DOI: 10.5061/dryad.5qfttdzdm
title: Phenotypic data from: from buds to shoots: insights into grapevine development from the Witch’s Broom bud sport

description: Background Bud sports occur spontaneously in plants when new growth
 exhibits a distinct phenotype from the rest of the parent plant. The
 Witch’s Broom bud sport occurs occasionally in various grapevine (Vitis
 vinifera) varieties and displays a suite of developmental defects,
 including dwarf features and reduced fertility. While it is highly
 detrimental for grapevine growers, it also serves as a useful tool for
 studying grapevine development. We used the Witch’s Broom bud sport in
 grapevine to understand the developmental trajectories of the bud sports,
 as well as the potential genetic basis. We analyzed the phenotypes of two
 independent cases of the Witch’s Broom bud sport, in the Dakapo and Merlot
 varieties of grapevine, alongside wild type counterparts. To do so, we
 quantified various shoot traits, performed 3D X-ray Computed Tomography on
 dormant buds, and landmarked leaves from the samples. We also performed
 Illumina and Oxford Nanopore sequencing on the samples and called genetic
 variants using these sequencing datasets. Results The Dakapo and Merlot
 cases of Witch’s Broom displayed severe developmental defects, with no
 fruit/clusters formed and dwarf vegetative features. However, the Dakapo
 and Merlot cases of Witch’s Broom studied were also phenotypically
 different from one another, with distinct differences in bud and leaf
 development. We identified 968–974 unique genetic mutations in our two
 Witch’s Broom cases that are potential causal variants of the bud sports.
 Examining gene function and validating these genetic candidates through
 PCR and Sanger-sequencing revealed one strong candidate mutation in Merlot
 Witch’s Broom impacting the gene GSVIVG01008260001. Conclusions The
 Witch’s Broom bud sports in both varieties studied had dwarf phenotypes,
 but the two instances studied were also vastly different from one another
 and likely have distinct genetic bases. Future work on Witch’s Broom bud
 sports in grapevine could provide more insight into development and the
 genetic pathways involved in grapevine.
description: See the manuscript for detailed methods used for collecting and
 analyzing these phenotypic data.
description: # Phenotypic data from: From buds to shoots: Insights into grapevine
 development from the Witch’s Broom bud sport
 [https://doi.org/10.5061/dryad.5qfttdzdm](https://doi.org/10.5061/dryad.5qfttdzdm) In "From buds to shoots: insights into grapevine development from the Witch’s Broom bud sport," we analyzed the phenotype and investigated the genetic basis of two independent cases of the Witch's Broom bud sport in the Dakapo and Merlot varieties of grapevine (*Vitis vinifera* L.). Here, we provide the phenotypic data from this manuscript and the link to the GitHub repository containing the code used for analyzing these data. The data provided includes i) the shoot observations used to characterize shoot traits and meristem fates, ii) the leaf scans used for comparing leaf size and shape between samples, and iii) dissecting microscope images and CT scans used to analyze internal bud morphologies. ## Description of the data and file structure The phenotypic data are divided into compressed files based on data type, with the description of each file below: * "shoot_observations.xlsx" - An Excel file containing observations of shoot phenotypes for all samples, including internode length, petiole length, lateral meristem fate, and leaf blade width and length. * "leaf_scans.zip" - A compressed folder containing the leaf scans used in this study for leaf landmarking analysis. The sample, shoot number, and nodes scanned are labeled in each scan. The scans are divided into folders based on sample and all file names follow the same structure: "[sample]-[shoot]-[first node in scan]-[last node in scan].tif" * "bud_dissecting_microscope_images.zip" - A compressed folder containing the dissecting microscope images of buds. All file names follow \ one of two structures: "[sample]-[bud #].jpg" if dissected or "[sample]-nondissected-[bud #].jpg" if not dissected * "bud_ct_scans.zip" - A compressed folder containing a representative image of CT scans for all buds scanned. The raw CT scan files have been omitted for space but are available on request. All file names follow the same structure: "[sample]_[bud #].jpg" ###### **Abbreviations used in file names and within files:** WT: wild type WB: Witch's Broom DWT: Dakapo wild type DWB: Dakapo Witch's Broom MWT: Merlot wild type MWB: Merlot Witch's Broom ## Code/Software The code used to analyze the phenotypic data as described in the manuscript is available on GitHub: [https://github.com/eleanore-ritter/witchs-broom/](https://github.com/eleanore-ritter/witchs-broom/).