@article{li_ecophysiological_2025,
	title = {Ecophysiological transition mediated by hybridization in a hybrid pine species complex},
	volume = {47},
	issn = {2468-2659},
	url = {https://www.sciencedirect.com/science/article/pii/S2468265925000952},
	doi = {10.1016/j.pld.2025.05.009},
	abstract = {Hybridization is a driving force in ecological transitions and speciation, yet direct evidence linking it to adaptive differentiation in natural systems remains limited. This study evaluates the role of hybridization in the speciation of Pinus densata, a keystone forest species on the southeastern Tibetan Plateau. By creating artificial interspecific F1s and a long-term common garden experiment on the plateau, we provide in situ assessments on 44 growth and physiological traits across four seasons, along with RNA sequencing. We found significant phenotypic divergence between P. densata and its putative parental species P. tabuliformis and P. yunnanensis, with P. densata demonstrating superior growth and dynamic balance between photosynthesis and photoprotection. The F1s closely resembled P. densata in most traits. Gene expression revealed 19\%–10\% of 34,000 examined genes as differentially expressed in P. densata and F1s relative to mid-parent expression values. Both additive (4\%) and non-additive gene actions (5\%–6\% in F1s, 10\%–12\% in P. densata) were common, while transgressive expression occurred more frequently in the stabilized natural hybrids, illustrating transcriptomic reprogramming brought by hybridization and further divergence by natural selection. We provide compelling evidence for hybridization-derived phenotypic divergence at both physiological and gene expression levels that could have contributed to the adaptation of P. densata to high plateau habitat where both parental species have low fitness. The altered physiology and gene expression in hybrids serve both as a substrate for novel ecological adaptation and as a mechanism for the initiation of reproductive isolation.},
	number = {4},
	urldate = {2025-08-01},
	journal = {Plant Diversity},
	author = {Li, Zhi-Chao and Xu, Chao-Qun and Zhao, Wei and Nie, Shuai and Bao, Yu-Tao and Liu, Hui and Xing, Zhen and Mao, Jian-Feng and Wang, Xiao-Ru},
	month = jul,
	year = {2025},
	keywords = {Ecological divergence, Gene action, Homoploid hybrid speciation, Physiological traits, RNA-Seq, Tibetan plateau},
	pages = {604--619},
}

Hybridization is a driving force in ecological transitions and speciation, yet direct evidence linking it to adaptive differentiation in natural systems remains limited. This study evaluates the role of hybridization in the speciation of Pinus densata, a keystone forest species on the southeastern Tibetan Plateau. By creating artificial interspecific F1s and a long-term common garden experiment on the plateau, we provide in situ assessments on 44 growth and physiological traits across four seasons, along with RNA sequencing. We found significant phenotypic divergence between P. densata and its putative parental species P. tabuliformis and P. yunnanensis, with P. densata demonstrating superior growth and dynamic balance between photosynthesis and photoprotection. The F1s closely resembled P. densata in most traits. Gene expression revealed 19%–10% of 34,000 examined genes as differentially expressed in P. densata and F1s relative to mid-parent expression values. Both additive (4%) and non-additive gene actions (5%–6% in F1s, 10%–12% in P. densata) were common, while transgressive expression occurred more frequently in the stabilized natural hybrids, illustrating transcriptomic reprogramming brought by hybridization and further divergence by natural selection. We provide compelling evidence for hybridization-derived phenotypic divergence at both physiological and gene expression levels that could have contributed to the adaptation of P. densata to high plateau habitat where both parental species have low fitness. The altered physiology and gene expression in hybrids serve both as a substrate for novel ecological adaptation and as a mechanism for the initiation of reproductive isolation.

@article{sharma_microbial_2025,
	title = {Microbial {Contributions} to {Plant} {Growth} and {StressTolerance}: {Mechanisms} for {Sustainable} {Plant} {Production}},
	issn = {2667-064X},
	shorttitle = {Microbial {Contributions} to {Plant} {Growth} and {StressTolerance}},
	url = {https://www.sciencedirect.com/science/article/pii/S2667064X25002349},
	doi = {10.1016/j.stress.2025.100966},
	abstract = {Plant growth-promoting rhizobacteria (PGPRs) play a crucial role in enhancing plant development through a variety of direct and indirect mechanisms. These include the production of phytohormones, nitrogen fixation, phosphate solubilization, siderophore-mediated iron acquisition, and biocontrol of plant pathogens. Predominantly inhabiting the rhizosphere, PGPRs interact with plant roots via complex molecular and ecological processes involving signalling molecules, metabolite exchanges, and modulation of plant immune responses. Such interactions enhance nutrient uptake and stress tolerance but also contribute to long-term plant health and productivity across diverse environmental conditions. This review focuses on the genera Pseudomonas and Bacillus, which are extensively studied for their strong colonization abilities, metabolic versability, and demonstrated potential in improving crop resilience. Advances in microbial genomics, metagenomics, and high-throughput phenotyping have greatly enhanced our ability to identify, characterize, and apply beneficial microbes across a range of crop systems. However, key challenges remain, including limited understanding of native soil microbiotas, the functional outcome of microbiome-soil-plant interactions, and the development of agricultural practices that efficiently integrate microbial solutions. With potato (Solanum tuberosum) as a model crop, this review synthesizes current knowledge on PGRP-mediated growth promotion - primarily by Pseudomonas and Bacillus acting alone or in microbial consortia, identifies critical research gaps, and outlines future directions for the application of PGPRs in sustainable crop production.},
	urldate = {2025-08-01},
	journal = {Plant Stress},
	author = {Sharma, Neha and Mahawar, Lovely and Mishra, Arti and Albrectsen, Benedicte Riber},
	month = jul,
	year = {2025},
	keywords = {Baseline soil microflora, PGPR, Plant Growth Promotion, Plant Stress Mitigation, Rethinking agricultural Practices},
	pages = {100966},
}

Plant growth-promoting rhizobacteria (PGPRs) play a crucial role in enhancing plant development through a variety of direct and indirect mechanisms. These include the production of phytohormones, nitrogen fixation, phosphate solubilization, siderophore-mediated iron acquisition, and biocontrol of plant pathogens. Predominantly inhabiting the rhizosphere, PGPRs interact with plant roots via complex molecular and ecological processes involving signalling molecules, metabolite exchanges, and modulation of plant immune responses. Such interactions enhance nutrient uptake and stress tolerance but also contribute to long-term plant health and productivity across diverse environmental conditions. This review focuses on the genera Pseudomonas and Bacillus, which are extensively studied for their strong colonization abilities, metabolic versability, and demonstrated potential in improving crop resilience. Advances in microbial genomics, metagenomics, and high-throughput phenotyping have greatly enhanced our ability to identify, characterize, and apply beneficial microbes across a range of crop systems. However, key challenges remain, including limited understanding of native soil microbiotas, the functional outcome of microbiome-soil-plant interactions, and the development of agricultural practices that efficiently integrate microbial solutions. With potato (Solanum tuberosum) as a model crop, this review synthesizes current knowledge on PGRP-mediated growth promotion - primarily by Pseudomonas and Bacillus acting alone or in microbial consortia, identifies critical research gaps, and outlines future directions for the application of PGPRs in sustainable crop production.

@article{lei_comprehensive_2025,
	title = {Comprehensive analysis of 1,771 transcriptomes from 7 tissues enhance genetic and biological interpretations of maize complex traits},
	issn = {2160-1836},
	url = {https://doi.org/10.1093/g3journal/jkaf140},
	doi = {10.1093/g3journal/jkaf140},
	abstract = {By reanalyzing 1,771 RNA-seq datasets from 7 tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation, evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex traits. Through an integrative analysis of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and several candidate genes for a number of agronomic traits, including leaf during the day for the anthesis-silking interval, leaf during the day for kernel Zeinoxanthin level, and root for ear height, highlighting the potential contribution of tissue-specific gene expression to variation in agronomic traits. Using transcriptome-wide association and colocalization analysis, we associated tissue-specific expression variation of 74 genes to agronomic traits variation. Our findings provide novel insights into the genetic and biological mechanisms underlying maize complex traits, and the multi-tissue regulatory atlas serves as a primary source for biological interpretation, functional validation, and genomic improvement of maize.},
	urldate = {2025-07-25},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Lei, Mengyu and Si, Huan and Zhu, Mingjia and Han, Yu and Liu, Wei and Dai, Yifei and Ji, Yan and Liu, Zhengwen and Hao, Fan and Hao, Ran and Zhao, Jiarui and Ye, Guoyou and Zan, Yanjun},
	month = jul,
	year = {2025},
	pages = {jkaf140},
}

By reanalyzing 1,771 RNA-seq datasets from 7 tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation, evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex traits. Through an integrative analysis of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and several candidate genes for a number of agronomic traits, including leaf during the day for the anthesis-silking interval, leaf during the day for kernel Zeinoxanthin level, and root for ear height, highlighting the potential contribution of tissue-specific gene expression to variation in agronomic traits. Using transcriptome-wide association and colocalization analysis, we associated tissue-specific expression variation of 74 genes to agronomic traits variation. Our findings provide novel insights into the genetic and biological mechanisms underlying maize complex traits, and the multi-tissue regulatory atlas serves as a primary source for biological interpretation, functional validation, and genomic improvement of maize.

@article{berggren_effects_2025,
	title = {Effects of propagation method and methyl jasmonate treatment on stem bark wound healing in {Norway} spruce seedlings},
	issn = {1612-4677},
	url = {https://doi.org/10.1007/s10342-025-01795-0},
	doi = {10.1007/s10342-025-01795-0},
	abstract = {Healing of stem bark wounds is important for minimizing pathogen infection risk, restoring nutrient transport and structural support in trees. Here, we explore how propagation through somatic embryogenesis (SE) and methyl jasmonate (MeJA) treatment affect wound healing ability in Norway spruce (Picea abies) plants. We inflicted a mechanical wound on the lower stem of MeJA- and non-treated plants produced via SE (emblings) or from seeds (seedlings). Visible signs of healing around the wound edges (onset of healing) were recorded 2 weeks post-wounding; wound size (exposed xylem) was measured every other week (June–September) in year 1, and May and September in year 2. Plant height and diameter were also measured. MeJA positively affected healing onset, with 48\% more MeJA- than non-treated plants exhibiting early healing. This resulted in a sharp decrease in wound size for MeJA-treated plants 2–4 weeks post-wounding. However, these benefits only occurred early on, as MeJA reduced the overall healing rate (tissue growth/day) by 9\%. For SE, fewer emblings (70\%) showed early healing signs compared to seedlings (91\%). Yet, non-treated emblings showed the highest healing rate during year 1; in year 2, these effects persisted with all emblings having a 61\% faster healing rate and 68\% more had completely closed their wounds relative to seedlings. Wounding did not affect growth, MeJA negatively affected diameter but not height, and overall emblings grew less than seedlings. We conclude that MeJA may stimulate stem wound healing initiation in Norway spruce, but slow down healing rate and vice versa for SE plants.},
	language = {en},
	urldate = {2025-07-25},
	journal = {European Journal of Forest Research},
	author = {Berggren, Kristina and Tudoran, Amelia and Chen, Yayuan and Tikkinen, Mikko and Bylund, Helena and Björkman, Christer and Egertsdotter, Ulrika and Puentes, Adriana},
	month = jun,
	year = {2025},
	keywords = {Arboriculture, Emblings, Jasmonic acid, Mechanical wounding, Picea abies, Plant regeneration, Plant tolerance, Regeneration, Seedlings, Shoot apical meristem, Somatic embryogenesis, Wound healing rate, Wounding},
}

Healing of stem bark wounds is important for minimizing pathogen infection risk, restoring nutrient transport and structural support in trees. Here, we explore how propagation through somatic embryogenesis (SE) and methyl jasmonate (MeJA) treatment affect wound healing ability in Norway spruce (Picea abies) plants. We inflicted a mechanical wound on the lower stem of MeJA- and non-treated plants produced via SE (emblings) or from seeds (seedlings). Visible signs of healing around the wound edges (onset of healing) were recorded 2 weeks post-wounding; wound size (exposed xylem) was measured every other week (June–September) in year 1, and May and September in year 2. Plant height and diameter were also measured. MeJA positively affected healing onset, with 48% more MeJA- than non-treated plants exhibiting early healing. This resulted in a sharp decrease in wound size for MeJA-treated plants 2–4 weeks post-wounding. However, these benefits only occurred early on, as MeJA reduced the overall healing rate (tissue growth/day) by 9%. For SE, fewer emblings (70%) showed early healing signs compared to seedlings (91%). Yet, non-treated emblings showed the highest healing rate during year 1; in year 2, these effects persisted with all emblings having a 61% faster healing rate and 68% more had completely closed their wounds relative to seedlings. Wounding did not affect growth, MeJA negatively affected diameter but not height, and overall emblings grew less than seedlings. We conclude that MeJA may stimulate stem wound healing initiation in Norway spruce, but slow down healing rate and vice versa for SE plants.

@article{bogdziewiez_q-warg_2025,
	title = {The {Q}-{Warg} {Pipeline}: {A} {Robust} and {Versatile} {Workflow} for {Quantitative} {Analysis} of {Protoplast} {Culture} {Conditions}},
	volume = {9},
	copyright = {© 2025 The Author(s). Plant Direct published by American Society of Plant Biologists and the Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {2475-4455},
	shorttitle = {The {Q}-{Warg} {Pipeline}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pld3.70090},
	doi = {10.1002/pld3.70090},
	abstract = {Single cells offer a simplified model for investigating complex mechanisms such as cell–cell adhesion. Protoplasts, plant cells without cell walls (CWs), have been instrumental in plant research, industrial applications, and breeding. However, because of the absence of a CW, protoplasts are not considered “true” plant cells, making them less relevant for biophysical studies. Current protocols for CW recovery in protoplasts vary widely among laboratories and starting materials, requiring lab-specific optimizations that often depend on expert knowledge and qualitative assessments. To address this, we have developed a user-friendly streamlined workflow, the Q-Warg pipeline, which enables quantitative comparison of various conditions for CW recovery post-protoplasting. This pipeline employs fluorescence imaging and tailored processing to measure parameters such as morphometry, cell viability, and CW staining intensity. Using this approach, we optimized culture conditions to obtain single plant cells (SPCs) with recovered CWs. Additionally, we demonstrated the robustness and versatility of the workflow by quantifying different fluorescent signals in protoplast suspensions. Overall, the Q-Warg pipeline provides a widely accessible and user-friendly solution for robust and unbiased characterization of protoplasts culture. The quantitative data generated by the pipeline will be useful in the future to decipher the mechanisms regulating protoplast viability and regeneration.},
	language = {en},
	number = {7},
	urldate = {2025-07-25},
	journal = {Plant Direct},
	author = {Bogdziewiez, Léa and Froeling, Rik and Schöppl, Patricia and Juquel, Jeanne and Antoniadi, Ioanna and Skalický, Vladimìr and Mathey, Ambroise and Fattaccioli, Jacques and Sprakel, Joris and Verger, Stéphane},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/pld3.70090},
	keywords = {Arabidopsis thaliana, cell wall, fluorescence, protoplasts, quantification, recovery, regeneration, viability},
	pages = {e70090},
}

Single cells offer a simplified model for investigating complex mechanisms such as cell–cell adhesion. Protoplasts, plant cells without cell walls (CWs), have been instrumental in plant research, industrial applications, and breeding. However, because of the absence of a CW, protoplasts are not considered “true” plant cells, making them less relevant for biophysical studies. Current protocols for CW recovery in protoplasts vary widely among laboratories and starting materials, requiring lab-specific optimizations that often depend on expert knowledge and qualitative assessments. To address this, we have developed a user-friendly streamlined workflow, the Q-Warg pipeline, which enables quantitative comparison of various conditions for CW recovery post-protoplasting. This pipeline employs fluorescence imaging and tailored processing to measure parameters such as morphometry, cell viability, and CW staining intensity. Using this approach, we optimized culture conditions to obtain single plant cells (SPCs) with recovered CWs. Additionally, we demonstrated the robustness and versatility of the workflow by quantifying different fluorescent signals in protoplast suspensions. Overall, the Q-Warg pipeline provides a widely accessible and user-friendly solution for robust and unbiased characterization of protoplasts culture. The quantitative data generated by the pipeline will be useful in the future to decipher the mechanisms regulating protoplast viability and regeneration.