Next generation shovelomics: set up a tent and REST

Tino Colombi; Norbert Kirchgessner; Chantal Andrée Le Marié; Larry Matthew York; Jonathan P. Lynch; Andreas Hund

doi:10.1007/s11104-015-2379-7

Next generation shovelomics: set up a tent and REST

Tino Colombi, Norbert Kirchgessner, Chantal Andrée Le Marié, Larry Matthew York, Jonathan P. Lynch, Andreas Hund

Research output: Contribution to journal › Article › peer-review

92 Scopus citations

Abstract

Aims: Root system architecture traits (RSAT) are crucial for crop productivity, especially under drought and low soil fertility. The “shovelomics” method of field excavation of mature root crowns followed by manual phenotyping enables a relatively high throughput as needed for breeding and quantitative genetics. We aimed to develop a new sampling protocol in combination with digital imaging and new software. Methods: Sampled rootstocks were split lengthwise, photographed under controlled illumination in an imaging tent and analysed using Root Estimator for Shovelomics Traits (REST). A set of 33 diverse maize hybrids, grown at 46 and 192 kg N ha⁻¹, was used to evaluate the method and software. Results: Splitting of the crowns enhanced soil removal and enabled access to occluded traits: REST-derived median gap size correlated negatively (r = −0.62) with lateral root density based on counting. The manually measured root angle correlated with the image-derived root angle (r = 0.89) and the horizontal extension of the root system (r = 0.91). The heritabilities of RSAT ranged from 0.45 to 0.81, comparable to heritabilities of plant height and leaf biomass. Conclusion: The combination of the novel crown splitting method, combined with imaging under controlled illumination followed by automatic analysis with REST, allowed for higher throughput while maintaining precision. The REST Software is available as supplement.

Original language	English
Pages (from-to)	1-20
Number of pages	20
Journal	Plant and Soil
Volume	388
Issue number	1-2
DOIs	https://doi.org/10.1007/s11104-015-2379-7
State	Published - Mar 2015
Externally published	Yes

Funding

The authors would like to thank the anonymous reviewers for their helpful suggestions and Achim Walter for his support. Thanks for assistance in the field go to Johan Prinsloo and the farmworkers in South Africa. Thanks to Claude Welcker for his assistance in assembling the EURoot maize panel and to Delley Seeds and Plants Ltd. for hybrid production. We kindly thank the donors of the genetic material: Department of Agroenvironmental Science and Technologies (DiSTA), University of Bologna, Italy (RootABA lines); Misión Biológica de Galicia (CSIC), Spain (EP52); Estación Experimental de Aula Dei (CSIC), Spain (EZ47, EZ11A, EZ37); Centro Investigaciones Agrarias de Mabegondo (CIAM), Spain (EC169); Misión Biológica de Galicia (CSIC), Spain, (EP52); University of Hohenheim, Versuchsstation für Pflanzenzüchtung, Germany (UH007, UH250); and INRA CNRS UPS AgroParisTech, France (supply of the remaining, public lines). We thank the Forschungszentrum Jülich GmbH, Germany for the MatLib package and Oliver Dressler for the CAD illustrations. Support for field research in South Africa was provided to Jonathan Lynch by the Howard G. Buffett Foundation. This research received funding from the European Community Seventh Framework Programme FP7-KBBE-2011-5 under grant agreement no.289300 and the Walter Hochstrasser-Stiftung.

Funders	Funder number
Seventh Framework Programme FP7-KBBE-2011-5	289300
Walter Hochstrasser-Stiftung

Keywords

Automated phenotyping
Heritability
Image processing
Maize
Root system architecture

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1007/s11104-015-2379-7

Cite this

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title = "Next generation shovelomics: set up a tent and REST",

abstract = "Aims: Root system architecture traits (RSAT) are crucial for crop productivity, especially under drought and low soil fertility. The “shovelomics” method of field excavation of mature root crowns followed by manual phenotyping enables a relatively high throughput as needed for breeding and quantitative genetics. We aimed to develop a new sampling protocol in combination with digital imaging and new software. Methods: Sampled rootstocks were split lengthwise, photographed under controlled illumination in an imaging tent and analysed using Root Estimator for Shovelomics Traits (REST). A set of 33 diverse maize hybrids, grown at 46 and 192 kg N ha−1, was used to evaluate the method and software. Results: Splitting of the crowns enhanced soil removal and enabled access to occluded traits: REST-derived median gap size correlated negatively (r = −0.62) with lateral root density based on counting. The manually measured root angle correlated with the image-derived root angle (r = 0.89) and the horizontal extension of the root system (r = 0.91). The heritabilities of RSAT ranged from 0.45 to 0.81, comparable to heritabilities of plant height and leaf biomass. Conclusion: The combination of the novel crown splitting method, combined with imaging under controlled illumination followed by automatic analysis with REST, allowed for higher throughput while maintaining precision. The REST Software is available as supplement.",

keywords = "Automated phenotyping, Heritability, Image processing, Maize, Root system architecture",

author = "Tino Colombi and Norbert Kirchgessner and {Le Mari{\'e}}, {Chantal Andr{\'e}e} and York, {Larry Matthew} and Lynch, {Jonathan P.} and Andreas Hund",

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doi = "10.1007/s11104-015-2379-7",

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AU - Colombi, Tino

AU - Kirchgessner, Norbert

AU - Le Marié, Chantal Andrée

AU - York, Larry Matthew

AU - Lynch, Jonathan P.

AU - Hund, Andreas

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AB - Aims: Root system architecture traits (RSAT) are crucial for crop productivity, especially under drought and low soil fertility. The “shovelomics” method of field excavation of mature root crowns followed by manual phenotyping enables a relatively high throughput as needed for breeding and quantitative genetics. We aimed to develop a new sampling protocol in combination with digital imaging and new software. Methods: Sampled rootstocks were split lengthwise, photographed under controlled illumination in an imaging tent and analysed using Root Estimator for Shovelomics Traits (REST). A set of 33 diverse maize hybrids, grown at 46 and 192 kg N ha−1, was used to evaluate the method and software. Results: Splitting of the crowns enhanced soil removal and enabled access to occluded traits: REST-derived median gap size correlated negatively (r = −0.62) with lateral root density based on counting. The manually measured root angle correlated with the image-derived root angle (r = 0.89) and the horizontal extension of the root system (r = 0.91). The heritabilities of RSAT ranged from 0.45 to 0.81, comparable to heritabilities of plant height and leaf biomass. Conclusion: The combination of the novel crown splitting method, combined with imaging under controlled illumination followed by automatic analysis with REST, allowed for higher throughput while maintaining precision. The REST Software is available as supplement.

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Next generation shovelomics: set up a tent and REST

Abstract

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Keywords

UN SDGs

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