@article{albrectsen_nordic_2025,
	title = {Nordic {Countries} as an {Opportunity} for {Sustainable}, {Low} {Pest} {Seed} {Potato} {Production} in a {Climate} {Change} {Scenario}},
	issn = {1871-4528},
	url = {https://doi.org/10.1007/s11540-025-09935-0},
	doi = {10.1007/s11540-025-09935-0},
	abstract = {Based on discussions within the Northern Tubers of Potato network (N’TOP-net), this review highlights northern Scandinavia’s potential for sustainable, low pest seed potato production. While long transport distances currently limit large-scale supply for consumption or processing, low pest pressure and stricter EU plant protection regulations increase its value for seed production. Climate change is expected to extend the growing season, driving renewed interest in Northern Scandinavia’s role in European food security. Finland exemplifies this potential, and parts of northern and central Sweden—historically suppliers of disease-free seed potatoes, even exported to Brazil—offer expansion opportunities. Nordic potato production, key biotic stressors, and opportunities for regional cooperation are examined, with a focus on novel farming practices, breeding innovations, and disease surveillance to improve resilience and sustainability. Despite shared values in cultivar selection, certification, and potato preferences, Nordic production strategies remain uncoordinated for long-term sustainability. We advocate for transnational, interdisciplinary collaboration to enhance Europe’s food security through joint efforts in three key areas: (1) soil-conserving farming, (2) breeding for adaptation to longer day length and resistance traits, and (3) transnational pest and disease surveillance. A Nordic potato initiative can strengthen European cooperation on sustainable production amid climate change. However, as policies must balance the benefits of longer growing seasons with emerging risks such as pests, droughts, and flooding, coordinated research, regulatory adaptation, and climate resilience investments are essential for safeguarding seed potato quality, food security, and supply chain stability.},
	language = {en},
	urldate = {2025-11-07},
	journal = {Potato Research},
	author = {Albrectsen, Benedicte Riber and Mäkinen, Kristiina and Mahawar, Lovely and Mishra, Arti and Abuley, Isaac Kwesi and Veillon, Isalyne and Gopan, Apsara Indhu and Sajeevan, Radha Sivarajan and Resjö, Svante and Andreasson, Erik and Liljeroth, Erland and Marhavý, Peter and Rossmann, Simeon Lim and Hansen, Jens Grønbech},
	month = oct,
	year = {2025},
	keywords = {Climate change adaptation, Food security strategy, Potato disease management, Seed potato production, Sustainable farming},
}

Based on discussions within the Northern Tubers of Potato network (N’TOP-net), this review highlights northern Scandinavia’s potential for sustainable, low pest seed potato production. While long transport distances currently limit large-scale supply for consumption or processing, low pest pressure and stricter EU plant protection regulations increase its value for seed production. Climate change is expected to extend the growing season, driving renewed interest in Northern Scandinavia’s role in European food security. Finland exemplifies this potential, and parts of northern and central Sweden—historically suppliers of disease-free seed potatoes, even exported to Brazil—offer expansion opportunities. Nordic potato production, key biotic stressors, and opportunities for regional cooperation are examined, with a focus on novel farming practices, breeding innovations, and disease surveillance to improve resilience and sustainability. Despite shared values in cultivar selection, certification, and potato preferences, Nordic production strategies remain uncoordinated for long-term sustainability. We advocate for transnational, interdisciplinary collaboration to enhance Europe’s food security through joint efforts in three key areas: (1) soil-conserving farming, (2) breeding for adaptation to longer day length and resistance traits, and (3) transnational pest and disease surveillance. A Nordic potato initiative can strengthen European cooperation on sustainable production amid climate change. However, as policies must balance the benefits of longer growing seasons with emerging risks such as pests, droughts, and flooding, coordinated research, regulatory adaptation, and climate resilience investments are essential for safeguarding seed potato quality, food security, and supply chain stability.

@article{rosenkranz_cis-_2025,
	title = {Cis- and trans-action of the cold-induced {lncRNAs}, {SVALKA} and {SVALNA}, regulate {CBF1} and {CBF3} in {Arabidopsis}},
	volume = {26},
	issn = {1469-221X},
	url = {https://www.embopress.org/doi/full/10.1038/s44319-025-00568-5},
	doi = {10.1038/s44319-025-00568-5},
	abstract = {Long noncoding RNAs (lncRNAs) are emerging as key regulatory players of coding gene expression in eukaryotes. Here, we investigate the roles of the lncRNAs SVALKA (SVK) and SVALNA (SVN) in regulating CBF1 and CBF3 gene expression in Arabidopsis under cold stress conditions. We integrated omics approaches, together with genetics and molecular biology, to uncover the transcriptional dynamics and regulatory mechanisms of SVK and SVN. Our results demonstrate that SVK functions as a cis- and trans-acting lncRNA, regulating both CBF1 and CBF3 through RNAPII collision and chromatin remodeling, while SVN serves a cis role by negatively regulating CBF3 via a RNAPII collision mechanism. We identified isoforms of SVK, originating from distinct transcription start sites and undergo alternative splicing which might be important to adapt stability, crucial for the regulatory functions. Furthermore, we show that two positionally conserved lncRNAs, originating from the upstream antisense strand of neighboring genes, can have different molecular mechanisms to regulate their targets. This study elucidates the complex interplay of lncRNAs in gene regulation, highlighting their essential roles in modulating responses to environmental stresses. Our findings contribute to a deeper understanding of the mechanisms underlying lncRNA functionality and their significance in gene regulatory networks in eukaryotes.},
	number = {20},
	urldate = {2025-11-07},
	journal = {EMBO reports},
	author = {Rosenkranz, Isabell and Mermet, Sarah and Zacharaki, Vasiliki and Kindgren, Peter},
	month = oct,
	year = {2025},
	note = {Num Pages: 5087
Publisher: John Wiley \& Sons, Ltd},
	keywords = {Arabidopsis, Cold Response, Epigenetic Regulation, Long Non-coding RNAs},
	pages = {5070--5087},
}

Long noncoding RNAs (lncRNAs) are emerging as key regulatory players of coding gene expression in eukaryotes. Here, we investigate the roles of the lncRNAs SVALKA (SVK) and SVALNA (SVN) in regulating CBF1 and CBF3 gene expression in Arabidopsis under cold stress conditions. We integrated omics approaches, together with genetics and molecular biology, to uncover the transcriptional dynamics and regulatory mechanisms of SVK and SVN. Our results demonstrate that SVK functions as a cis- and trans-acting lncRNA, regulating both CBF1 and CBF3 through RNAPII collision and chromatin remodeling, while SVN serves a cis role by negatively regulating CBF3 via a RNAPII collision mechanism. We identified isoforms of SVK, originating from distinct transcription start sites and undergo alternative splicing which might be important to adapt stability, crucial for the regulatory functions. Furthermore, we show that two positionally conserved lncRNAs, originating from the upstream antisense strand of neighboring genes, can have different molecular mechanisms to regulate their targets. This study elucidates the complex interplay of lncRNAs in gene regulation, highlighting their essential roles in modulating responses to environmental stresses. Our findings contribute to a deeper understanding of the mechanisms underlying lncRNA functionality and their significance in gene regulatory networks in eukaryotes.

@article{liu_genome_2025,
	title = {Genome and transcriptome analysis provide insights into the genetics and breeding of {Salix} suchowensis growth traits},
	volume = {56},
	issn = {1573-5095},
	url = {https://doi.org/10.1007/s11056-025-10132-7},
	doi = {10.1007/s11056-025-10132-7},
	abstract = {Shrub willow species (Salix sp.) are ideal for cultivation as bioenergy source and can serve as effective models for genetic research due to their rapid growth rates. Understanding the genetic basis of growth traits in willows can enhance the development of high-quality cultivars. In this study, we performed genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) mapping, and transcriptome-wide association analyses to investigate the genetic basis of plant height (Height) and ground diameter (GD) in a full-sib population of Salix suchowensis derived from eight parental lines, which were phenotyped across three sites in southwest China. We identified 15 quantitative trait loci (QTLs) associated with Height and 10 QTLs associated with GD. Furthermore, we identified 938 eQTLs influencing the expression of 685 genes, including a trans-eQTL hub, as well as eight co-expression modules correlated with Height and GD. Transcriptome-wide association studies (TWAS) revealed five genes linked to Height and three genes associated with GD. By jointly modeling genetic variations and environmental factors, we developed a multi-site predictive model that outperformed the genomic best linear unbiased prediction. This study provides valuable insights into the genetic regulatory mechanisms underlying key growth traits in S. suchowensis and establishes a genomic prediction model to facilitate the rapid genetic improvement of the species.},
	language = {en},
	number = {6},
	urldate = {2025-11-07},
	journal = {New Forests},
	author = {Liu, Wei and Gu, Shaobo and Zhu, Mingjia and Han, Yu and Dai, Xiaogang and Wu, Huaitong and Yin, Tongming and Guo, Linjie and Feng, Landi and Zan, Yanjun and Liu, Jianquan},
	month = oct,
	year = {2025},
	keywords = {Breeding prediction, Ground diameter, Plant height, QTL, QTL-by-environment interactions, Salix suchowensis},
	pages = {63},
}

Shrub willow species (Salix sp.) are ideal for cultivation as bioenergy source and can serve as effective models for genetic research due to their rapid growth rates. Understanding the genetic basis of growth traits in willows can enhance the development of high-quality cultivars. In this study, we performed genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) mapping, and transcriptome-wide association analyses to investigate the genetic basis of plant height (Height) and ground diameter (GD) in a full-sib population of Salix suchowensis derived from eight parental lines, which were phenotyped across three sites in southwest China. We identified 15 quantitative trait loci (QTLs) associated with Height and 10 QTLs associated with GD. Furthermore, we identified 938 eQTLs influencing the expression of 685 genes, including a trans-eQTL hub, as well as eight co-expression modules correlated with Height and GD. Transcriptome-wide association studies (TWAS) revealed five genes linked to Height and three genes associated with GD. By jointly modeling genetic variations and environmental factors, we developed a multi-site predictive model that outperformed the genomic best linear unbiased prediction. This study provides valuable insights into the genetic regulatory mechanisms underlying key growth traits in S. suchowensis and establishes a genomic prediction model to facilitate the rapid genetic improvement of the species.

@article{zacharaki_convergent_2025,
	title = {Convergent antisense transcription primes hosting genes for stress responsiveness in plants},
	volume = {18},
	issn = {1674-2052},
	url = {https://www.sciencedirect.com/science/article/pii/S167420522500351X},
	doi = {10.1016/j.molp.2025.10.001},
	abstract = {Plants need to constantly surveil their surroundings to adapt to environmental fluctuations, which they achieve primarily through transcriptional reprogramming. Thus, plants are excellent models for identifying novel transcriptional regulatory mechanisms. In this study, we characterize the regulation mediated by long non-coding transcription that initiates on the complementary strand in the 5ʹ end of coding genes (convergent antisense transcription, CASt). In Arabidopsis, CASt is associated with stress-responsive genes that are highly expressed. Our analysis shows that CASt depends on a specific gene architecture that is evolutionarily conserved in higher plants. CASt is present in genes with an extended first intron and over-represented in genes encoding functional transporters in Arabidopsis, such as the AMINO ACID PERMEASE (AAP) transporter family. Experimental evidence points to a role for CASt in priming their host genes for stress responsiveness in evolutionary divergent plant species. Furthermore, we were able to predict stress responsiveness in rice AAP genes based on the presence of a long first intron and CASt. Collectively, we show an evolutionary strategy and regulatory mechanism specific to plants for enhancing stress responsiveness through modification of gene architecture and antisense transcription.},
	number = {11},
	urldate = {2025-11-07},
	journal = {Molecular Plant},
	author = {Zacharaki, Vasiliki and Quevedo, Marti and Nardeli, Sarah Muniz and Meena, Shiv Kumar and Monte, Elena and Kindgren, Peter},
	month = nov,
	year = {2025},
	keywords = {Antisense transcription, Arabidopsis, Cold acclimation, Transporters, antisense transcription, cold acclimation, transporters},
	pages = {1920--1931},
}

Plants need to constantly surveil their surroundings to adapt to environmental fluctuations, which they achieve primarily through transcriptional reprogramming. Thus, plants are excellent models for identifying novel transcriptional regulatory mechanisms. In this study, we characterize the regulation mediated by long non-coding transcription that initiates on the complementary strand in the 5ʹ end of coding genes (convergent antisense transcription, CASt). In Arabidopsis, CASt is associated with stress-responsive genes that are highly expressed. Our analysis shows that CASt depends on a specific gene architecture that is evolutionarily conserved in higher plants. CASt is present in genes with an extended first intron and over-represented in genes encoding functional transporters in Arabidopsis, such as the AMINO ACID PERMEASE (AAP) transporter family. Experimental evidence points to a role for CASt in priming their host genes for stress responsiveness in evolutionary divergent plant species. Furthermore, we were able to predict stress responsiveness in rice AAP genes based on the presence of a long first intron and CASt. Collectively, we show an evolutionary strategy and regulatory mechanism specific to plants for enhancing stress responsiveness through modification of gene architecture and antisense transcription.

@article{fenech_cyp71a_2025,
	title = {The {CYP71A}, {NIT}, {AMI}, and {IAMH} gene families are dispensable for indole-3-acetaldoxime-mediated auxin biosynthesis in {Arabidopsis}},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koaf242},
	doi = {10.1093/plcell/koaf242},
	abstract = {The auxin indole-3-acetic acid (IAA) governs plant development and environmental responses. Although the indole-3-pyruvic acid (IPyA) pathway is the predominant route for IAA biosynthesis, other pathways have been proposed, such as the indole-3-acetaldoxime (IAOx) pathway. The IAOx pathway has garnered attention due to its supposed activation in auxin-overproducing mutants (e.g., sur1, sur2, ugt74b1) and the auxin-like responses triggered by exogenous application of its proposed intermediates IAOx, indole-3-acetonitrile (IAN), and indole-3-acetamide (IAM). However, despite the supporting evidence for individual steps of the IAOx pathway, its overall physiological relevance remains inconclusive. Here, using a comprehensive genetic approach combined with metabolic and phenotypic profiling, we demonstrate that mutating gene families proposed to function in the IAOx pathway in Arabidopsis (Arabidopsis thaliana) does not result in prominent auxin-deficient phenotypes, nor are these genes required for the high auxin production in the sur2 mutant. Our findings also challenge the previously postulated linear IAOx pathway. Exogenously provided IAOx, IAN, and IAM can be converted to IAA in vivo, but they do not act as precursors for each other. Finally, our findings question the physiological relevance of IAM and IAN as IAA precursors in plants and suggest the existence of a yet-uncharacterized route for IAA production in the sur2 mutant, likely involving IAOx as an intermediate. The identification of the metabolic steps and the corresponding genes in this pathway may uncover another IAA biosynthesis route in plants.},
	urldate = {2025-10-17},
	journal = {The Plant Cell},
	author = {Fenech, M and Brumos, J and Pěnčík, A and Edwards, B and Belcapo, S and DeLacey, J and Patel, A and Kater, M M and Li, X and Ljung, K and Novak, O and Alonso, J M and Stepanova, A N},
	month = oct,
	year = {2025},
	pages = {koaf242},
}

The auxin indole-3-acetic acid (IAA) governs plant development and environmental responses. Although the indole-3-pyruvic acid (IPyA) pathway is the predominant route for IAA biosynthesis, other pathways have been proposed, such as the indole-3-acetaldoxime (IAOx) pathway. The IAOx pathway has garnered attention due to its supposed activation in auxin-overproducing mutants (e.g., sur1, sur2, ugt74b1) and the auxin-like responses triggered by exogenous application of its proposed intermediates IAOx, indole-3-acetonitrile (IAN), and indole-3-acetamide (IAM). However, despite the supporting evidence for individual steps of the IAOx pathway, its overall physiological relevance remains inconclusive. Here, using a comprehensive genetic approach combined with metabolic and phenotypic profiling, we demonstrate that mutating gene families proposed to function in the IAOx pathway in Arabidopsis (Arabidopsis thaliana) does not result in prominent auxin-deficient phenotypes, nor are these genes required for the high auxin production in the sur2 mutant. Our findings also challenge the previously postulated linear IAOx pathway. Exogenously provided IAOx, IAN, and IAM can be converted to IAA in vivo, but they do not act as precursors for each other. Finally, our findings question the physiological relevance of IAM and IAN as IAA precursors in plants and suggest the existence of a yet-uncharacterized route for IAA production in the sur2 mutant, likely involving IAOx as an intermediate. The identification of the metabolic steps and the corresponding genes in this pathway may uncover another IAA biosynthesis route in plants.