Low-cost rhizotron imaging and zero-shot deep-learning resolve temporal, spatial, and genetic variation in grapevine rootstock root systems
- 1University of California, Davis
Abstract
Root system architecture shapes how grapevine rootstocks take up water and nutrients, yet roots remain the least phenotyped grapevine organ because they are hidden and hard to image. We present a low-cost phenotyping pipeline that pairs custom acrylic rhizotrons (about US$30 each) with a consumer flatbed scanner and BiRefNet, a general-purpose deep-learning model used without training on root images, followed by automated mask cleaning, skeleton-based trait extraction, and soil moisture mapping. We tested it on nine commercial rootstocks scanned 16 times over 42 days after transplanting (DAT), with half under a ten-day water deficit. From 1,108 images we extracted 21 whole-root, depth-resolved, and topological traits. Genotypes differed in nearly every trait and in how they changed over time. Heritability of size and branching traits peaked at 0.92-0.93 between 21 and 31 DAT and fell for width, depth, and convex hull once roots reached the rhizotron walls, defining the best measurement window. The image-derived soil moisture map accurately tracked the deficit and its recovery. Deficit plants shifted new root growth to deeper soil without growing less overall, and the substrate dried fastest around older and denser roots. Root brightness decreased with root age and local moisture, and transport segments (axes serving several tips) were brighter than terminal laterals in every genotype. Root system size was associated with stomatal conductance in well-watered plants, and stomatal recovery after re-watering correlated with new root growth. The pipeline turns simple hardware into a quantitative, time-resolved root phenotyping platform suitable for breeding.
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BibTeX
@misc{diazgarcia2026lowcost,
title = {{Low-cost rhizotron imaging and zero-shot deep-learning resolve temporal, spatial, and genetic variation in grapevine rootstock root systems}},
author = {L. Diaz-Garcia and J. R. Munoz and E. Torres-Lomas and A. J. McElrone and S. Sharma and Y. Lupo},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.10.750709},
url = {https://www.biorxiv.org/content/10.64898/2026.09.10.750709v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Low-cost rhizotron imaging and zero-shot deep-learning resolve temporal, spatial, and genetic variation in grapevine rootstock root systems
AU - L. Diaz-Garcia
AU - J. R. Munoz
AU - E. Torres-Lomas
AU - A. J. McElrone
AU - S. Sharma
AU - Y. Lupo
PY - 2026
DA - 2026/09/10
PB - bioRxiv
DO - 10.64898/2026.09.10.750709
UR - https://www.biorxiv.org/content/10.64898/2026.09.10.750709v1
AB - Root system architecture shapes how grapevine rootstocks take up water and nutrients, yet roots remain the least phenotyped grapevine organ because they are hidden and hard to image. We present a low-cost phenotyping pipeline that pairs custom acrylic rhizotrons (about US$30 each) with a consumer flatbed scanner and BiRefNet, a general-purpose deep-learning model used without training on root images, followed by automated mask cleaning, skeleton-based trait extraction, and soil moisture mapping. We tested it on nine commercial rootstocks scanned 16 times over 42 days after transplanting (DAT), with half under a ten-day water deficit. From 1,108 images we extracted 21 whole-root, depth-resolved, and topological traits. Genotypes differed in nearly every trait and in how they changed over time. Heritability of size and branching traits peaked at 0.92-0.93 between 21 and 31 DAT and fell for width, depth, and convex hull once roots reached the rhizotron walls, defining the best measurement window. The image-derived soil moisture map accurately tracked the deficit and its recovery. Deficit plants shifted new root growth to deeper soil without growing less overall, and the substrate dried fastest around older and denser roots. Root brightness decreased with root age and local moisture, and transport segments (axes serving several tips) were brighter than terminal laterals in every genotype. Root system size was associated with stomatal conductance in well-watered plants, and stomatal recovery after re-watering correlated with new root growth. The pipeline turns simple hardware into a quantitative, time-resolved root phenotyping platform suitable for breeding.
ER -