@article{akhter_cone-setting_2022,
	title = {Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway},
	volume = {n/a},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18449},
	doi = {10.1111/nph.18449},
	abstract = {Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their mRNA and miRNA fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, microRNA156 and the conifer specific microRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these micro-RNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.},
	language = {en},
	number = {n/a},
	urldate = {2022-09-16},
	journal = {New Phytologist},
	author = {Akhter, Shirin and Westrin, Karl Johan and Zivi, Nathan and Nordal, Veronika and Kretzschmar, Warren W. and Delhomme, Nicolas and Street, Nathaniel R. and Nilsson, Ove and Emanuelsson, Olof and Sundström, Jens F.},
	month = sep,
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18449},
	keywords = {Cone-setting, Flowering, Gymnosperm, Picea abies, Reproductive development, SPL-gene family, Transcriptome},
}

Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their mRNA and miRNA fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, microRNA156 and the conifer specific microRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these micro-RNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.

@article{li_teasing_2022,
	title = {Teasing apart the joint effect of demography and natural selection in the birth of a contact zone},
	volume = {n/a},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18480},
	doi = {10.1111/nph.18480},
	abstract = {Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. During glacial periods species were confined to low latitude refugia from which they recolonized higher latitudes as the climate improved. This multi-pronged recolonization led to many lineages that later met and formed large contact zones. We leverage genomic data from 5,000 P. abies trees to test for the presence of natural selection during recolonization and establishment of a contact zone in Scandinavia. Scandinavian P. abies is today made up of a southern genetic cluster originating from the Baltics, and a northern one originating from Northern Russia. The contact zone delineating them closely matches the limit between two major climatic regions. We show that natural selection contributed to its establishment and maintenance. First, an isolation-with-migration model with genome-wide linked selection fits the data better than a purely neutral one. Second, many loci show signature of selection or are associated with environmental variables. These loci, regrouped in clusters on chromosomes, are often related to phenology. Altogether, our results illustrate how climatic cycles, recolonization and selection can establish strong local adaptation along contact zones and affect the genetic architecture of adaptive traits.},
	language = {en},
	number = {n/a},
	urldate = {2022-09-16},
	journal = {New Phytologist},
	author = {Li, Lili and Milesi, Pascal and Tiret, Mathieu and Chen, Jun and Sendrowski, Janek and Baison, John and Chen, Zhi-qiang and Zhou, Linghua and Karlsson, Bo and Berlin, Mats and Westin, Johan and Garcia-Gil, Maria Rosario and Wu, Harry X. and Lascoux, Martin},
	month = sep,
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18480},
	keywords = {Climate change, Contact zone, Demography, Last Glacial Maximum, Local adaptation, Natural selection, Picea abies},
}

Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. During glacial periods species were confined to low latitude refugia from which they recolonized higher latitudes as the climate improved. This multi-pronged recolonization led to many lineages that later met and formed large contact zones. We leverage genomic data from 5,000 P. abies trees to test for the presence of natural selection during recolonization and establishment of a contact zone in Scandinavia. Scandinavian P. abies is today made up of a southern genetic cluster originating from the Baltics, and a northern one originating from Northern Russia. The contact zone delineating them closely matches the limit between two major climatic regions. We show that natural selection contributed to its establishment and maintenance. First, an isolation-with-migration model with genome-wide linked selection fits the data better than a purely neutral one. Second, many loci show signature of selection or are associated with environmental variables. These loci, regrouped in clusters on chromosomes, are often related to phenology. Altogether, our results illustrate how climatic cycles, recolonization and selection can establish strong local adaptation along contact zones and affect the genetic architecture of adaptive traits.

@article{chen_genetic_2022,
	title = {Genetic architecture behind developmental and seasonal control of tree growth and wood properties in {Norway} spruce},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.927673},
	abstract = {Genetic control of tree growth and wood formation varies depending on the age of the tree and the time of the year. Single-locus, multi-locus, and multi-trait genome-wide association studies (GWAS) were conducted on 34 growth and wood property traits in 1,303 Norway spruce individuals using exome capture to cover {\textasciitilde}130K single-nucleotide polymorphisms (SNPs). GWAS identified associations to the different wood traits in a total of 85 gene models, and several of these were validated in a progenitor population. A multi-locus GWAS model identified more SNPs associated with the studied traits than single-locus or multivariate models. Changes in tree age and annual season influenced the genetic architecture of growth and wood properties in unique ways, manifested by non-overlapping SNP loci. In addition to completely novel candidate genes, SNPs were located in genes previously associated with wood formation, such as cellulose synthases and a NAC transcription factor, but that have not been earlier linked to seasonal or age-dependent regulation of wood properties. Interestingly, SNPs associated with the width of the year rings were identified in homologs of Arabidopsis thaliana BARELY ANY MERISTEM 1 and rice BIG GRAIN 1, which have been previously shown to control cell division and biomass production. The results provide tools for future Norway spruce breeding and functional studies.},
	urldate = {2022-09-01},
	journal = {Frontiers in Plant Science},
	author = {Chen, Zhi-Qiang and Zan, Yanjun and Zhou, Linghua and Karlsson, Bo and Tuominen, Hannele and García-Gil, Maria Rosario and Wu, Harry X.},
	month = aug,
	year = {2022},
	keywords = {⛔ No DOI found},
}

Genetic control of tree growth and wood formation varies depending on the age of the tree and the time of the year. Single-locus, multi-locus, and multi-trait genome-wide association studies (GWAS) were conducted on 34 growth and wood property traits in 1,303 Norway spruce individuals using exome capture to cover ~130K single-nucleotide polymorphisms (SNPs). GWAS identified associations to the different wood traits in a total of 85 gene models, and several of these were validated in a progenitor population. A multi-locus GWAS model identified more SNPs associated with the studied traits than single-locus or multivariate models. Changes in tree age and annual season influenced the genetic architecture of growth and wood properties in unique ways, manifested by non-overlapping SNP loci. In addition to completely novel candidate genes, SNPs were located in genes previously associated with wood formation, such as cellulose synthases and a NAC transcription factor, but that have not been earlier linked to seasonal or age-dependent regulation of wood properties. Interestingly, SNPs associated with the width of the year rings were identified in homologs of Arabidopsis thaliana BARELY ANY MERISTEM 1 and rice BIG GRAIN 1, which have been previously shown to control cell division and biomass production. The results provide tools for future Norway spruce breeding and functional studies.

@article{linden_circum-arctic_2022,
	title = {Circum-{Arctic} distribution of chemical anti-herbivore compounds suggests biome-wide trade-off in defence strategies in {Arctic} shrubs},
	issn = {1600-0587},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ecog.06166},
	doi = {10.1111/ecog.06166},
	abstract = {Spatial variation in plant chemical defence towards herbivores can help us understand variation in herbivore top–down control of shrubs in the Arctic and possibly also shrub responses to global warming. Less defended, non-resinous shrubs could be more influenced by herbivores than more defended, resinous shrubs. However, sparse field measurements limit our current understanding of how much of the circum-Arctic variation in defence compounds is explained by taxa or defence functional groups (resinous/non-resinous). We measured circum-Arctic chemical defence and leaf digestibility in resinous (Betula glandulosa, B. nana ssp. exilis) and non-resinous (B. nana ssp. nana, B. pumila) shrub birches to see how they vary among and within taxa and functional groups. Using liquid chromatography–mass spectrometry (LC–MS) metabolomic analyses and in vitro leaf digestibility via incubation in cattle rumen fluid, we analysed defence composition and leaf digestibility in 128 samples from 44 tundra locations. We found biogeographical patterns in anti-herbivore defence where mean leaf triterpene concentrations and twig resin gland density were greater in resinous taxa and mean concentrations of condensing tannins were greater in non-resinous taxa. This indicates a biome-wide trade-off between triterpene- or tannin-dominated defences. However, we also found variations in chemical defence composition and resin gland density both within and among functional groups (resinous/non-resinous) and taxa, suggesting these categorisations only partly predict chemical herbivore defence. Complex tannins were the only defence compounds negatively related to in vitro digestibility, identifying this previously neglected tannin group as having a potential key role in birch anti-herbivore defence. We conclude that circum-Arctic variation in birch anti-herbivore defence can be partly derived from biogeographical distributions of birch taxa, although our detailed mapping of plant defence provides more information on this variation and can be used for better predictions of herbivore effects on Arctic vegetation.},
	language = {en},
	urldate = {2022-09-08},
	journal = {Ecography},
	author = {Lindén, Elin and te Beest, Mariska and Aubreu, Ilka and Moritz, Thomas and Sundqvist, Maja K. and Barrio, Isabel C. and Boike, Julia and Bryant, John P. and Bråthen, Kari Anne and Buchwal, Agata and Bueno, C. Guillermo and Currier, Alain and Egelkraut, Dagmar D. and Forbes, Bruce C. and Hallinger, Martin and Heijmans, Monique and Hermanutz, Luise and Hik, David S. and Hofgaard, Annika and Holmgren, Milena and Huebner, Diane C. and Høye, Toke T. and Jónsdóttir, Ingibjörg S. and Kaarlejärvi, Elina and Kissler, Emilie and Kumpula, Timo and Limpens, Juul and Myers-Smith, Isla H. and Normand, Signe and Post, Eric and Rocha, Adrian V. and Schmidt, Niels Martin and Skarin, Anna and Soininen, Eeva M. and Sokolov, Aleksandr and Sokolova, Natalia and Speed, James D. M. and Street, Lorna and Tananaev, Nikita and Tremblay, Jean-Pierre and Urbanowicz, Christine and Watts, David A. and Zimmermann, Heike and Olofsson, Johan},
	month = aug,
	year = {2022},
	keywords = {Arctic, Betula, birch, herbivory, metabolomics, plant chemical defence, shrubs, tundra},
	pages = {e06166},
}

Spatial variation in plant chemical defence towards herbivores can help us understand variation in herbivore top–down control of shrubs in the Arctic and possibly also shrub responses to global warming. Less defended, non-resinous shrubs could be more influenced by herbivores than more defended, resinous shrubs. However, sparse field measurements limit our current understanding of how much of the circum-Arctic variation in defence compounds is explained by taxa or defence functional groups (resinous/non-resinous). We measured circum-Arctic chemical defence and leaf digestibility in resinous (Betula glandulosa, B. nana ssp. exilis) and non-resinous (B. nana ssp. nana, B. pumila) shrub birches to see how they vary among and within taxa and functional groups. Using liquid chromatography–mass spectrometry (LC–MS) metabolomic analyses and in vitro leaf digestibility via incubation in cattle rumen fluid, we analysed defence composition and leaf digestibility in 128 samples from 44 tundra locations. We found biogeographical patterns in anti-herbivore defence where mean leaf triterpene concentrations and twig resin gland density were greater in resinous taxa and mean concentrations of condensing tannins were greater in non-resinous taxa. This indicates a biome-wide trade-off between triterpene- or tannin-dominated defences. However, we also found variations in chemical defence composition and resin gland density both within and among functional groups (resinous/non-resinous) and taxa, suggesting these categorisations only partly predict chemical herbivore defence. Complex tannins were the only defence compounds negatively related to in vitro digestibility, identifying this previously neglected tannin group as having a potential key role in birch anti-herbivore defence. We conclude that circum-Arctic variation in birch anti-herbivore defence can be partly derived from biogeographical distributions of birch taxa, although our detailed mapping of plant defence provides more information on this variation and can be used for better predictions of herbivore effects on Arctic vegetation.

@article{liu_plant_2022,
	title = {The {Plant} trans-{Golgi} {Network} {Component} {ECHIDNA} {Regulates} {Defense}, {Cell} {Death}, and {Endoplasmic} {Reticulum} {Stress}},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac400},
	doi = {10.1093/plphys/kiac400},
	abstract = {The trans-Golgi network (TGN) acts as a central platform for sorting and secreting various cargoes to the cell surface, thus being essential for the full execution of plant immunity. However, the fine-tuned regulation of TGN components in plant defense and stress response has been not fully elucidated. Our study revealed that despite largely compromising penetration resistance, the loss-of-function mutation of the TGN component protein ECHIDNA (ECH) induced enhanced post-invasion resistance to powdery mildew in Arabidopsis thaliana. Genetic and transcriptome analyses and hormone profiling demonstrated that ECH loss resulted in salicylic acid (SA) hyperaccumulation via the ISOCHORISMATE SYNTHASE 1 biosynthesis pathway, thereby constitutively activating SA-dependent innate immunity that was largely responsible for the enhanced post-invasion resistance. Furthermore, the ech mutant displayed accelerated SA-independent spontaneous cell death and constitutive POWDERY MILDEW RESISTANCE 4-mediated callose depositions. In addition, ECH loss led to a chronically prolonged endoplasmic reticulum stress in the ech mutant. These results provide insights into understanding the role of TGN components in the regulation of plant immunity and stress responses.},
	urldate = {2022-09-01},
	journal = {Plant Physiology},
	author = {Liu, Lijiang and Qin, Li and Safdar, Luqman Bin and Zhao, Chuanji and Cheng, Xiaohui and Xie, Meili and Zhang, Yi and Gao, Feng and Bai, Zetao and Huang, Junyan and Bhalerao, Rishikesh P and Liu, Shengyi and Wei, Yangdou},
	month = aug,
	year = {2022},
	pages = {kiac400},
}

The trans-Golgi network (TGN) acts as a central platform for sorting and secreting various cargoes to the cell surface, thus being essential for the full execution of plant immunity. However, the fine-tuned regulation of TGN components in plant defense and stress response has been not fully elucidated. Our study revealed that despite largely compromising penetration resistance, the loss-of-function mutation of the TGN component protein ECHIDNA (ECH) induced enhanced post-invasion resistance to powdery mildew in Arabidopsis thaliana. Genetic and transcriptome analyses and hormone profiling demonstrated that ECH loss resulted in salicylic acid (SA) hyperaccumulation via the ISOCHORISMATE SYNTHASE 1 biosynthesis pathway, thereby constitutively activating SA-dependent innate immunity that was largely responsible for the enhanced post-invasion resistance. Furthermore, the ech mutant displayed accelerated SA-independent spontaneous cell death and constitutive POWDERY MILDEW RESISTANCE 4-mediated callose depositions. In addition, ECH loss led to a chronically prolonged endoplasmic reticulum stress in the ech mutant. These results provide insights into understanding the role of TGN components in the regulation of plant immunity and stress responses.