Complementary Phenotyping of Maize Root System Architecture by Root Pulling Force and X-Ray Imaging

Shao, Mon‐Ray; Ni, Jinfu; Li, M.; Howard, Angela; Lehner, Kevin; Mullen, Jack L.; Gunn, Shayla L.; McKay, John; Topp, Christopher N.

doi:10.34133/2021/9859254

Cited by 22 publications

(13 citation statements)

References 63 publications

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“…RPF showed the greatest positive correlation with root mass and area. This is consistent with our previous study of 3D X-ray tomography measurements from the root crowns of a subset of SAM lines, where RPF was highly associated with root volume and surface area (Shao et al, 2021). As further evidence for the utility of RPF as a sampling method, estimates of heritability for RPF were greater than or equal to those for RSA traits (Figure 3).…”

Section: Rootsupporting

confidence: 91%

“…While RPF can serve as a simple measure for root architecture traits, the extracted root systems remain amenable to image-based measurements as in excavationbased root extraction. Imaging of pulled root systems has shown RPF to be highly indicative of root system volume and surface area (Shao et al, 2021). Due to the simplicity and individual plant sampling of the RPF method, it is also amenable to automation to increase the throughput of RSA measurements in the field for improved mapping studies.…”

Section: Introductionmentioning

confidence: 99%

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Root Pulling Force Across Drought in Maize Reveals Genotype by Environment Interactions and Candidate Genes

et al. 2022

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High-throughput, field-based characterization of root systems for hundreds of genotypes in thousands of plots is necessary for breeding and identifying loci underlying variation in root traits and their plasticity. We designed a large-scale sampling of root pulling force, the vertical force required to extract the root system from the soil, in a maize diversity panel under differing irrigation levels for two growing seasons. We then characterized the root system architecture of the extracted root crowns. We found consistent patterns of phenotypic plasticity for root pulling force for a subset of genotypes under differential irrigation, suggesting that root plasticity is predictable. Using genome-wide association analysis, we identified 54 SNPs as statistically significant for six independent root pulling force measurements across two irrigation levels and four developmental timepoints. For every significant GWAS SNP for any trait in any treatment and timepoint we conducted post hoc tests for genotype-by-environment interaction, using a mixed model ANOVA. We found that 8 of the 54 SNPs showed significant GxE. Candidate genes underlying variation in root pulling force included those involved in nutrient transport. Although they are often treated separately, variation in the ability of plant roots to sense and respond to variation in environmental resources including water and nutrients may be linked by the genes and pathways underlying this variation. While functional validation of the identified genes is needed, our results expand the current knowledge of root phenotypic plasticity at the whole plant and gene levels, and further elucidate the complex genetic architecture of maize root systems.

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Section: Rootsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Root Pulling Force Across Drought in Maize Reveals Genotype by Environment Interactions and Candidate Genes

et al. 2022

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“…In addition, it allows quantification of root architecture over time and in response to environmental stress by analyzing root 3D models derived from CT images. Shao et al (2021) generated highly precise 3D models of maize root crowns via CT and created computations pipelines that could measure 71 features from each sample. Herrero-Huerta et al (2021) developed a spatial-temporal root architecture modeling method based on CT, enabling the extraction of key root traits, including root number, length, angle, diameter, and volume of lateral roots.…”

Section: Survey Methodologymentioning

confidence: 99%

Recent advances in methods for in situ root phenotyping

Zhu

et al. 2022

PeerJ

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Roots assist plants in absorbing water and nutrients from soil. Thus, they are vital to the survival of nearly all land plants, considering that plants cannot move to seek optimal environmental conditions. Crop species with optimal root system are essential for future food security and key to improving agricultural productivity and sustainability. Root systems can be improved and bred to acquire soil resources efficiently and effectively. This can also reduce adverse environmental impacts by decreasing the need for fertilization and fresh water. Therefore, there is a need to improve and breed crop cultivars with favorable root system. However, the lack of high-throughput root phenotyping tools for characterizing root traits in situ is a barrier to breeding for root system improvement. In recent years, many breakthroughs in the measurement and analysis of roots in a root system have been made. Here, we describe the major advances in root image acquisition and analysis technologies and summarize the advantages and disadvantages of each method. Furthermore, we look forward to the future development direction and trend of root phenotyping methods. This review aims to aid researchers in choosing a more appropriate method for improving the root system.

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“…This means that dense root crowns or areas of thick matted lateral roots are not resolvable. Thus, we are considering the potential to complement the photogrammetry derived point cloud with X-ray CT derived root crown reconstructions (Shao et al, 2021;Zeng et al, 2021).…”

Section: The Importance Of Capturing Entire 3d Root System Architectu...mentioning

confidence: 99%

Root System Architecture and Environmental Flux Analysis in Mature Crops using 3D Root Mesocosms

Dowd

Bagnall

et al. 2022

Preprint

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Current methods of root sampling typically only obtain small or incomplete sections of root systems and do not capture their true complexity. To facilitate the visualization and analysis of full-sized plant root systems in 3-dimensions, we developed customized mesocosm growth containers. While highly scalable, the design presented here uses an internal volume of 45 ft3 (1.27 m3), suitable for large crop and bioenergy grass root systems to grow largely unconstrained. Furthermore, they allow for the excavation and preservation of 3-dimensional RSA, and facilitate the collection of time-resolved subterranean environmental data. Sensor arrays monitoring matric potential, temperature and CO2 levels are buried in a grid formation at various depths to assess environmental fluxes at regular intervals. Methods of 3D data visualization of fluxes were developed to allow for comparison with root system architectural traits. Following harvest, the recovered root system can be digitally reconstructed in 3D through photogrammetry, which is an inexpensive method requiring only an appropriate studio space and a digital camera. We developed a pipeline to extract features from the 3D point clouds, or from derived skeletons that include point cloud voxel number as a proxy for biomass, total root system length, volume, depth, convex hull volume and solidity as a function of depth. Ground-truthing these features with biomass measurements from manually dissected root systems showed a high correlation. We evaluated switchgrass, maize, and sorghum root systems to highlight the capability for species wide comparisons. We focused on two switchgrass ecotypes, upland (VS16) and lowland (WBC3), in identical environments to demonstrate widely different root system architectures that may be indicative of core differences in their rhizoeconomic foraging strategies. Finally, we imposed a strong physiological water stress and manipulated the growth medium to demonstrate whole root system plasticity in response to environmental stimuli. Hence, these new 3D Root Mesocosms and accompanying computational analysis provides a new paradigm for study of mature crop systems and the environmental fluxes that shape them.

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Complementary Phenotyping of Maize Root System Architecture by Root Pulling Force and X-Ray Imaging

Cited by 22 publications

References 63 publications

Root Pulling Force Across Drought in Maize Reveals Genotype by Environment Interactions and Candidate Genes

Root Pulling Force Across Drought in Maize Reveals Genotype by Environment Interactions and Candidate Genes

Recent advances in methods for in situ root phenotyping

Root System Architecture and Environmental Flux Analysis in Mature Crops using 3D Root Mesocosms

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