Traitmill™: a functional genomics platform for the phenotypic analysis of cereals

Abstract

The improvement of quality and quantitative traits in industrial crops is among the most important goals in plant breeding. Many traits of interest are controlled by multiple genes and improvements have so far only been obtained through conventional breeding. The use of biotechnological tools to modify quantitative traits is highly challenging. CropDesign has developed TraitMill™, an automated plant evaluation platform allowing high-throughput testing of the effect of plant-based transgenes on agronomically valuable traits in crop plants. The focus of the platform is currently on rice, a good model for other important cereals such as maize and wheat. TraitMill™ offers a high-throughput prediction of gene function. Genes of validated function that confer trait improvement can then be transferred to other cereal crop species such as maize, but also to dicots, trees and ornamentals. TraitMill™ involves the following key components: (i) selection of candidate trait improvement genes among genes involved in signal transduction, cell cycle control, transcription, nutrient metabolism, etc.; (ii) a suite of validated constitutive or tissue-specific promoters from rice allowing for the selection of the most appropriate promoter–gene combination in view of the desired trait improvement; (iii) an industrialized plant transformation system generating tens of thousands of transgenic plants annually; and (iv) a robotized trait evaluation set-up for plant evaluation, proprietary image analysis software for measuring plant performance parameters and statistical analysis of results.

3D sorghum reconstructions from depth images identify QTL regulating shoot architecture

“…Commercial platforms, including the Scanalyzer series from Lemnatec (http:// www.lemnatec.com/products/; accessed February 2016) and the Traitmill platform from CropDesign (http:// www.cropdesign.com/general.php; accessed February 2016), have gained adoption in the research community and have promoted the development of additional software (beyond that which the respective companies provide) to analyze the images produced by the platform (Reuzeau, 2007;Hartmann et al, 2011;Fahlgren et al, 2015a). A variety of noncommercial platforms and methods developed by the research community also exist and have been demonstrated to perform well (White et al, 2012;Fiorani and Schurr, 2013;Sirault et al, 2013;Pound et al, 2014).…”

Mathematical Models Light Up Plant Signaling

“…In addition, some models require various types of high-throughput data. In this respect, the rapid development of large-scale phenotyping technologies may provide part of the solution (Granier et al, 2006;Reuzeau et al, 2006;Tisné et al, 2013).…”

“…These nondestructive systems are equipped with computer algorithms to analyze the images and calculate hypocotyl length, apical hook opening, and phototropic bending. For older plants, some automated platforms can capture the image and weigh each plant (Granier et al, 2006;Reuzeau et al, 2006;Tisné et al, 2013). Besides the whole-plant monitoring systems described above, high-resolution imaging technologies at the organ and cellular level are also under rapid development.…”

Discovering Transgenic Elite Events: Using Information from Early Screening Trials for Improving Experimental Design

“…To demonstrate the methods developed in this paper, we will use a real example of transgenic screening experiments using TraitMill, a high-throughput screening platform for rice (Reuzeau et al 2005). This example will be used throughout and be further elaborated in the last section of the paper.…”