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1. Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Author

Salojärvi, J. (Jarkko), Smolander, O.-P. (Olli-Pekka), Nieminen, K. (Kaisa), Rajaraman, S. (Sitaram), Safronov, O. (Omid), Safdari, P. (Pezhman), Lamminmäki, A. (Airi), Immanen, J. (Juha), Lan, T. (Tianying), Tanskanen, J. (Jaakko), Rastas, P. (Pasi), Amiryousefi, A. (Ali), Jayaprakash, B. (Balamuralikrishna), Kammonen, J. I. (Juhana I.), Hagqvist, R. (Risto), Eswaran, G. (Gugan), Ahonen, V. H. (Viivi Helena), Serra, J. A. (Juan Alonso), Asiegbu, F. O. (Fred O.), Barajas-Lopez, J. d. (Juan de Dios), Blande, D. (Daniel), Blokhina, O. (Olga), Blomster, T. (Tiina), Broholm, S. (Suvi), Brosche, M. (Mikael), Cui, F. (Fuqiang), Dardick, C. (Chris), Ehonen, S. E. (Sanna E.), Elomaa, P. (Paula), Escamez, S. (Sacha), Fagerstedt, K. V. (Kurt V.), Fujii, H. (Hiroaki), Gauthier, A. (Adrien), Gollan, P. J. (Peter J.), Halimaa, P. (Pauliina), Heino, P. I. (Pekka I.), Himanen, K. (Kristiina), Hollender, C. (Courtney), Kangasjärvi, S. (Saijaliisa), Kauppinen, L. (Leila), Kelleher, C. T. (Colin T.), Kontunen-Soppela, S. (Sari), Koskinen, J. P. (J. Patrik), Kovalchuk, A. (Andriy), Kärenlampi, S. O. (Sirpa O.), Kärkönen, A. K. (Anna K.), Lim, K.-J. (Kean-Jin), Leppälä, J. (Johanna), Macpherson, L. (Lee), Mikola, J. (Juha), Mouhu, K. (Katriina), Mähönen, A. P. (Ari Pekka), Niinemets, Ü. (Ülo), Oksanen, E. (Elina), Overmyer, K. (Kirk), Palva, E. T. (E. Tapio), Pazouki, L. (Leila), Pennanen, V. (Ville), Puhakainen, T. (Tuula), Poczai, P. (Peter), Possen, B. J. (Boy J. H. M.), Punkkinen, M. (Matleena), Rahikainen, M. M. (Moona M.), Rousi, M. (Matti), Ruonala, R. (Raili), van der Schoot, C. (Christiaan), Shapiguzov, A. (Alexey), Sierla, M. (Maija), Sipilä, T. P. (Timo P.), Sutela, S. (Suvi), Teeri, T. H. (Teemu H.), Tervahauta, A. I. (Arja I.), Vaattovaara, A. (Aleksia), Vahala, J. (Jorma), Vetchinnikova, L. (Lidia), Welling, A. (Annikki), Wrzaczek, M. (Michael), Xu, E. (Enjun), Paulin, L. G. (Lars G.), Schulman, A. H. (Alan H.), Lascoux, M. (Martin), Albert, V. A. (Victor A.), Auvinen, P. (Petri), Helariutta, Y. (Ykä), Kangasjärvi, J. (Jaakko), Salojärvi, J. (Jarkko), Smolander, O.-P. (Olli-Pekka), Nieminen, K. (Kaisa), Rajaraman, S. (Sitaram), Safronov, O. (Omid), Safdari, P. (Pezhman), Lamminmäki, A. (Airi), Immanen, J. (Juha), Lan, T. (Tianying), Tanskanen, J. (Jaakko), Rastas, P. (Pasi), Amiryousefi, A. (Ali), Jayaprakash, B. (Balamuralikrishna), Kammonen, J. I. (Juhana I.), Hagqvist, R. (Risto), Eswaran, G. (Gugan), Ahonen, V. H. (Viivi Helena), Serra, J. A. (Juan Alonso), Asiegbu, F. O. (Fred O.), Barajas-Lopez, J. d. (Juan de Dios), Blande, D. (Daniel), Blokhina, O. (Olga), Blomster, T. (Tiina), Broholm, S. (Suvi), Brosche, M. (Mikael), Cui, F. (Fuqiang), Dardick, C. (Chris), Ehonen, S. E. (Sanna E.), Elomaa, P. (Paula), Escamez, S. (Sacha), Fagerstedt, K. V. (Kurt V.), Fujii, H. (Hiroaki), Gauthier, A. (Adrien), Gollan, P. J. (Peter J.), Halimaa, P. (Pauliina), Heino, P. I. (Pekka I.), Himanen, K. (Kristiina), Hollender, C. (Courtney), Kangasjärvi, S. (Saijaliisa), Kauppinen, L. (Leila), Kelleher, C. T. (Colin T.), Kontunen-Soppela, S. (Sari), Koskinen, J. P. (J. Patrik), Kovalchuk, A. (Andriy), Kärenlampi, S. O. (Sirpa O.), Kärkönen, A. K. (Anna K.), Lim, K.-J. (Kean-Jin), Leppälä, J. (Johanna), Macpherson, L. (Lee), Mikola, J. (Juha), Mouhu, K. (Katriina), Mähönen, A. P. (Ari Pekka), Niinemets, Ü. (Ülo), Oksanen, E. (Elina), Overmyer, K. (Kirk), Palva, E. T. (E. Tapio), Pazouki, L. (Leila), Pennanen, V. (Ville), Puhakainen, T. (Tuula), Poczai, P. (Peter), Possen, B. J. (Boy J. H. M.), Punkkinen, M. (Matleena), Rahikainen, M. M. (Moona M.), Rousi, M. (Matti), Ruonala, R. (Raili), van der Schoot, C. (Christiaan), Shapiguzov, A. (Alexey), Sierla, M. (Maija), Sipilä, T. P. (Timo P.), Sutela, S. (Suvi), Teeri, T. H. (Teemu H.), Tervahauta, A. I. (Arja I.), Vaattovaara, A. (Aleksia), Vahala, J. (Jorma), Vetchinnikova, L. (Lidia), Welling, A. (Annikki), Wrzaczek, M. (Michael), Xu, E. (Enjun), Paulin, L. G. (Lars G.), Schulman, A. H. (Alan H.), Lascoux, M. (Martin), Albert, V. A. (Victor A.), Auvinen, P. (Petri), Helariutta, Y. (Ykä), and Kangasjärvi, J. (Jaakko)

Abstract

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.

Published
2017

2. Tree architecture: A strigolactone-deficient mutant reveals a connection between branching order and auxin gradient along the tree stem.

Author

Su C, Kokosza A, Xie X, Pěnčík A, Zhang Y, Raumonen P, Shi X, Muranen S, Topcu MK, Immanen J, Hagqvist R, Safronov O, Alonso-Serra J, Eswaran G, Venegas MP, Ljung K, Ward S, Mähönen AP, Himanen K, Salojärvi J, Fernie AR, Novák O, Leyser O, Pałubicki W, Helariutta Y, and Nieminen K

Subjects
Trees, Lactones, Gene Expression Regulation, Plant, Indoleacetic Acids, Plant Growth Regulators
Abstract

Due to their long lifespan, trees and bushes develop higher order of branches in a perennial manner. In contrast to a tall tree, with a clearly defined main stem and branching order, a bush is shorter and has a less apparent main stem and branching pattern. To address the developmental basis of these two forms, we studied several naturally occurring architectural variants in silver birch ( Betula pendula ). Using a candidate gene approach, we identified a bushy kanttarelli variant with a loss-of-function mutation in the BpMAX1 gene required for strigolactone (SL) biosynthesis. While kanttarelli is shorter than the wild type (WT), it has the same number of primary branches, whereas the number of secondary branches is increased, contributing to its bush-like phenotype. To confirm that the identified mutation was responsible for the phenotype, we phenocopied kanttarelli in transgenic BpMAX1::RNAi birch lines. SL profiling confirmed that both kanttarelli and the transgenic lines produced very limited amounts of SL. Interestingly, the auxin (IAA) distribution along the main stem differed between WT and BpMAX1::RNAi . In the WT, the auxin concentration formed a gradient, being higher in the uppermost internodes and decreasing toward the basal part of the stem, whereas in the transgenic line, this gradient was not observed. Through modeling, we showed that the different IAA distribution patterns may result from the difference in the number of higher-order branches and plant height. Future studies will determine whether the IAA gradient itself regulates aspects of plant architecture., Competing Interests: Competing interests statement:The authors declare no competing interest.

Published
2023
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3. ELIMÄKI Locus Is Required for Vertical Proprioceptive Response in Birch Trees.

Author

Alonso-Serra J, Shi X, Peaucelle A, Rastas P, Bourdon M, Immanen J, Takahashi J, Koivula H, Eswaran G, Muranen S, Help H, Smolander OP, Su C, Safronov O, Gerber L, Salojärvi J, Hagqvist R, Mähönen AP, Helariutta Y, and Nieminen K

Subjects
Betula growth & development, Cambium genetics, Mutation, Plant Stems genetics, Proprioception genetics, Trees genetics, Trees growth & development, Betula genetics, Cambium growth & development, Genes, Plant, Plant Stems growth & development
Abstract

Tree architecture has evolved to support a top-heavy above-ground biomass, but this integral feature poses a weight-induced challenge to trunk stability. Maintaining an upright stem is expected to require vertical proprioception through feedback between sensing stem weight and responding with radial growth. Despite its apparent importance, the principle by which plant stems respond to vertical loading forces remains largely unknown. Here, by manipulating the stem weight of downy birch (Betula pubescens) trees, we show that cambial development is modulated systemically along the stem. We carried out a genetic study on the underlying regulation by combining an accelerated birch flowering program with a recessive mutation at the ELIMÄKI locus (EKI), which causes a mechanically defective response to weight stimulus resulting in stem collapse after just 3 months. We observed delayed wood morphogenesis in eki compared with WT, along with a more mechanically elastic cambial zone and radial compression of xylem cell size, indicating that rapid tissue differentiation is critical for cambial growth under mechanical stress. Furthermore, the touch-induced mechanosensory pathway was transcriptionally misregulated in eki, indicating that the ELIMÄKI locus is required to integrate the weight-growth feedback regulation. By studying this birch mutant, we were able to dissect vertical proprioception from the gravitropic response associated with reaction wood formation. Our study provides evidence for both local and systemic responses to mechanical stimuli during secondary plant development., Competing Interests: Declaration of Interests The authors declare no competing interest, (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Published
2020
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