Accelerating root system phenotyping of seedlings through a computer-assisted processing pipeline

Background: There are numerous systems and techniques to measure the growth of plant roots. However, phenotyping large numbers of plant roots for breeding and genetic analyses remains challenging. One major difficulty is to achieve high throughput and resolution at a reasonable cost per plant sample. Here we describe a cost-effective root phenotyping pipeline, on which we perform time and accuracy benchmarking to identify bottlenecks in such pipelines and strategies for their acceleration. Results: Our root phenotyping pipeline was assembled with custom software and low cost material and equipment. Results show that sample preparation and handling of samples during screening are the most time consuming task in root phenotyping. Algorithms can be used to speed up the extraction of root traits from image data, but when applied to large numbers of images, there is a trade-off between time of processing the data and errors contained in the database. Conclusions: Scaling-up root phenotyping to large numbers of genotypes will require not only automation of sample preparation and sample handling, but also efficient algorithms for error detection for more reliable replacement of manual interventions

An ErbB2/c-Src axis links bioenergetics with PRC2 translation to drive epigenetic 2 reprogramming and mammary tumourigenesis

Dysregulation of histone modifications promotes carcinogenesis by altering transcription. Breast cancers frequently overexpress the histone methyltransferase EZH2, the catalytic subunit of Polycomb Repressor Complex 2 (PRC2). However, the role of EZH2 in this setting is unclear due to the context-dependent functions of PRC2 and the heterogeneity of breast cancer. Moreover, the mechanisms underlying PRC2 overexpression in cancer are obscure. Here, using multiple models of breast cancer driven by the oncogene ErbB2, we show that the tyrosine kinase c-Src links energy sufficiency with PRC2 overexpression via control of mRNA translation. By stimulating mitochondrial ATP production, c-Src suppresses energy stress, permitting sustained activation of the mammalian/mechanistic target of rapamycin complex 1 (mTORC1), which increases the translation of mRNAs encoding the PRC2 subunits Ezh2 and Suz12. We show that Ezh2 overexpression and activity are pivotal in ErbB2-mediated mammary tumourigenesis. These results reveal the hitherto unknown c-Src/mTORC1/PRC2 axis, which is essential for ErbB2-driven carcinogenesis

Which root architectural elements contribute the best to anchorage of Pinus species? Insights from in silico experiments

Background and Aims Root anchorage function is crucial for tree survival as most trees are exposed to recurrent wind throughout their lifespan. Trees exhibit a large variability of root system architecture (RSA) due genetic and environmental factors. This study aims to understand the links between RSA and tree stability.Methods A 3D biomechanical model was used to simulate tree overturning. To capture the variability of sinker RSA, fourteen virtual root patterns were created from an ensemble average of measured Pinus pinaster root systems. Root virtual patterns and tree-pulling simulations were verified against experimental data.Results The model predicts realistic tree anchorage strength, root stress, and failure patterns. Only a few root components contribute significantly to anchorage strength. The taproot contributes the most to anchorage rigidity, representing 61 % of the anchorage strength. The windward roots failure drives ultimate anchorage failure, representing 25 % of the anchorage strength. Simulations show that root secondary thickening induces higher anchorage rigidity and increases anchorage strength by 58 %.Conclusions This innovative approach appears promising for describing tree stability and its acclimation to external constraints