DOI: 10.5061/dryad.47d7wm3pp
title: A machine learning enabled approach to assess trade-offs between growth and stress tolerance in Pooideae grasses following domestication

description: Plant domestication may create trade-offs between growth and stress
 tolerance, raising concerns about yield stability in future climates.
 Previous studies have found limited direct evidence for such trade-offs,
 often focusing on weakened defenses associated with higher growth rates.
 Trade-offs can also occur when traits optimized for favorable conditions
 perform less efficiently under stress. Deciphering these mechanisms is
 crucial for maintaining growth in changing environments. We examine one
 key aspect of vegetative growth, leaf elongation, in six species of
 grasses. We use a machine learning-enabled pipeline to extract cell
 dimensions and positions from leaf microscope images to study cell
 kinematics. We find that domesticated plants generally have longer leaves,
 larger division zones, and higher cell production rates. While no clear
 trade-off is observed between domestication and drought response in final
 leaf length, a trade-off occurs in development; wild species exhibit a
 smaller decrease in the elongation zone size under drought compared with
 domesticated species. This pattern points to compensatory mechanisms, such
 as extended elongation duration or increased cell production, mitigating
 drought effects in domesticated plants. These nuanced trade-offs
 associated with domestication highlight the importance of robustly
 phenotyping developmental and physiological traits, possibly informing
 breeding strategies to enhance crop resilience in future climates.
description: The species studied are listed in Table 1. Both domesticated
 wheat varieties (Triticum turgidum L. var. Durum 'Langdon' and
 'Svevo', Triticum aestivum 'Chinese Spring') and wild
 emmer wheat (Triticum turgidum L. subsp. dicoccoides 'Zavitan'
 and 'Vavilovii') were subjected to a pre-germination treatment
 at 32°C dry conditions for 7 days, followed by 4°C dry conditions for 2
 days. Domesticated oat (Avena sativa cv. 'Sang'), wild oat
 (Avena insularis 'BYU 207'), domesticated barley (Hordeum
 vulgare 'Morex'), wild barley (Hordeum vulgare L. subsp.
 spontaneum), and Brachypodium distachyon (Bd21) seeds were placed at 4°C
 in water for 7 days to synchronize germination. After cold treatment, all
 seeds were soaked in Gibberellic Acid for 1 day to promote uniform
 germination. Seeds were then planted in Kord square pots (the HC
 Companies, OH, USA) filled with 70g of Profile porous ceramic rooting
 media (Profile Products, Buffalo Grove, IL). 
 Common
 name Scientific
 name Accession
 identifier Name
 symbol Domestication
 status ploidy
 wheat (wild emmer) <em>Triticum turgidum ssp.
 dicoccoides</em> Zavitan Wheat-Z-Wild Wild 4x wheat (bread wheat) <em>Triticum
 aestivum</em> Chinese
 Spring Wheat-CS-Domesticated Domesticated 6x wheat (durum wheat) <em>Triticum turgidum L. var.
 durum</em> Langdon Wheat-L- Domesticated Domesticated 4x wheat (durum wheat) <em>Triticum turgidum L. var.
 durum</em> Svevo* Wheat-S- Domesticated Domesticated 4x wheat (wild emmer) <em>Triticum turgidum L. subsp.
 dicoccoides</em> Vavilovii*(GRIN:PI 352322) Wheat-V-Wild Wild 4x oat <em>Avena sativa L.</em>
 Sang (NPGS:PI386171) Oat- Domesticated Domesticated 6x oat <em>Avena insularis</em>
 BYU 207 Oat-Wild Wild 4x barley <em>Hordeum vulgare L. subsp.
 spontaneous</em> (GRIN:PI 662181) Barley-Wild Wild 2x barley <em>Hordeum vulgare</em>
 Morex Barley- Domesticated Domesticated 2x purple false brome <em>Brachypodium
 distachyon</em> Bd21 Bd21 Wild 2x 
 *The two species are only used for leaf elongation
 in this study, while the rest are used for both leaf elongation and cell
 elongation. Before planting, the dry weight (DW) of
 each pot and its field capacity (FC) for water were recorded. FC was
 determined by saturating the pot with water and allowing it to drain
 overnight under gravity, with the weight difference between the saturated
 and dry pot used as the basis for subsequent soil dry-down control. The
 plants were grown in growth chambers (Biochambers FXC-9) with controlled
 conditions: 60% humidity, 500 µmol photons m-2 s-1 light intensity, and a
 temperature regime of 25°C during the day and 20°C at night (16h/8h
 day/night cycle). Initially, the plants were bottom watered every other
 day with tap water (pH 5-6), supplemented with DYNA-GRO GROW Liquid Plant
 Food 7-9-5 (Dyna-Gro, Richmond, CA, USA) until the appearance of the
 second leaf. From the appearance of the second leaf stage, control plants
 continued to be watered nightly without fertilizer, while drought
 treatment plants were subjected to controlled soil dry-down. Soil water
 content in the drought treatment group was reduced to 45% FC, and then
 water content maintained between 45-55% by watering at 10 a.m., 4 p.m.,
 and 10 p.m. daily.  The third leaf was regularly
 checked at each watering. For both control and drought-treated groups,
 four to six replicates were used to measure the entire process of the
 third leaf’s elongation, and an additional four to six replicates were
 harvested on the fifth day after leaf appearance (approximately at the
 steady state of elongation) for microscopy.  The third
 leaf of plants used for leaf elongation were photographed every four hours
 using a Raspberry Pi camera. Leaf length was measured from the leaf base
 to tip using ImageJ, with a length scale correction applied based on a
 predefined standard to adjust for the perspective of each image.
 We used a second set of plants for leaf cell measurements. We
 carefully unwrapped an emergent third leaf from older leaves, and
 dissected as close as possible to its connection to the seed. This is done
 on the fifth day after the appearance of the third leaf, which corresponds
 to a steady state of leaf elongation as observed in the whole-leaf
 measurements, above. At this stage, the ligule is within 1mm of the leaf
 base. Dental impression material (Defend Impression Material, IL, USA )
 was applied to the base region (for leaves &gt; 50mm) or whole leaf
 (&lt;50mm) of the abaxial surface to create an imprint of the leaf.
 Thereafter, a thin layer of nail polish was applied to the imprint, then
 dried, and placed onto a microscope slide. Microscopy images of imprints
 are taken with Zeiss Axiolab 5 with Axiocam 208 CCD camera (Carl Zeiss AG,
 Germany) with 10x magnification. A sequence of images were taken from the
 base of the leaf towards the tip with &gt;20% overlap between
 images. This dataset contains leaf elongation dataset,
 and original microscopy images of the leaf surface imprints. 
description: # A machine learning enabled approach to assess trade-offs between growth
 and stress tolerance in Pooideae grasses following domestication
 [https://doi.org/10.5061/dryad.47d7wm3pp](https://doi.org/10.5061/dryad.47d7wm3pp) This folder contains data and microscopy images for the paper:  Jie Yun, Chenyang Yuan, Katherine Irelan, Marie-Jeanne Kabongo, Eldar Urkumbayev, David L Des Marais, A machine learning enabled approach to assess trade-offs between growth and stress tolerance in Pooideae grasses following domestication, *Journal of Experimental Botany* Comments and requests should be addressed to Jie Yun ([jyun@mit.edu](mailto:jyun@mit.edu)). This folder contains * leaf_elongation_data.xlsx  This dataset includes the tab leaf_elongation_data, which has the 3rd leaf length measurement along with thermal time in samples harvested for leaf elongation. The tab sample_info has sample species and conditions. In the leaf_elongation_data tab, columns are thermal time, and rows are names of samples, with values showing the leaf length (mm). The empty cells are missing values, before the start of the measurement, or after stopping the measurement once the leaf lengths are stable.  In the sample_info tab, it has Sample (name), Crop type (or Brachypodium), Domestication status, Treatment, Batch, and Accessions. To be specific, domestication has two levels: W (wild) and D (domesticated); treatment has two levels: ww (well watered) and wd (water deficit); batch has two levels: batch 1 and batch 2. Accessions are consistent with the abbreviations in the table in Methods.   * original_microscopy_images.zip This folder includes microscopy images of the 3rd leaf for samples harvested for cell elongation. Each sample is saved in a folder. In each folder, they are numbered as sequential images from the leaf meristem to the tip. The details of the samples can be found in microscopy_samples_info.xlsx.  In microscopy_samples_info.xlsx, it has rows: Domestication status, Sample, Treatment, Crop type (or Brachypodium), and Sample folder name. Domestication has two levels: W (wild) and D (domesticated); treatment has two levels: ww (well watered) and wd (water deficit).