaptation, selection and evolutionary history. Exome capture is a cost‐effective method for providing sequencing data from protein‐coding parts of the genes. C0t‐1 DNA blockers consist of repetitive DNA and are used in exome captures to prevent the hybridisation of repetitive DNA sequences to capture baits or bait‐bound genomic DNA. Universal blockers target repetitive regions shared by many species, while species‐specific c0t‐1 DNA is prepared from the DNA of the studied species, thus perfectly matching the repetitive DNA contents of the species. So far, the use of species‐specific c0t‐1 DNA has been limited to a few model species. Here, we evaluated the performance of blocker treatments in exome captures of Pinus sylvestris, a widely distributed conifer species with a large (> 20 Gbp) and highly repetitive genome. We compared treatment with a commercial universal blocker to treatments with species‐specific c0t‐1 (30,000 and 60,000 ng). Species‐specific c0t‐1 captured more unique exons than the initial set of targets leading to increased SNP discovery and reduced sequencing of tandem repeats compared to the universal blocker. Based on our results, we recommend optimising exome captures using at least 60,000 ng of species‐specific c0t‐1 DNA. It is relatively easy and fast to prepare and can also be used with existing bait set designs. [ABSTRACT FROM AUTHOR]

Published
2024
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