@incollection{johansson_perennial_2022,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {The {Perennial} {Clock} {Is} an {Essential} {Timer} for {Seasonal} {Growth} {Events} and {Cold} {Hardiness}},
	isbn = {978-1-07-161912-4},
	url = {https://doi.org/10.1007/978-1-0716-1912-4_18},
	abstract = {Over the last several decades, changes in global temperatures have led to changes in local environments affecting the growth conditions for many species. This is a trend that makes it even more important to understand how plants respond to local variations and seasonal changes in climate.To detect daily and seasonal changes as well as acute stress factors such as cold and drought, plants rely on a circadian clock. This chapter introduces the current knowledge and literature about the setup and function of the circadian clock in various tree and perennial species, with a focus on the Populus genus.},
	language = {en},
	urldate = {2021-12-01},
	booktitle = {Plant {Circadian} {Networks}: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Johansson, Mikael and Ibáñez, Cristian and Takata, Naoki and Eriksson, Maria E.},
	editor = {Staiger, Dorothee and Davis, Seth and Davis, Amanda Melaragno},
	year = {2022},
	doi = {10.1007/978-1-0716-1912-4_18},
	keywords = {Bud burst, Bud set, Circadian clock, Cold tolerance, Growth, Perennial plants, Populus, Seasonal regulation},
	pages = {227--242},
}

Over the last several decades, changes in global temperatures have led to changes in local environments affecting the growth conditions for many species. This is a trend that makes it even more important to understand how plants respond to local variations and seasonal changes in climate.To detect daily and seasonal changes as well as acute stress factors such as cold and drought, plants rely on a circadian clock. This chapter introduces the current knowledge and literature about the setup and function of the circadian clock in various tree and perennial species, with a focus on the Populus genus.

@incollection{johansson_monitoring_2022,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {Monitoring {Seasonal} {Bud} {Set}, {Bud} {Burst}, and {Cold} {Hardiness} in {Populus}},
	isbn = {978-1-07-161912-4},
	url = {https://doi.org/10.1007/978-1-0716-1912-4_17},
	abstract = {Using a perennial model plant allows the study of reoccurring seasonal events in a way that is not possible using a fast-growing annual such as A. thaliana (Arabidopsis). In this study, we present a hybrid aspen (Populus tremula × P. tremuloides) as our perennial model plant. These plants can be grown in growth chambers to shorten growth periods and manipulate day length and temperature in ways that would be impossible under natural conditions. In addition, the use of growth chambers allows easy monitoring of height and diameter expansion, accelerating the collection of data from new strategies that allow evaluation of promoters or inhibitors of growth. Here, we describe how to study and quantify responses to seasonal changes (mainly using P. tremula × P. tremuloides) by measuring growth rate and key events under different photoperiodic cycles.},
	language = {en},
	urldate = {2021-12-01},
	booktitle = {Plant {Circadian} {Networks}: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Johansson, Mikael and Takata, Naoki and Ibáñez, Cristian and Eriksson, Maria E.},
	editor = {Staiger, Dorothee and Davis, Seth and Davis, Amanda Melaragno},
	year = {2022},
	doi = {10.1007/978-1-0716-1912-4_17},
	keywords = {Bud burst, Bud set, Cold acclimation, Critical day length, Freezing tolerance, Perennial, Photoperiod, Populus},
	pages = {215--226},
}

Using a perennial model plant allows the study of reoccurring seasonal events in a way that is not possible using a fast-growing annual such as A. thaliana (Arabidopsis). In this study, we present a hybrid aspen (Populus tremula × P. tremuloides) as our perennial model plant. These plants can be grown in growth chambers to shorten growth periods and manipulate day length and temperature in ways that would be impossible under natural conditions. In addition, the use of growth chambers allows easy monitoring of height and diameter expansion, accelerating the collection of data from new strategies that allow evaluation of promoters or inhibitors of growth. Here, we describe how to study and quantify responses to seasonal changes (mainly using P. tremula × P. tremuloides) by measuring growth rate and key events under different photoperiodic cycles.

@article{igamberdiev_pyrophosphate_2021,
	title = {Pyrophosphate as an alternative energy currency in plants},
	volume = {478},
	issn = {0264-6021},
	url = {https://doi.org/10.1042/BCJ20200940},
	doi = {10.1042/BCJ20200940},
	abstract = {In the conditions of [Mg2+] elevation that occur, in particular, under low oxygen stress and are the consequence of the decrease in [ATP] and increase in [ADP] and [AMP], pyrophosphate (PPi) can function as an alternative energy currency in plant cells. In addition to its production by various metabolic pathways, PPi can be synthesized in the combined reactions of pyruvate, phosphate dikinase (PPDK) and pyruvate kinase (PK) by so-called PK/PPDK substrate cycle, and in the reverse reaction of membrane-bound H+-pyrophosphatase, which uses the energy of electrochemical gradients generated on tonoplast and plasma membrane. The PPi can then be consumed in its active forms of MgPPi and Mg2PPi by PPi-utilizing enzymes, which require an elevated [Mg2+]. This ensures a continuous operation of glycolysis in the conditions of suppressed ATP synthesis, keeping metabolism energy efficient and less dependent on ATP.},
	language = {en},
	number = {8},
	urldate = {2021-06-03},
	journal = {Biochemical Journal},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = apr,
	year = {2021},
	pages = {1515--1524},
}

In the conditions of [Mg2+] elevation that occur, in particular, under low oxygen stress and are the consequence of the decrease in [ATP] and increase in [ADP] and [AMP], pyrophosphate (PPi) can function as an alternative energy currency in plant cells. In addition to its production by various metabolic pathways, PPi can be synthesized in the combined reactions of pyruvate, phosphate dikinase (PPDK) and pyruvate kinase (PK) by so-called PK/PPDK substrate cycle, and in the reverse reaction of membrane-bound H+-pyrophosphatase, which uses the energy of electrochemical gradients generated on tonoplast and plasma membrane. The PPi can then be consumed in its active forms of MgPPi and Mg2PPi by PPi-utilizing enzymes, which require an elevated [Mg2+]. This ensures a continuous operation of glycolysis in the conditions of suppressed ATP synthesis, keeping metabolism energy efficient and less dependent on ATP.

@article{dob_jasmonate_2021,
	title = {Jasmonate inhibits adventitious root initiation through repression of {CKX1} and activation of {RAP2}.{6L} transcription factor in {Arabidopsis}},
	volume = {72},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erab358},
	doi = {10.1093/jxb/erab358},
	abstract = {Adventitious rooting is a de novo organogenesis process that enables plants to propagate clonally and cope with environmental stresses. Adventitious root initiation (ARI) is controlled by interconnected transcriptional and hormonal networks, but there is little knowledge of the genetic and molecular programs orchestrating these networks. Thus, we have applied genome-wide transcriptome profiling to elucidate the profound transcriptional reprogramming events preceding ARI. These reprogramming events are associated with the downregulation of cytokinin (CK) signaling and response genes, which could be triggers for ARI. Interestingly, we found that CK free-base (iP, tZ, cZ and DHZ) content declined during ARI, due to downregulation of de novo CK biosynthesis and upregulation of CK inactivation pathways. We also found that MYC2-dependent jasmonate (JA) signaling inhibits ARI by downregulating the expression of the CYTOKININ OXIDASE/DEHYDROGENASE1 (CKX1) gene. We also demonstrated that JA and CK synergistically activate expression of RELATED to APETALA2.6 LIKE (RAP2.6L) transcription factor, and constitutive expression of this transcription factor strongly inhibits ARI. Collectively, our findings reveal that previously unknown genetic interactions between JA and CK play key roles in ARI},
	number = {20},
	urldate = {2021-08-18},
	journal = {Journal of Experimental Botany},
	author = {Dob, Asma and Lakehal, Abdellah and Novak, Ondrej and Bellini, Catherine},
	month = jul,
	year = {2021},
	pages = {7107--7118},
}

Adventitious rooting is a de novo organogenesis process that enables plants to propagate clonally and cope with environmental stresses. Adventitious root initiation (ARI) is controlled by interconnected transcriptional and hormonal networks, but there is little knowledge of the genetic and molecular programs orchestrating these networks. Thus, we have applied genome-wide transcriptome profiling to elucidate the profound transcriptional reprogramming events preceding ARI. These reprogramming events are associated with the downregulation of cytokinin (CK) signaling and response genes, which could be triggers for ARI. Interestingly, we found that CK free-base (iP, tZ, cZ and DHZ) content declined during ARI, due to downregulation of de novo CK biosynthesis and upregulation of CK inactivation pathways. We also found that MYC2-dependent jasmonate (JA) signaling inhibits ARI by downregulating the expression of the CYTOKININ OXIDASE/DEHYDROGENASE1 (CKX1) gene. We also demonstrated that JA and CK synergistically activate expression of RELATED to APETALA2.6 LIKE (RAP2.6L) transcription factor, and constitutive expression of this transcription factor strongly inhibits ARI. Collectively, our findings reveal that previously unknown genetic interactions between JA and CK play key roles in ARI

@article{rendon-anaya_adaptive_2021,
	title = {Adaptive introgression facilitate adaptation to high latitudes in {European} aspen ({Populus} tremula {L}.)},
	volume = {38},
	issn = {1537-1719},
	url = {https://doi.org/10.1093/molbev/msab229},
	doi = {10.1093/molbev/msab229},
	abstract = {Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole genome re-sequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum (LGM), we detected an adaptive introgression event in a genome region of ∼500kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin - probably Russian - of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results therefore emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits.},
	language = {eng},
	number = {11},
	journal = {Molecular Biology and Evolution},
	author = {Rendón-Anaya, Martha and Wilson, Jonathan and Sveinsson, Sæmundur and Fedorkov, Aleksey and Cottrell, Joan and Bailey, Mark E. S. and Ruņģis, Dainis and Lexer, Christian and Jansson, Stefan and Robinson, Kathryn M. and Street, Nathaniel R. and Ingvarsson, Pär K.},
	month = jul,
	year = {2021},
	pages = {5034--5050},
}

Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole genome re-sequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum (LGM), we detected an adaptive introgression event in a genome region of ∼500kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin - probably Russian - of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results therefore emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits.