Root phenomics of crops: opportunities and challenges

Abstract

Reliable techniques for screening large numbers of plants for root traits are still being developed, but include aeroponic, hydroponic and agar plate systems. Coupled with digital cameras and image analysis software, these systems permit the rapid measurement of root numbers, length and diameter in moderate (typically <1000) numbers of plants. Usually such systems are employed with relatively small seedlings, and information is recorded in 2D. Recent developments in X-ray microtomography have facilitated 3D non-invasive measurement of small root systems grown in solid media, allowing angular distributions to be obtained in addition to numbers and length. However, because of the time taken to scan samples, only a small number can be screened (typically <10 per day, not including analysis time of the large spatial datasets generated) and, depending on sample size, limited resolution may mean that fine roots remain unresolved. Although agar plates allow differences between lines and genotypes to be discerned in young seedlings, the rank order may not be the same when the same materials are grown in solid media. For example, root length of dwarfing wheat (Triticum aestivum L.) lines grown on agar plates was increased by ~40% relative to wild-type and semi-dwarfing lines, but in a sandy loam soil under well watered conditions it was decreased by 24–33%. Such differences in ranking suggest that significant soil environment–genotype interactions are occurring. Developments in instruments and software mean that a combination of high-throughput simple screens and more in-depth examination of root–soil interactions is becoming viable.

Large root systems: are they useful in adapting wheat to dry environments?

“…For example, Wojciechowski et al (2009) showed that the effect of Rht genes on root growth was strongly positive in gel cultures but strongly negative in soil. Potential approaches for efficient phenotyping of root traits under controlled conditions have recently been reviewed by Gregory et al (2009), who indicated significant emerging capability. However, field screening remains difficult.…”

Analyzing Lateral Root Development: How to Move Forward

“…These include growth on moistened germination paper rolls or pouches, sand rhizotrons, rhizoboxes, in compost followed by washing, soil columns and gelbased systems where phenotypic effects can be imaged using flatbed scanners, digital cameras, lasers, or even x-ray computed tomography (CT) (Hetz et al, 1996;Whiting et al, 2000;Bengough et al, 2004;Fang et al, 2009;French et al, 2009;Gregory et al, 2009;Hammond et al, 2009;Iyer-Pascuzzi et al, 2010;Trachsel et al, 2010;Tracy et al, 2010Tracy et al, , 2011Chapman et al, 2011;Lobet et al, 2011;Lucas et al, 2011). Magnetic resonance imaging (for noninvasive analysis of root structures) and positron emission tomography (for analysis of carbon transport and accumulation) can be combined to study the dynamics of structure-function relationships of roots in real soils in a noninvasive manner .…”

Development of a novel semi-hydroponic phenotyping system for studying root architecture

“…Root architecture directly impacts the capture of such soil resources and is, therefore, fundamental to crop productivity (Lynch 1995;Casson and Lindsey 2003;Malamy 2005;Watt et al 2006;Dunbabin 2007;Fita et al 2008;Gregory et al 2009). Changes in root system architecture and exploitation of soil water influence the accumulation of crop biomass (Hammer et al 2009).…”

“…Quantifying the architecture of root systems is essential because crop productivity is almost always influenced by the availability and accessibility of water and nutrients that are heterogeneously distributed in the soil (Miller et al 2003;Cichy et al 2009;Gregory et al 2009). Root architecture directly impacts the capture of such soil resources and is, therefore, fundamental to crop productivity (Lynch 1995;Casson and Lindsey 2003;Malamy 2005;Watt et al 2006;Dunbabin 2007;Fita et al 2008;Gregory et al 2009).…”

“…However, reliable approaches for phenotyping large numbers of plants are still being developed. Several non soil-filled methods for evaluating roots are available, including hydroponic, aeroponic and agar-plate systems (Gregory et al 2009). The soil-filled root observation chambers (Manschadi et al 2008) or rhizotrons (Wiese et al 2005), and growth pouches (Bonser et al 1996;Liao et al 2004) are often used in studying roots.…”