In Silico Roots: Room for Growth

Rutten, Jacob Pieter; Tusscher, Kirsten ten

doi:10.1016/j.tplants.2018.11.005

Cited by 15 publications

(19 citation statements)

References 58 publications

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“…Today, computer models have become a central tool for wet-lab scientists to quickly explore possible mechanisms underlying morphogenesis before designing and implementing effective experimental strategies. To date, computer models of root development have been instrumental in understanding root maturation in the context of biochemical flow over nongrowing (Band et al, 2014;Rutten and ten Tusscher, 2019) or idealized templates (Grieneisen et al, 2007). On contrary, little to no attempts were made to couple mechanisms of cell polarity establishment and realistic tissue biomechanics at single cell resolution to mechanistically understand how a root emerges from small populations of cells.…”

Section: Discussionmentioning

confidence: 99%

“…The main source of auxin during globular root embryogenesis comes from the shoot, and tends to accumulate in vascular tissue, root tip and epidermis 20,21 . Many aspects of auxin transport by PIN efflux carriers are well understood, however the connections between these mechanisms and the effect on root growth are largely obscure [22][23][24] .…”

Section: General Model Assumptionsmentioning

confidence: 99%

“…Computer models are becoming increasingly important tools to provide a mechanistic understanding of processes underlying organ morphogenesis. In the last decade, several computational models of plant development had produced critical insights in the auxindependent growth and zonation of mature roots [22][23][24][25] . However, most of these models incorporate pre-defined experimental patterns of cell polarities on idealized geometries(e.g.…”

Section: Introductionmentioning

confidence: 99%

“…This apparent complexity of root growth and patterning mechanisms has long attracted theoreticians on the quest to identify the underlying principles. In the last decade, several computational models of root development yielded important insights about auxin-dependent growth and zonation of mature roots (Morales-Tapia and Ruz-Ramírez, 2016;Rutten and ten Tusscher, 2019;Wabnik et al, 2011). However, these root models typically incorporate pre-defined patterns of polar auxin flow on idealized geometries (e.g.…”

Section: Introductionmentioning

confidence: 99%

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A coupled mechano-biochemical framework for root meristem morphogenesis

Marconi

Gallemí

Benková

et al. 2021

Preprint

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Understanding how an independent organ develops from the stem cell populations in the process called morphogenesis is a pressing challenge in developmental biology and medicine. Plants build up new organs such as roots to adjust their bodies to dynamic changes in the environment, thereby providing a tractable model to address this challenge. Here, we combined empirical data with advanced computer modeling techniques to build a mechanistic cell-based framework for the morphogenesis of the plant root. Our framework relies on experimentally supported design principles underlying the multi-layered feedback between tissue mechanics, cell growth, and directional cell-to-cell transport of growth regulator auxin. Model simulations reconstruct experimentally-observed patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Furthermore, our model provides new insights into mechanisms of sustained root growth and cell polarity establishment. This work reveals that mobile auxin signal feeds back on cell polarity and growth mechanics to instruct the morphogenesis of an independent organ.

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Section: Discussionmentioning

confidence: 99%

Section: General Model Assumptionsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

A coupled mechano-biochemical framework for root meristem morphogenesis

Marconi

Gallemí

Benková

et al. 2021

Preprint

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“…Answers to these questions require the ability to analyze and image roots and signals within the roots on a three-dimensional level and at different scales of cellular organizations, ideally ranging from subcellular organization, to single cells, tissues, whole organ, and whole plant. Such studies should be combined with cell-specific whole-genome ‘omics’ and analyzed using a system biology approach and computational modeling [128,129,130]. In addition, the molecular mechanisms underlying signal perception and transduction need to be elucidated down to their atomic level structures, because sensing and transducing cellular signals may be explained by specific atomic-level changes within a single molecule, or within a complex of molecules.…”

Section: Discussionmentioning

confidence: 99%

Root Plasticity in the Pursuit of Water

Fromm

2019

Plants

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One of the greatest challenges of terrestrial vegetation is to acquire water through soil-grown roots. Owing to the scarcity of high-quality water in the soil and the environment’s spatial heterogeneity and temporal variability, ranging from extreme flooding to drought, roots have evolutionarily acquired tremendous plasticity regarding their geometric arrangement of individual roots and their three-dimensional organization within the soil. Water deficiency has also become an increasing threat to agriculture and dryland ecosystems due to climate change. As a result, roots have become important targets for genetic selection and modification in an effort to improve crop resilience under water-limiting conditions. This review addresses root plasticity from different angles: Their structures and geometry in response to the environment, potential genetic control of root traits suitable for water-limiting conditions, and contemporary and future studies of the principles underlying root plasticity post-Darwin’s ‘root-brain’ hypothesis. Our increasing knowledge of different disciplines of plant sciences and agriculture should contribute to a sustainable management of natural and agricultural ecosystems for the future of mankind.

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Root anatomy and soil resource capture

et al. 2021

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Background Suboptimal water and nutrient availability are primary constraints in global agriculture. Root anatomy plays key roles in soil resource acquisition. In this article we summarize evidence that root anatomical phenotypes present opportunities for crop breeding. Scope Root anatomical phenotypes influence soil resource acquisition by regulating the metabolic cost of soil exploration, exploitation of the rhizosphere, the penetration of hard soil domains, the axial and radial transport of water, and interactions with soil biota including mycorrhizal fungi, pathogens, insects, and the rhizosphere microbiome. For each of these topics we provide examples of anatomical phenotypes which merit attention as selection targets for crop improvement. Several cross-cutting issues are addressed including the importance of phenotypic plasticity, integrated phenotypes, C sequestration, in silico modeling, and novel methods to phenotype root anatomy including image analysis tools. Conclusions An array of anatomical phenes have substantial importance for the acquisition of water and nutrients. Substantial phenotypic variation exists in crop germplasm. New tools and methods are making it easier to phenotype root anatomy, determine its genetic control, and understand its utility for plant fitness. Root anatomical phenotypes are underutilized yet attractive breeding targets for the development of the efficient, resilient crops urgently needed in global agriculture.

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In Silico Roots: Room for Growth

Cited by 15 publications

References 58 publications

A coupled mechano-biochemical framework for root meristem morphogenesis

A coupled mechano-biochemical framework for root meristem morphogenesis

Root Plasticity in the Pursuit of Water

Root anatomy and soil resource capture

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