title: Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis.
abstract: The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions.
authors.affiliation: The SIMBIOS Centre, Abertay University, Dundee, DD1 1HG, UK.|Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.
authors.forename: H F
authors.initials: HF
authors.lastname: Downie
authors.affiliation: Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.|Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Leicestershire, LE12 5RD, UK.
authors.forename: M O
authors.initials: MO
authors.lastname: Adu
authors.affiliation: The SIMBIOS Centre, Abertay University, Dundee, DD1 1HG, UK.
authors.forename: S
authors.initials: S
authors.lastname: Schmidt
authors.affiliation: The SIMBIOS Centre, Abertay University, Dundee, DD1 1HG, UK.
authors.forename: W
authors.initials: W
authors.lastname: Otten
authors.affiliation: Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.
authors.forename: L X
authors.initials: LX
authors.lastname: Dupuy
authors.affiliation: Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.|King Saud University, Riyadh, Saudi Arabia.
authors.forename: P J
authors.initials: PJ
authors.lastname: White
authors.affiliation: Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.
authors.forename: T A
authors.initials: TA
authors.lastname: Valentine
mesh_terms: D005838:Genotype; D010641:Phenotype; D018517:Plant Roots / Q000166:cytology* / Q000254:growth & development / Q000502:physiology; D058441:Rhizosphere; D012984:Software; D012987:Soil; D014867:Water / Q000378:metabolism
chemical_list: D012987:Soil; D014867:Water
keywords: abiotic interactions; automation; biotic interactions; computed tomography; microscopy; root system architecture (RSA); root:soil interactions; soil