@article{kareem_tmo5_2025,
	title = {{TMO5} regulates {PIN1} polarity convergence and organogenesis downstream of {MONOPTEROS} in the {Arabidopsis} shoot},
	volume = {152},
	issn = {0950-1991},
	url = {https://doi.org/10.1242/dev.205255},
	doi = {10.1242/dev.205255},
	abstract = {Plants continuously produce lateral organs, such as leaves and flowers, from the shoot apical meristem (SAM). This process is guided by the accumulation of the plant hormone auxin and the polar localization of the efflux protein PIN-FORMED1 (PIN1). The transcription factor MONOPTEROS (MP) plays a crucial role in orienting PIN1 polarity, thereby facilitating auxin-driven organogenesis. In this study, we investigate genes downstream of MP that may regulate PIN1 polarity and organogenesis, discovering that the downstream vascular transcription factor TMO5 can promote PIN1 polarity convergence non-cell-autonomously and that TMO5 and its family members promote organ initiation in the SAM. By examining the role of auxin and cytokinin downstream of these genes, we provide evidence that the TMO5-like genes control PIN1 polarity and drive organogenesis by coordinating multiple hormonal signalling pathways.},
	number = {24},
	urldate = {2026-09-07},
	journal = {Development},
	author = {Kareem, Abdul and Ohno, Carolyn and Heisler, Marcus G.},
	month = dec,
	year = {2025},
	pages = {dev205255},
}

Plants continuously produce lateral organs, such as leaves and flowers, from the shoot apical meristem (SAM). This process is guided by the accumulation of the plant hormone auxin and the polar localization of the efflux protein PIN-FORMED1 (PIN1). The transcription factor MONOPTEROS (MP) plays a crucial role in orienting PIN1 polarity, thereby facilitating auxin-driven organogenesis. In this study, we investigate genes downstream of MP that may regulate PIN1 polarity and organogenesis, discovering that the downstream vascular transcription factor TMO5 can promote PIN1 polarity convergence non-cell-autonomously and that TMO5 and its family members promote organ initiation in the SAM. By examining the role of auxin and cytokinin downstream of these genes, we provide evidence that the TMO5-like genes control PIN1 polarity and drive organogenesis by coordinating multiple hormonal signalling pathways.

@article{kareem_water_2025,
	title = {Water availability positions auxin response maxima to determine plant regeneration fates},
	volume = {11},
	copyright = {2025 The Author(s)},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-025-02029-2},
	doi = {10.1038/s41477-025-02029-2},
	abstract = {Wounding and hormones serve as diverse triggers for regeneration in animals and plants. Despite important advances in understanding various types of regeneration, the mechanism by which plants determine regeneration outcomes remains largely unknown. Here we demonstrate in Arabidopsis that a trade-off between two regeneration fates, wound-induced callus and root regeneration, was driven by distinct molecular pathways related to cambium and root development, respectively. We discovered that local water availability near the wound site determined the early stages of regeneration fates in Arabidopsis and tomato, with high water triggering root fate and low water initiating callus fate. Distinct spatial distributions of auxin response maxima around the wound, shaped by water availability, were critical for determining root or callus fates. We found that, by perturbing auxin response or auxin transport dynamics, we could change regeneration outcomes. Moreover, high water availability enhanced ethylene and jasmonic acid responses, whereas treatments with these hormones could modify auxin transport dynamics or the location of auxin response maxima, thus influencing regeneration fates. We propose that, through stress hormones, water availability modifies the auxin response distribution to control regeneration outcomes, thus allowing environmental control of regeneration and providing a means to improve in vitro regeneration by changing the water potential.},
	language = {en},
	number = {7},
	urldate = {2026-09-07},
	journal = {Nature Plants},
	publisher = {Nature Publishing Group},
	author = {Kareem, Abdul and van Wüllen, Anna K. and Zhang, Ai and Walckiers, Gabriel and Fasth, Ellen and Melnyk, Charles W.},
	month = jul,
	year = {2025},
	keywords = {Cell fate, Plant regeneration},
	pages = {1367--1379},
}

Wounding and hormones serve as diverse triggers for regeneration in animals and plants. Despite important advances in understanding various types of regeneration, the mechanism by which plants determine regeneration outcomes remains largely unknown. Here we demonstrate in Arabidopsis that a trade-off between two regeneration fates, wound-induced callus and root regeneration, was driven by distinct molecular pathways related to cambium and root development, respectively. We discovered that local water availability near the wound site determined the early stages of regeneration fates in Arabidopsis and tomato, with high water triggering root fate and low water initiating callus fate. Distinct spatial distributions of auxin response maxima around the wound, shaped by water availability, were critical for determining root or callus fates. We found that, by perturbing auxin response or auxin transport dynamics, we could change regeneration outcomes. Moreover, high water availability enhanced ethylene and jasmonic acid responses, whereas treatments with these hormones could modify auxin transport dynamics or the location of auxin response maxima, thus influencing regeneration fates. We propose that, through stress hormones, water availability modifies the auxin response distribution to control regeneration outcomes, thus allowing environmental control of regeneration and providing a means to improve in vitro regeneration by changing the water potential.

@article{feng_genetic_2026,
	title = {Genetic structure and diversity of four {Chinese} fir breeding populations over 60 years},
	volume = {22},
	issn = {1614-2950},
	url = {https://doi.org/10.1007/s11295-026-01750-z},
	doi = {10.1007/s11295-026-01750-z},
	abstract = {Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is the most commercially important conifer species in southern China. Since 2015, the Fujian Province has launched its fourth cycle of genetic improvement, yet the impact of intensive artificial selection for growth and wood quality traits on the genetic diversity of advanced-cycle populations remains unclear. In this study, genotyping-by-sequencing (GBS) was used to genotype 310 individuals sampled from four consecutive breeding populations (first to fourth cycle). Across cycles, diversity indices remained relatively stable, with the fourth-cycle population showing slightly higher values (Ho = 0.325, He = 0.272). The broadening of breeding objectives to include wood quality and resistance traits, together with the introduction of external elite germplasm from the second cycle onward, may have contributed to this balance. Consequently, genetic differentiation among the populations from different breeding cycles was minimal (Fst {\textless} 0.01). Comparison of the genomic and pedigree-based relationship matrices revealed discrepancies for some pairs, indicating that genomic estimates provide complementary information for characterizing relatedness. Overall, genetic diversity was maintained across the four breeding cycles. These results provide a genomic basis for managing genetic diversity and relatedness in advanced-cycle Chinese fir breeding.},
	language = {en},
	number = {5},
	urldate = {2026-09-02},
	journal = {Tree Genetics \& Genomes},
	author = {Feng, Qihang and Chen, Zhi-Qiang and Zhao, Benwen and Zhang, Long and Su, Shunde and Zhang, Xie and Chen, Yu and El-Kassaby, Yousry A. and Wu, Harry X. and Bian, Liming},
	month = aug,
	year = {2026},
	keywords = {Breeding population, Chinese fir, Genetic diversity, Genomic kinship},
	pages = {29},
}

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is the most commercially important conifer species in southern China. Since 2015, the Fujian Province has launched its fourth cycle of genetic improvement, yet the impact of intensive artificial selection for growth and wood quality traits on the genetic diversity of advanced-cycle populations remains unclear. In this study, genotyping-by-sequencing (GBS) was used to genotype 310 individuals sampled from four consecutive breeding populations (first to fourth cycle). Across cycles, diversity indices remained relatively stable, with the fourth-cycle population showing slightly higher values (Ho = 0.325, He = 0.272). The broadening of breeding objectives to include wood quality and resistance traits, together with the introduction of external elite germplasm from the second cycle onward, may have contributed to this balance. Consequently, genetic differentiation among the populations from different breeding cycles was minimal (Fst \textless 0.01). Comparison of the genomic and pedigree-based relationship matrices revealed discrepancies for some pairs, indicating that genomic estimates provide complementary information for characterizing relatedness. Overall, genetic diversity was maintained across the four breeding cycles. These results provide a genomic basis for managing genetic diversity and relatedness in advanced-cycle Chinese fir breeding.

@article{rodriguez_comparative_2026,
	title = {Comparative regulomics of wood formation across dicot and conifer trees},
	volume = {17},
	copyright = {2026 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-026-75624-2},
	doi = {10.1038/s41467-026-75624-2},
	abstract = {Understanding the regulatory program underlying wood formation is key to improving biomass production and carbon sequestration in trees. However, how wood formation evolved and how these programs have been rewired across lineages remains unclear. Here, we present the first high-spatial-resolution evo-devo resource for wood transcriptomes spanning multiple dicots and conifers, representing the two major tree-containing lineages separated by more than 300 million years of evolution. Using orthology-aware co-expression network analysis, we identified genes with conserved and lineage-specific expression patterns. By integrating chromatin accessibility data and transcription factor motif analysis, we further inferred candidate regulatory networks for xylem differentiation and secondary cell wall formation. We demonstrate how this dataset can be used to answer long standing questions in wood biology related to differences in acetylation of cell wall polymers and master regulators of xylem specification across dicot and conifer tree species. The data offer a resource for the tree biology and evo-devo communities, and are publicly available at PlantGenIE.org.},
	language = {en},
	number = {1},
	urldate = {2026-09-02},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Rodriguez, Eduardo and Birkeland, Siri and Chapple, Ellen Dimmen and Fredriksson, Samuel and Carracedo Lorenzo, Zulema and Ahlgren Kalman, Teitur and Kumar, Vikash and Mccann, Jamie and Hill, Jason and Soundiramourtty, Sivagamy and Voxeur, Aline and Røhr, Åsmund Kjendseth and Tuominen, Hannele and Mellerowicz, Ewa J. and Street, Nathaniel R. and Hvidsten, Torgeir R.},
	month = jul,
	year = {2026},
	keywords = {Comparative genomics, Gene regulatory networks, Plant evolution, Plant genetics},
	pages = {8916},
}

Understanding the regulatory program underlying wood formation is key to improving biomass production and carbon sequestration in trees. However, how wood formation evolved and how these programs have been rewired across lineages remains unclear. Here, we present the first high-spatial-resolution evo-devo resource for wood transcriptomes spanning multiple dicots and conifers, representing the two major tree-containing lineages separated by more than 300 million years of evolution. Using orthology-aware co-expression network analysis, we identified genes with conserved and lineage-specific expression patterns. By integrating chromatin accessibility data and transcription factor motif analysis, we further inferred candidate regulatory networks for xylem differentiation and secondary cell wall formation. We demonstrate how this dataset can be used to answer long standing questions in wood biology related to differences in acetylation of cell wall polymers and master regulators of xylem specification across dicot and conifer tree species. The data offer a resource for the tree biology and evo-devo communities, and are publicly available at PlantGenIE.org.

@article{liu_loss_2026,
	title = {Loss of function of the {AP2}/{ERF} transcription factor {StGAME9} abolishes activation and induction of steroidal glycoalkaloid biosynthesis in potato plants},
	volume = {237},
	issn = {0981-9428},
	url = {https://www.sciencedirect.com/science/article/pii/S0981942826005474},
	doi = {10.1016/j.plaphy.2026.111561},
	abstract = {Steroidal glycoalkaloids (SGAs) are toxic defense substances present in certain species of the Solanaceae, including major crops such as eggplant, tomato, and potato. GLYCOALKALOID METABOLISM 9 (GAME9) was first identified in tomato and potato as an APETALA 2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor regulating key genes in SGA biosynthesis. However, the spatial effects of endogenous GAME9 in potato remain largely unexplored, particularly in tubers, highlighting a knowledge gap in understanding activation and induction of SGA biosynthesis in this important staple food crop. Here, we generated StGAME9 knockout mutants in potato via DNA-free CRISPR/Cas9. Compared to the wild type, knockout mutants contained significantly reduced SGA levels in leaves, and were almost free of SGAs in tubers. Notably, SGA accumulation remained minimal in the mutant tubers even under two SGA-inducing conditions; wounding and light exposure, indicating a loss of inducible SGA biosynthesis. Integrated transcriptomic and metabolomic characterization of knockout mutants (Stgame9) revealed extensive reprogramming of gene expression and metabolism, affecting not only SGA and sterol pathways but also a broader range of metabolic processes, with stress-related metabolic responses being attenuated in Stgame9 tubers. Despite these changes, Stgame9 plants displayed a normal growth phenotype under both greenhouse and field conditions. Our findings substantiate a pivotal role of GAME9 in potato for the regulation of basal and induced SGA biosynthesis. The results further indicate that StGAME9 is involved in the regulation of a broader, complex, and interconnected network along biosynthetic pathways, where potato metabolism exhibits substantial robustness and compensatory capacity to buffer the loss of StGAME9.},
	urldate = {2026-09-02},
	journal = {Plant Physiology and Biochemistry},
	author = {Liu, Ying and Merino, Irene and Potgieter, Lizel and Flöhr, Adam and Johansson, Annika I. and Andersson, Mariette and Sitbon, Folke and Hofvander, Per},
	month = aug,
	year = {2026},
	keywords = {AP2/ERF transcription factor, Abiotic stress, Glycoalkaloids, Metabolomics, Potato (), Transcriptomics},
	pages = {111561},
}

Steroidal glycoalkaloids (SGAs) are toxic defense substances present in certain species of the Solanaceae, including major crops such as eggplant, tomato, and potato. GLYCOALKALOID METABOLISM 9 (GAME9) was first identified in tomato and potato as an APETALA 2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor regulating key genes in SGA biosynthesis. However, the spatial effects of endogenous GAME9 in potato remain largely unexplored, particularly in tubers, highlighting a knowledge gap in understanding activation and induction of SGA biosynthesis in this important staple food crop. Here, we generated StGAME9 knockout mutants in potato via DNA-free CRISPR/Cas9. Compared to the wild type, knockout mutants contained significantly reduced SGA levels in leaves, and were almost free of SGAs in tubers. Notably, SGA accumulation remained minimal in the mutant tubers even under two SGA-inducing conditions; wounding and light exposure, indicating a loss of inducible SGA biosynthesis. Integrated transcriptomic and metabolomic characterization of knockout mutants (Stgame9) revealed extensive reprogramming of gene expression and metabolism, affecting not only SGA and sterol pathways but also a broader range of metabolic processes, with stress-related metabolic responses being attenuated in Stgame9 tubers. Despite these changes, Stgame9 plants displayed a normal growth phenotype under both greenhouse and field conditions. Our findings substantiate a pivotal role of GAME9 in potato for the regulation of basal and induced SGA biosynthesis. The results further indicate that StGAME9 is involved in the regulation of a broader, complex, and interconnected network along biosynthetic pathways, where potato metabolism exhibits substantial robustness and compensatory capacity to buffer the loss of StGAME9.