Use of Imaging Technologies for High Throughput Phenotyping

Abstract

In this chapter we describe a high throughput phenotyping system that we have developed for raspberry and other soft fruit crops and its application to against individual (water stress regimes, vine weevil and Phytophthora root rot) and combined stresses. The term phenotype is used to describe the morphology, physiology, biochemistry and ontogeny of a plant, encompassing the diverse array of traits that contribute to the plant’s functional form. Plant phenotype is expressed as a consequence of the interaction between the plant genetic background (i.e. genotype) and the biotic and abiotic conditions experienced by the plant in its growing environment. A key focus of raspberry and other crop breeding is to understand the genetic control of desirable plant traits and the influence of environmental conditions on trait expression, which relies on the ability to collect quantitative information on target traits across genetically-characterised populations of plants. The process of characterising plant traits in detail, referred to as plant phenotyping, is a major challenge when relating plant genetic information to traits for plants in realistic growing environments. Advances in genetics and genomics methods in raspberry including high throughput DNA sequencing which has provided a new GbS linkage map and genome scaffolds, developments in microarray and RNA seq data and data analysis tools have provided large amounts of detailed information on raspberry. There is, however, a lack of corresponding methodology for high throughput plant phenotyping, which limits the quantity of available trait information, and creates a bottleneck in raspberry and other crop breeding (Fahlgren et al. 2015; Pauli et al. 2016a, b). The key factor in understanding traits at a genetic level is an ability to accurately phenotype. The main limitation is the significant effort and complexity of measurements, depending on trait, required to capture phenotyping data from plants grown in relevant environments – i.e. field conditions.