@article{wahl_plant_2026,
	title = {The plant energy management machinery: an essential hub for stress resilience and developmental dynamics with great potential for crop improvement},
	volume = {77},
	issn = {0022-0957},
	shorttitle = {The plant energy management machinery},
	url = {https://doi.org/10.1093/jxb/erag032},
	doi = {10.1093/jxb/erag032},
	abstract = {Plants coordinate resource uptake, developmental pace, and morphological efficiency. This ensures that energy use is balanced across time and tissues, enabling resilience and stable growth under fluctuating environmental conditions. The plant energy management machinery encompasses the interconnected signalling and metabolic networks that coordinate energy acquisition, storage, mobilization, and utilization to support growth, development, and environmental adaptation. In contrast to animals, where dedicated organs such as fat bodies in Drosophila and the liver in mammals, play crucial roles in energy metabolism and sensing (Chatterjee and Perrimon, 2021), plants exhibit a more integrative concept of nutrient and energy regulation. Here, the term ‘nutrients’ extends beyond simple energy carriers to include a broad spectrum of organic and inorganic compounds, such as sugars, amino acids, nitrate, phosphate, and lipids, that function both as metabolic substrates and as signalling molecules, influencing gene expression, enzyme activity, developmental transitions, and growth.},
	number = {5},
	urldate = {2026-03-10},
	journal = {Journal of Experimental Botany},
	author = {Wahl, Vanessa and Hanson, Johannes and Menand, Benoît},
	month = mar,
	year = {2026},
	pages = {1357--1361},
}

Plants coordinate resource uptake, developmental pace, and morphological efficiency. This ensures that energy use is balanced across time and tissues, enabling resilience and stable growth under fluctuating environmental conditions. The plant energy management machinery encompasses the interconnected signalling and metabolic networks that coordinate energy acquisition, storage, mobilization, and utilization to support growth, development, and environmental adaptation. In contrast to animals, where dedicated organs such as fat bodies in Drosophila and the liver in mammals, play crucial roles in energy metabolism and sensing (Chatterjee and Perrimon, 2021), plants exhibit a more integrative concept of nutrient and energy regulation. Here, the term ‘nutrients’ extends beyond simple energy carriers to include a broad spectrum of organic and inorganic compounds, such as sugars, amino acids, nitrate, phosphate, and lipids, that function both as metabolic substrates and as signalling molecules, influencing gene expression, enzyme activity, developmental transitions, and growth.

@article{mahawar_straw_2026,
	title = {Straw {Mulching} {Differentially} {Shapes} the {Structure} and {Function} of {Below}-{Ground} {Bacterial} {Communities} in {Potato} {Depending} on {eDNA} {Source} and {Cultivar}},
	volume = {7},
	copyright = {© 2026 The Author(s). Plant-Environment Interactions published by New Phytologist Foundation and John Wiley \& Sons Ltd.},
	issn = {2575-6265},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pei3.70131},
	doi = {10.1002/pei3.70131},
	abstract = {Potato is the world's third most important food crop, yet its production relies heavily on pesticides, creating a need for sustainable alternatives. We assessed how straw mulching, a practice known to improve soil fertility, enrich microbial activity, and suppress diseases, affects below-ground bacterial community structure and functional potential across different potato-associated sample types. A field experiment was conducted in northern Sweden using two potato cultivars under mulched and control soil conditions. Samples from the rhizosphere, root, soil, and tuber peel were analyzed using 16S ribosomal RNA (rRNA) gene sequencing (Illumina platform) to assess bacterial diversity and community composition. Straw mulching significantly increased bacterial richness and altered community structure across sample types and cultivars. Copiotrophic genera, which thrive in nutrient-rich environments, included Rhodanobacter, Mucilaginibacter, Flavobacterium, and Pseudomonas, and were enriched in rhizosphere, root, and tuber peel. Oligotrophs such as Bryobacter and Candidatus Solibacter dominated the soil and are known to contribute to organic matter turnover and plant growth. Notably, in the peel of one cultivar (King Edward), the abundance of Pseudomonas increased 5–7-fold, correlating with elevated starch and ascorbic acid contents of the tubers. In conclusion, the effect of straw mulching on soil bacterial communities and tuber quality appears to be diverse and cultivar dependent. Long-term and large-scale studies are needed to evaluate cumulative impacts on soil health, yield, and resilience.},
	language = {en},
	number = {1},
	urldate = {2026-02-20},
	journal = {Plant-Environment Interactions},
	author = {Mahawar, Lovely and Mishra, Arti and Tsitouri, Angeliki and Albrectsen, Benedicte Riber},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/pei3.70131},
	keywords = {bacterial communities, cv King Edward, cv Mandel, illumina amplicon sequencing, metabarcoding},
	pages = {e70131},
}

Potato is the world's third most important food crop, yet its production relies heavily on pesticides, creating a need for sustainable alternatives. We assessed how straw mulching, a practice known to improve soil fertility, enrich microbial activity, and suppress diseases, affects below-ground bacterial community structure and functional potential across different potato-associated sample types. A field experiment was conducted in northern Sweden using two potato cultivars under mulched and control soil conditions. Samples from the rhizosphere, root, soil, and tuber peel were analyzed using 16S ribosomal RNA (rRNA) gene sequencing (Illumina platform) to assess bacterial diversity and community composition. Straw mulching significantly increased bacterial richness and altered community structure across sample types and cultivars. Copiotrophic genera, which thrive in nutrient-rich environments, included Rhodanobacter, Mucilaginibacter, Flavobacterium, and Pseudomonas, and were enriched in rhizosphere, root, and tuber peel. Oligotrophs such as Bryobacter and Candidatus Solibacter dominated the soil and are known to contribute to organic matter turnover and plant growth. Notably, in the peel of one cultivar (King Edward), the abundance of Pseudomonas increased 5–7-fold, correlating with elevated starch and ascorbic acid contents of the tubers. In conclusion, the effect of straw mulching on soil bacterial communities and tuber quality appears to be diverse and cultivar dependent. Long-term and large-scale studies are needed to evaluate cumulative impacts on soil health, yield, and resilience.

@article{ibanez_circadian_2025,
	title = {The circadian clock of {Populus} affects physiological, transcriptional and metabolomic responses to osmotic and ionic components of salt stress},
	volume = {2},
	copyright = {2025 The Author(s)},
	issn = {2948-281X},
	url = {https://www.nature.com/articles/s44323-025-00052-2},
	doi = {10.1038/s44323-025-00052-2},
	abstract = {The circadian oscillator is an innate timing mechanism present in most organisms, including plants. In this study, Populus tremula × P. tremuloides (Populus) trees with reduced expression of circadian clock components were exposed to gradually increases in the osmotic and ionic components of salt stress. Reduced levels of the morning components PttLATE ELONGATED HYPOCOTYL 1 and 2 (PttLHY1,2) or of the evening components PttPSEUDO-RESPONSE REGULATOR 7a and b (PttPRR7a,b) and PttGIGANTEA1,2 (PttGI1,2) affected growth adaptation under stress conditions. PttLHY1,2 regulated growth under NaCl treatment via the control of PttCyclin D3 expression. PttPRR7a,b and PttGI1,2 were instrumental in maintaining growth in roots by enabling effective adaptation of the metabolome. Major changes in the root metabolome under prolonged stress included alterations in carbohydrate, amino acids, and fatty acids. This study places the circadian clock at the centre of adaptation to adverse conditions in trees and will help the development of stress-resistant trees.},
	language = {en},
	number = {1},
	urldate = {2025-10-03},
	journal = {npj Biological Timing and Sleep},
	publisher = {Nature Publishing Group},
	author = {Ibáñez, Cristian and Vergara, Alexander and Castro, David and Bascunan-Godoy, Luisa and Sjölander, Johan and Jurca, Manuela and Pin, Pierre A. and Nilsson, Ove and Eriksson, Maria E.},
	month = oct,
	year = {2025},
	keywords = {Circadian rhythm signalling peptides and proteins, Plant sciences},
	pages = {34},
}

The circadian oscillator is an innate timing mechanism present in most organisms, including plants. In this study, Populus tremula × P. tremuloides (Populus) trees with reduced expression of circadian clock components were exposed to gradually increases in the osmotic and ionic components of salt stress. Reduced levels of the morning components PttLATE ELONGATED HYPOCOTYL 1 and 2 (PttLHY1,2) or of the evening components PttPSEUDO-RESPONSE REGULATOR 7a and b (PttPRR7a,b) and PttGIGANTEA1,2 (PttGI1,2) affected growth adaptation under stress conditions. PttLHY1,2 regulated growth under NaCl treatment via the control of PttCyclin D3 expression. PttPRR7a,b and PttGI1,2 were instrumental in maintaining growth in roots by enabling effective adaptation of the metabolome. Major changes in the root metabolome under prolonged stress included alterations in carbohydrate, amino acids, and fatty acids. This study places the circadian clock at the centre of adaptation to adverse conditions in trees and will help the development of stress-resistant trees.

@article{brun_chip-ms_2026,
	title = {{ChIP}-{MS} in {Plant} {Systems}: {Mapping} the {H3K27ac} {Proteome} {During} the {Greening} {Process}},
	volume = {178},
	copyright = {© 2026 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	shorttitle = {{ChIP}-{MS} in {Plant} {Systems}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70797},
	doi = {10.1111/ppl.70797},
	abstract = {We have established a method for chromatin immunoprecipitation coupled to mass spectrometry (ChIP-MS) in Arabidopsis thaliana. We demonstrate its utility by investigating proteins associated with histone H3 lysine 27 acetylation (H3K27ac), a key epigenetic mark regulating photosynthesis-associated nuclear genes (PhANGs) during chloroplast development and establishment of photosynthesis. Purification of chromatin-associated proteins from light-grown Arabidopsis cell cultures identified 66 proteins associated with H3K27ac that met the selection criteria in the two replicate experiments: (i) 2-fold change in relation to IgG, (ii) at least two unique peptides, and (iii) relevant biological annotations. The identified proteins included chromatin remodelers, chromatin regulators and transcription factors with potential roles in H3K27ac deposition. To evaluate the physiological role of the candidates associated with the H3K27ac mark, we developed a rapid and reproducible phenotyping method based on controlled light scanning to determine chlorophyll accumulation in mutant seedlings. We complemented with pigment quantification and analysis of photosynthesis-associated nuclear genes (PhANGs) expression. Several mutants displayed altered greening, pigment accumulation, or affected photosynthetic gene expression consistent with a role during chloroplast development. Notably, chr11, chr17, and atpds5a mutants showed impaired pigment accumulation and reduced expression of PhANGs, whereas hmgb4 and mbd10 mutants exhibited increased greening and induction of PhANGs. Together, these findings establish ChIP-MS as a robust approach to identify histone mark-associated proteins in plants and provide a first set of candidate regulators of H3K27ac during chloroplast biogenesis. This technical advance opens new possibilities to discover chromatin-based regulation of plant development and environmental responses.},
	language = {en},
	number = {1},
	urldate = {2026-02-20},
	journal = {Physiologia Plantarum},
	author = {Brun, Alexis and Quevedo, Marti and Sterling, Luis A. and Dekkers, Dick H. W. and Demmers, Jeroen and Hudson, Elton Paul and Strand, Åsa},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70797},
	keywords = {MS, chromatin, histone modifications, photosynthesis},
	pages = {e70797},
}

We have established a method for chromatin immunoprecipitation coupled to mass spectrometry (ChIP-MS) in Arabidopsis thaliana. We demonstrate its utility by investigating proteins associated with histone H3 lysine 27 acetylation (H3K27ac), a key epigenetic mark regulating photosynthesis-associated nuclear genes (PhANGs) during chloroplast development and establishment of photosynthesis. Purification of chromatin-associated proteins from light-grown Arabidopsis cell cultures identified 66 proteins associated with H3K27ac that met the selection criteria in the two replicate experiments: (i) 2-fold change in relation to IgG, (ii) at least two unique peptides, and (iii) relevant biological annotations. The identified proteins included chromatin remodelers, chromatin regulators and transcription factors with potential roles in H3K27ac deposition. To evaluate the physiological role of the candidates associated with the H3K27ac mark, we developed a rapid and reproducible phenotyping method based on controlled light scanning to determine chlorophyll accumulation in mutant seedlings. We complemented with pigment quantification and analysis of photosynthesis-associated nuclear genes (PhANGs) expression. Several mutants displayed altered greening, pigment accumulation, or affected photosynthetic gene expression consistent with a role during chloroplast development. Notably, chr11, chr17, and atpds5a mutants showed impaired pigment accumulation and reduced expression of PhANGs, whereas hmgb4 and mbd10 mutants exhibited increased greening and induction of PhANGs. Together, these findings establish ChIP-MS as a robust approach to identify histone mark-associated proteins in plants and provide a first set of candidate regulators of H3K27ac during chloroplast biogenesis. This technical advance opens new possibilities to discover chromatin-based regulation of plant development and environmental responses.

@article{han_development_2026,
	title = {Development and application of a genotyping by target sequencing single-nucleotide polymorphism array panel in {Salix} suchowensis},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/s12864-026-12690-2},
	doi = {10.1186/s12864-026-12690-2},
	abstract = {Salix suchowensis is an important species of Salix, known for its rapid growth property and wide application in environmental construction, ecological restoration, wicker production, and biomass energy production. Due to its significance as a sustainable biological resource, S. suchowensis has been the centre of intensive breeding. However, rapid improvement of growth and biomass has been hindered by a lack of genomic resources. To address this limitation, we designed a liquid-phase probe array by genotyping by target sequencing technology. Using whole-genome resequencing data, a total of 39,076 SNPs were selected for the array panel, consisting of trait-associated SNPs, intragenic SNPs, and intergenic SNPs. This panel was validated by genotyping 550 new samples, demonstrating high call rates and effective capture of the population structure. Genome-wide association analysis identified 72 SNPs associated with plant height and ground diameter. Additionally, the array panel shows a high potential for genomic selection, with high prediction accuracy for various traits. These results highlight the efficiency of this panel in capturing genomic variations that are highly valuable for future genetic research and breeding applications.},
	language = {en},
	urldate = {2026-03-09},
	journal = {BMC Genomics},
	author = {Han, Yu and Gu, Shaobo and Zhu, Mingjia and Liu, Wei and Feng, Landi and Yin, Tongming and Gao, Xuemeng and Zan, Yanjun and Huang, Rui and Ji, Yan and Liu, Jianquan},
	month = mar,
	year = {2026},
	keywords = {Genome-wide association study, Genomic selection, Ground diameter, Liquid-phase probe array, Plant height},
}

Salix suchowensis is an important species of Salix, known for its rapid growth property and wide application in environmental construction, ecological restoration, wicker production, and biomass energy production. Due to its significance as a sustainable biological resource, S. suchowensis has been the centre of intensive breeding. However, rapid improvement of growth and biomass has been hindered by a lack of genomic resources. To address this limitation, we designed a liquid-phase probe array by genotyping by target sequencing technology. Using whole-genome resequencing data, a total of 39,076 SNPs were selected for the array panel, consisting of trait-associated SNPs, intragenic SNPs, and intergenic SNPs. This panel was validated by genotyping 550 new samples, demonstrating high call rates and effective capture of the population structure. Genome-wide association analysis identified 72 SNPs associated with plant height and ground diameter. Additionally, the array panel shows a high potential for genomic selection, with high prediction accuracy for various traits. These results highlight the efficiency of this panel in capturing genomic variations that are highly valuable for future genetic research and breeding applications.