Delivering low-cost, high-throughput root phenotyping screens for arable crops

Plant roots are essential for the uptake of water and nutrients from soil. Consequently, root growth has significant effects on crop establishment and yield. Previous work by the project team, and others, has shown strong relationships between early root growth traits and the performance of arable crops in the field. However, measuring roots and selecting varieties with improved root systems in the field is time consuming, laborious and expensive. Using laboratory techniques, root growth can be measured quickly and cheaply - for 1000s of plants a year. Genotypes with better root growth and root architectures can be identified in the laboratory and assessments of selected plants can be made under field conditions to validate laboratory screens and assess field performance.

In this proposal we will use low cost, high-throughput methods to define the early root system of >1,600 different oilseed rape (OSR), barley and wheat genotypes in the laboratory. The roots of individual plants will be imaged at two time points. These images will then be analysed to determine the number of roots, root branching rates, root lengths, root growth rates and root angles. To validate and test the utility of measurements made in the laboratory, we will compare them with (1) measurements of root systems made in the field, and (2) data collected from new and legacy field trials assessing large numbers of new crop varieties for National and Recommended Lists to identify root traits correlated with establishment and yield for breeding.

Root growth and architecture are genetically controlled. We will identify genetic loci in large populations of OSR, barley and wheat affecting root growth and architecture traits that correlate with resource acquisition, establishment and yield in the field. An understanding of how best to combine beneficial alleles will be assessed through modelling approaches. To identify genetic targets for breeding we will develop mathematical models describing root growth and architecture in OSR that incorporate the effects of genetic variation. These mathematical models will be extended to predict the effects of root architecture on P acquisition and, thereby, identify potential genotypes with improved rooting and greater P acquisition for sustainable agriculture.

In summary, this proposal will deliver low cost, high-throughput platforms for root phenotyping. These will be of direct benefit to the breeding industry, allowing them to assess germplasm for root growth and architecture that correlate with improved establishment and yield. Genetic loci affecting root growth and architecture will be identified to accelerate the breeding of new varieties. Mathematical models will allow genotypes associated with improved root systems to be identified.

We will develop low cost, high-throughput (HTP) phenotyping platforms to quantify root growth and architecture in oilseed rape (OSR), barley and wheat. We will phenotype >1,600 distinct genotypes, comprising >800 OSR, 580 barley and 250 wheat genotypes in the laboratory. Root systems will be imaged at two time points and root number, length, angle, branching and growth rates will be determined using ImageJ and bespoke image analysis software. Data from HTP phenotyping will be correlated with (1) field performance data, including establishment and yield from new field experiments and from industry/legacy data, and (2) 3D imaging of root systems using micro-computed tomography (micro-CT). These data will be integrated in two databases, one for root images and one for all other project data. We will identify genetic loci in large populations of OSR, barley and wheat affecting root growth and architecture traits that correlate with resource acquisition, establishment and yield in the field. In OSR, this will include the development of a new mapping population, the development of gene expression markers and expression QTL networks. It will also include fine mapping previously-identified candidate loci in an existing mapping population, through an ongoing UK-China collaboration. In barley, this will comprise genome-wide association mapping techniques. In wheat, this will comprise the use of new populations of step-wise alien introgressions from wild relatives. An understanding of how best to combine beneficial alleles will be assessed through modelling approaches. To identify genetic targets for breeding we will develop mathematical models describing root growth and architecture in OSR that incorporate the effects of genetic variation. These mathematical models will be extended to predict the effects of root architecture on P acquisition. Root data obtained from laboratory and field experiments will be used to parameterise and validate these models.

Roots are an untapped breeding resource to facilitate crop establishment, increase crop yield potential and improve resource use efficiency. This project is designed to meet industry-driven demands for low-cost, high-throughput screening platforms for key root growth and architectural traits in a wide range of germplasm. The main outputs are: (1) simple, low-cost, high-throughput root phenotyping platforms for arable crops, (2) data on key root traits for oilseed rape (OSR), barley and wheat germplasm, (3) identification of root traits that are correlated with the breeding targets of establishment and commercial yield in the field, (4) a new dynamic model of the OSR root system incorporating the effects of genotype for predicting root architectures with improved capture of soil resources, and (5) identification of genetic loci associated with root development and architecture traits. The Pathways to Impact statement defines the activities that will expedite the utilisation of these outputs, primarily by industry but also by academic and public stakeholders.

The main impact, in the short term, will be achieved through interactions with industry groups, including companies involved in breeding new OSR, barley and wheat varieties. These groups will benefit immediately from the development of low cost, high-throughput root phenotyping during the project. Germplasm contributed by Industry Partners will be screened and the genetic potential for breeding new elite lines for root traits that improve resource acquisition, establishment or yield will be identified. This will bring competitive advantage through 'first mover' positioning and IP. In addition, genetic loci and markers associated with beneficial root traits will allow marker-assisted selection of genotypes with these traits and accelerate the breeding process in the medium and longer-terms. Results and outputs from the project will be disseminated to Industry Partners through CIRC meetings, and to the wider industry through joint industry-academic meetings, trade shows and the trade press, under the guidance of a Steering Committee.

Secondary impact will be achieved through academic routes. Thus, the academic research community will benefit from (1) improved knowledge of root development and architecture traits in crop plants, (2) the identification of genetic loci associated with root development and architecture traits in crop plants, and (3) new mathematical models describing the development of OSR root systems incorporating the effects of genotype.

Ultimately, impact will be felt by the wider society. To feed the world's burgeoning population, agricultural production must double in the next three decades within unpredictable environmental constraints. The development of crop varieties with improved resource use efficiency, establishment and yield through the selection of root traits, will serve to increase the food supplied from a given area. This will contribute to agricultural sustainability and greater food security.