Expression quantitative trait loci mapping identified <i>PtrXB38</i> as a key hub gene in adventitious root development in <i>Populus</i>

Yao, Tao; Zhang, Jin; Yates, Timothy B.; Shrestha, Him K.; Engle, Nancy L.; Ployet, Raphael; John, Cai; Feng, Kai; Bewg, William Patrick; Chen, Margot S. S.; Lu, Haiwei; Harding, Scott A.; Qiao, Zhenzhen; Jawdy, Sara S.; Shu, Mengjun; Yuan, Wenya; Mozaffari, Khadijeh; Harman‐Ware, Anne E.; Happs, Renee M.; York, Larry M.; Binder, Brad M.; Yoshinaga, Yuko; Daum, Christopher; Tschaplinski, Timothy J.; Abraham, Paul E.; Tsai, Chung‐Jui; Barry, Kerrie; Lipzen, Anna; Schmutz, Jeremy; Tuskan, Gerald A.; Chen, Jin‐Gui; Muchero, Wellington

doi:10.1111/nph.19126

Cited by 5 publications

(3 citation statements)

References 89 publications

(127 reference statements)

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“…To further amplify the potential benefits of SA catabolism, we repeated these experiments using a P. tremula x P. alba INRA 717-1B4 mutant that overexpresses the PtrXB38 gene [37]. This mutant has been shown to produce significantly higher concentrations of salicin in the roots (Figure S4).…”

Section: Effects Of Epistatic Interactions That Benefit Sa Catabolizersmentioning

confidence: 99%

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Catabolic pathway acquisition by soil pseudomonads readily enables growth with salicyl alcohol but does not affect colonization ofPopulusroots

Christel,

Carrell,

Burdick

et al. 2024

Preprint

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Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally reproduced one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol into soil isolates from the Pseudomonas genus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferred by HGT but is selectively neutral under environmentally-relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting, because the selective benefits are small and negative frequency-dependent.

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Section: Effects Of Epistatic Interactions That Benefit Sa Catabolizersmentioning

confidence: 99%

“…Sorbitol (75 µL of 1mg/mL aqueous solution) was added to the first extract as an internal standard [37]. The two extracts were combined, and a 1 mL aliquot was dried under nitrogen for analysis.…”

Section: Metabolite Analysismentioning

confidence: 99%

Catabolic pathway acquisition by soil pseudomonads readily enables growth with salicyl alcohol but does not affect colonization ofPopulusroots

Christel,

Carrell,

Burdick

et al. 2024

Preprint

Self Cite

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“…Since its publication, the authors of Yao et al (2023) have identified an error in their article. An image for 'OE-72' was duplicated in Fig.…”

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confidence: 99%

Corrigendum to: Expression quantitative trait loci mapping identified PtrXB38 as a key hub gene in adventitious root development in Populus

2024

New Phytologist

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A multi-tissue genome-scale model of Populus trichocarpa elucidates overexpression targets for improving drought tolerance

Simas Coutinho Barbosa,

Schroeder,

Suthers

et al. 2024

In Silico Plants

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Populus trichocarpa (poplar) is a fast-growing model tree whose lignocellulosic biomass is a promising biofuel feedstock. Enhancing its viability and yield in non-arable drought-prone lands can reduce biomass cost and accelerate adoption as a biofuel crop. Data from extensive -omics and phenotypic studies were leveraged herein to reconstruct a multi-tissue (root, stem, and leaf) genome-scale model (GSM) of poplar, iPotri3463, encompassing 14,360 reactions, 12,402 metabolites, and 3,463 genes. Two condition-specific GSMs were extracted from iPotri3463: iPotri3016C (control) and iPotri2999D (drought), supported by condition-specific transcript levels and reaction essentiality for growth. Physiological constraints consistent with experimental measurements of drought-stressed plants were imposed to growth, photorespiration, and carbon assimilation rates. Calculated increased flux capacity through the violaxanthin cycle and GABA biosynthetic pathways agree with established key strategies for improving drought tolerance. Differential gene expression analysis was performed on existing transcriptomes of poplar under different watering regimes. Computational flux knockdown was applied to reactions with increased flux capacity under drought which were associated with at least one downregulated gene. Several such reactions were essential for maintaining observed biomass yield and their associated genes are candidates for overexpression to improve drought tolerance. Glutamine synthetase is one whose overexpression in poplar confirms in silico predictions. However, the two most promising candidates are genes encoding ferulate-5-hydroxylase, Potri.007G016400 and Potri.005G117500, as their overexpression in other plant species led to demonstrably improved drought tolerance while previous overexpression in poplar reduced biomass recalcitrance. iPotri3463 is the first poplar-specific whole-plant GSM and the second one available for a woody plant.

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Expression quantitative trait loci mapping identified PtrXB38 as a key hub gene in adventitious root development in Populus

Cited by 5 publications

References 89 publications

Catabolic pathway acquisition by soil pseudomonads readily enables growth with salicyl alcohol but does not affect colonization ofPopulusroots

Catabolic pathway acquisition by soil pseudomonads readily enables growth with salicyl alcohol but does not affect colonization ofPopulusroots

Corrigendum to: Expression quantitative trait loci mapping identified PtrXB38 as a key hub gene in adventitious root development in Populus

A multi-tissue genome-scale model of Populus trichocarpa elucidates overexpression targets for improving drought tolerance

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