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A low-cost greenhouse-based high-throughput phenotyping platform for genetic studies: a case study in maize under inoculation with plant growth-promoting bacteria

View ORCID ProfileRafael Massahiro Yassue, View ORCID ProfileGiovanni Galli, View ORCID ProfileRonaldo Borsato Junior, View ORCID ProfileHao Cheng, View ORCID ProfileGota Morota, View ORCID ProfileRoberto Fritsche-Neto
doi: https://doi.org/10.1101/2021.08.12.456112
Rafael Massahiro Yassue
1Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, São Paulo, Brazil
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Giovanni Galli
1Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, São Paulo, Brazil
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Ronaldo Borsato Junior
1Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, São Paulo, Brazil
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Hao Cheng
2Department of Animal Science, University of California, Davis, USA
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Gota Morota
3Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, USA
4Center for Advanced Innovation in Agriculture, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
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  • For correspondence: morota@vt.edu r.fritscheneto@irri.org
Roberto Fritsche-Neto
1Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, São Paulo, Brazil
5Quantitative Genetics and Biometrics Cluster, International Rice Research Institute, Los Baños, Philippines
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  • For correspondence: morota@vt.edu r.fritscheneto@irri.org
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Abstract

Greenhouse-based high-throughput phenotyping (HTP) presents a useful approach for studying novel plant growth-promoting bacteria (PGPB). Despite the potential of this approach to leverage genetic variability for breeding new maize cultivars exhibiting highly stable symbiosis with PGPB, greenhouse-based HTP platforms are not yet widely used because they are highly expensive; hence, it is challenging to perform HTP studies under a limited budget. In this study, we built a low-cost greenhouse-based HTP platform to collect growth-related image-derived phenotypes. We assessed 360 inbred maize lines with or without PGPB inoculation under nitrogen-limited conditions. Plant height, canopy coverage, and canopy volume obtained from photogrammetry were evaluated five times during early maize development. A plant biomass index was constructed as a function of plant height and canopy coverage. Inoculation with PGPB promoted plant growth. Phenotypic correlations between the image-derived phenotypes and manual measurements were at least 0.6. The genomic heritability estimates of the image-derived phenotypes ranged from 0.23 to 0.54. Moderate-to-strong genomic correlations between the plant biomass index and shoot dry mass (0.24–0.47) and between HTP-based plant height and manually measured plant height (0.55–0.68) across the developmental stages showed the utility of our HTP platform. Collectively, our results demonstrate the usefulness of the low-cost HTP platform for large-scale genetic and management studies to capture plant growth.

Core ideas

  • A low-cost greenhouse-based HTP platform was developed.

  • Image-derived phenotypes presented moderate to high genomic heritabilities and correlations.

  • Plant growth-promoting bacteria can improve plant resilience under nitrogen-limited conditions.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Email addresses: rafael.yassue{at}usp.br (RMY), giovannigalli{at}alumni.usp.br (GG), ronaldoborsatojr{at}usp.br (RBJ), qtlcheng{at}ucdavis.edu (HC), morota{at}vt.edu (GM), and r.fritscheneto{at}irri.org (RFN)

  • Abbreviations

    (CC)
    canopy coverage
    (CV)
    canopy volume
    (GBLUP)
    genomic best linear unbiased prediction
    (GCP)
    ground control points
    (GRO)
    ground resolution of the orthomosaics
    (GDD)
    growing degree days
    (HTP)
    high-throughput phenotyping
    (PHHTP)
    high-throughput phenotyping plant height
    (LB)
    Luria-Bertani medium
    (NDVI)
    normalized difference vegetation index
    (NL)
    number of fully expanded leaves
    (PGPB)
    plant growth-promoting bacteria
    (PH)
    plant height
    (RTK)
    real time kinematic
    (SDM)
    shoot dry mass
    (SNP)
    single-nucleotide polymorphism
    (UAV)
    unoccupied aerial vehicle
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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    Posted August 13, 2021.
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    A low-cost greenhouse-based high-throughput phenotyping platform for genetic studies: a case study in maize under inoculation with plant growth-promoting bacteria
    Rafael Massahiro Yassue, Giovanni Galli, Ronaldo Borsato Junior, Hao Cheng, Gota Morota, Roberto Fritsche-Neto
    bioRxiv 2021.08.12.456112; doi: https://doi.org/10.1101/2021.08.12.456112
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    A low-cost greenhouse-based high-throughput phenotyping platform for genetic studies: a case study in maize under inoculation with plant growth-promoting bacteria
    Rafael Massahiro Yassue, Giovanni Galli, Ronaldo Borsato Junior, Hao Cheng, Gota Morota, Roberto Fritsche-Neto
    bioRxiv 2021.08.12.456112; doi: https://doi.org/10.1101/2021.08.12.456112

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