About

Lance Cadle-Davidson is an Adjunct Associate Professor in the School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section at Cornell AgriTech. He is also a Research Plant Pathologist at the USDA Grape Genetics Research Unit in Geneva, NY. His research program addresses critical needs for the sustainable management of grapevine fungal and oomycete diseases. His collaborative research aims to develop new grape varieties that are healthy, delicious, and disease resistant, exemplified by his co-leadership of the VitisGen project. His work involves analyzing billions of data points to better understand the biology of host and pathogen co-evolution and how their DNA sequences influence disease outcomes. This basic scientific research employs cutting-edge genomic tools to enhance traditional breeding approaches, with the goal of developing eco-friendly disease resistance that will last for future generations.

Selected publications

• Diagnostic KASP Markers for Flower Sex and Stenospermocarpic Seedlessness in Diverse Vitis, Muscadinia, and Wide Hybrid Populations

  Journal of the American Society for Horticultural Science · 2026-03-04

  articleOpen access

  The genus Vitis is composed of two subgenera, Vitis (2n = 38) and Muscadinia (2n = 40), which are both cultivated for fresh-market, juice, and wine industries. Stenospermocarpic seedless and perfect-flowered vines are highly desired in both Vitis vinifera and muscadine ( Muscadinia rotundifolia ) breeding programs. Stenospermocarpy has recently been introgressed from V. vinifera to muscadines through conventional breeding despite their differing chromosome number, but no molecular markers for this trait have been validated in muscadine germplasm. Wild vines in both subgenera are dioecious, but perfect-flowered forms were independently selected during domestication to enhance reproductive efficiency and fruit production. This study reports the development and validation of two Kompetitive allele-specific PCR (KASP) markers targeting causal polymorphisms within candidate genes for male sterility ( VviINP1 ) and stenospermocarpy ( VviAGL11 ). Sequence alignments with published M. rotundifolia genomes suggested that the seedless_Arg197Leu_site56 and female_INP_indel_site56 KASP markers might be broadly effective across diverse species within Vitis and Muscadinia . Marker performance was evaluated using a validation panel including 918 Vitis × Muscadinia hybrid seedlings from the University of Arkansas Fruit Breeding Program and a diverse set of cultivated and wild accessions (209 accessions evaluated with the seedless marker and 315 accessions with the flower sex marker). After excluding incomplete phenotype and genotype data, the stenospermocarpic marker (seedless_Arg197Leu_site56) accurately predicted seedlessness in 921 of 924 (99.7%) entries. Additionally, 148 of 203 seedlings that failed to produce fruit across both growing seasons were predicted to be stenospermocarpic with the seedless KASP marker, suggesting that seedless Vitis × Muscadinia hybrids may have partial sterility or lack cold hardiness. The flower sex marker (female_INP_indel_site56) correctly predicted flower sex in all 1138 (100%) entries. Together, these KASP markers provide highly accurate and cost-effective tools for early selection of seedless and perfect-flowered genotypes across Vitis , Muscadinia , and hybrid breeding programs.

  PublisherDOI

• Population Analysis of the US Department of Agriculture, Agricultural Research Service Vitis Repository with rhAmpSeq Markers

  Journal of the American Society for Horticultural Science · 2026-04-13

  articleOpen access

  Grape ( Vitis spp.) is an economically and culturally significant crop grown in a wide array of climates, including cooler areas that regularly experience freezing temperatures. To better adapt grapes for cultivation in cooler climates, wild grape relatives and hybrids have been and continue to be used in breeding efforts. The US Department of Agriculture, Agricultural Research Service maintains a collection of cultivated and wild cold-hardy grapes in Geneva, NY, USA. This collection contains more than one dozen species, mostly of North American origin, as well as an extensive set of hybrid breeding lines and cultivars. We demonstrate the genetic variation present in the collection using newly developed rhAmpSeq markers to explore phylogenetic relationships. Our findings match those of previous analyses that showed Eurasian species nested within the North American species, suggesting a North American origin of the Vitis genus. In addition, an analysis of ancestry and genetic distance suggested taxonomic identities of 18 previously unidentified accessions and 36 putatively misidentified accessions. The data presented here advance the understanding of the Vitis clade and provide support for ongoing research, conservation, and breeding efforts.

  PublisherDOI

• Challenges and Suggestions for Tissue Culture–Free Transformation and Genome Editing in De Novo Grapevine Meristems

  PhytoFrontiers™ · 2026-02-09

  articleOpen access

  Producing plants with transgenes or genome edits often requires regeneration systems that take time, expertise, and resources. Some species, cultivars, and explants regenerate well and others poorly, inconsistently, or not at all. Moreover, tissue culture can introduce somaclonal variation, adding further complexity and unpredictability to regeneration outcomes. Tissue culture–free genome editing is an attractive potential alternative to conventional transformation methods, particularly for recalcitrant crops such as grapevine, where regeneration remains a major bottleneck. Developmental regulators (DRs) have been shown to enhance plant regeneration and transformation, and, in some species, can induce de novo meristem formation to enable genome editing without tissue culture. Here, we present evaluation of DR-mediated, tissue culture–free transformation carried out independently by two research groups, using Agrobacterium-based delivery of ISOPENTENYL TRANSFERASE in soil-grown grapevine. One group included gene editing reagents and the other a luciferase reporter. Across more than 1,500 total inoculations involving multiple cultivars, Agrobacterium strains, and tested protocol modifications, no stably transformed or genome-edited shoots were recovered. Wound scarring, lignification, and rapid activation of nearby prompt lateral meristems were identified as likely biological barriers to DR-mediated de novo meristem formation. By documenting these negative but informative outcomes, we aim to help prevent fruitless repetition and to provide guidance for further research toward robust in planta transformation and genome-editing in grapevine and other recalcitrant species. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

  PublisherDOI

• Integrating Large Multi-Modal Models for Automated Powdery Mildew Phenotyping in Grapevines

  SSRN Electronic Journal · 2026-01-01

  preprintOpen access
  PublisherDOI

• Journal Name: Plant Physiology and Biochemistryeffect of Grapevine Rootstock and Foliar Biostimulants in Regulating Scion Physiology, Secondary Metabolites, and Root Architectural Adaptation to Drought Stress

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access
  PublisherDOI

• A Novel Susceptibility Locus to <i>Erysiphe necator</i> (<i>SEN2</i>) Identified by Genetic Mapping of Automated Microscopy Computer Vision Data in Grapevines

  Plant Disease · 2025-01-15

  article

  Powdery mildew, caused by the fungus Erysiphe necator, is one of the primary causes of grape yield loss across the globe. Although numerous resistance loci have been identified in various grapevine species, the genetic determinants of susceptibility to E. necator remain largely unexplored. Understanding the genetics of susceptibility for pathogenesis is equally important for developing durable resistance grapevines against this pathogen. To identify these factors in Vitis interspecific hybrid ‘Chambourcin,’ a controlled leaf disc assay was conducted for 2 years using an automated microscopy phenotyping system with 273 F 1 genotypes from a cross of ‘Chambourcin’ and V. vinifera ‘Cabernet Sauvignon.’ Additionally, a high-resolution linkage map using the same number of ‘Chambourcin’-derived hybrids was constructed with 355 simple sequence repeats and 1,394 RNaseH2-dependent amplicon sequencing–derived haplotype markers that clustered into 19 linkage groups. A quantitative trait locus analysis identified a susceptibility locus (here named Sen2) on linkage group 7 explaining 8.90 to 12.57% of the total phenotypic variance. The markers associated with this susceptibility locus were used to identify 78 accessions in the U.S. Department of Agriculture Agricultural Research Service cold-hardy Vitis collection at Geneva, NY, that carry Sen2 and can be used to selectively exclude susceptible progenies. Additionally, six accessions carry the alternative haplotype encoding recessive resistance and can be used for resistance breeding. The identification of powdery mildew susceptibility loci is crucial for identifying genes that could be targeted for gene knockout, gene editing, RNA interference, or selection among breeding genotypes to enhance sustainable protection against pathogens.

  PublisherDOI

• A Device for Computer Vision Analysis of Fungal Features Outperforms Quantitative Manual Microscopy by Experts in Discerning a Host Resistance Locus

  Phytopathology · 2025-04-02 · 4 citations

  article

  Accurate, quantitative phenotyping aids in the discovery of quantitative trait loci, particularly those with minor effects. Previously, we optimized replicated precision phenotyping of mapping families after inoculation of leaf discs with the grapevine powdery mildew pathogen ( Erysiphe necator). Pathogen colonies were stained, and hyphal density was estimated using hyphal transects. This approach outperformed field evaluations and other controlled phenotyping methods but required one or two person-months of microscopy per experiment to evaluate resistance across 300 host genotypes. More recently, we combined advanced macrophotography, robotic sample positioning, and convolutional neural networks to produce a high-throughput phenotyping device, which was modified and commercialized as “Blackbird.” Here, that device was tested for nondestructive image collection and computer vision quantification of foliar grapevine powdery mildew. Blackbird outpaced manual microscopy up to 60-fold and nondestructively generated time-series segregating phenotypes from 2 to 9 days postinoculation (dpi). Paired analysis of these phenotypes with RNase H2-amplicon sequencing haplotype markers targeting the Vitis core genome detected REN13 on chromosome 8. Genetic analysis of Blackbird convolutional neural network data explained a greater proportion of the phenotypic variance via hyphae at 4 dpi (24.5%) and conidia at 9 dpi (24.0%) than manual microscopy at 8 dpi (15.8%). As a moderate-effect resistance locus in the widely planted resistant variety ‘Norton’, which already produces commercial wine quality, REN13 could significantly delay epidemics and could be useful in grape breeding programs to increase the durability of stronger resistance loci (e.g., RUN1, REN4, or REN12) in resistance gene stacks while maintaining fruit quality.

  PublisherDOI

• Realistic Scenarios of Phenotypic Variation and Errors in High-Throughput Phenotyping Experiments Minimally Impact the Results of Quantitative Trait Locus Mapping Analysis

  Phytopathology · 2025-02-25

  articleSenior author

  High-throughput phenotyping technologies increase the efficiency of breeding programs, but with larger datasets, errors can accumulate. Plant breeders often conduct quantitative trait locus (QTL) mapping, where large sample size and accurate quantitative response estimates are important for detecting small-effect QTLs. This study examined how phenotype error, inconsistency, and replication changed QTL magnitude and location. Three real sets of phenotype data were used from microscopy robot analysis of grapevine powdery mildew ( Erysiphe necator) severity, which previously resulted in discovery of large ( R 2 = 85%), intermediate ( R 2 = 45%), and small ( R 2 = 9%) effect QTLs. Custom R scripts were written to induce several realistic sources of error, inconsistency, and varied replication. The results were remarkably robust to these changes. Swapping or shifting 2% of samples or changing disease severity by 50% on one replicate had negligible impact on QTLs. Unreplicated simulations produced the largest logarithm of the odds score range (5.55 to 8.27) and mean logarithm of the odds score deviation (−1.72 to −3.22; Cohen's D = 1.48 to 2.12). The large-effect-size QTL ( REN12) was always detected. The intermediate-effect-size QTL ( REN13) was detected except when three of the eight replicates were analyzed individually. Even for the small-effect-size locus ( NYVPLG9), error scenarios rarely (2 of 9,000 cases) eliminated significant QTL detection, versus no replication (9 of 10). Thus, the benefits of data volume associated with high-throughput phenotyping technologies outweigh the cost of the increased errors tested here. Instead, the focus should be on examining how each experimental replicate contributes to the results of the QTL mapping analysis.

  PublisherDOI

• PhytoPatholoBot: Autonomous Ground Robot for Near‐Real‐Time Disease Scouting in the Vineyard

  Journal of Field Robotics · 2025-08-25

  article

  ABSTRACT The grape and wine industry suffers substantial losses annually due to diseases like downy mildew and grapevine leafroll‐associated virus 3. Effective control of these diseases hinges on precise and timely diagnosis, which is often hindered by the shortage of highly skilled disease scouts. This highlights the urgent need for alternative, scalable solutions. We introduce PhytoPatholoBot (PPB), a fully autonomous ground robot equipped with a custom imaging system and onboard analysis pipeline for near‐real‐time disease detection and severity quantification, enabling rapid disease assessments in vineyards. The imaging system uses active illumination to enhance image quality and consistency, addressing a key challenge in ensuring the generalizability of analysis models. The analysis pipeline incorporates a disease mapping near‐real‐time model, a custom segmentation model designed for deployment on low‐power edge computing devices, allowing near‐real‐time inference. PPB was deployed in both research and commercial vineyards for field‐based disease scouting. Experimental results demonstrated that its disease detection and severity quantification performance was comparable to those of experienced human scouts and advanced offline computer vision models, while maintaining high computational efficiency and low‐power consumption suited to field robots. PPB's ability to map disease progression over the growing season and manage multiple disease types in previously unseen vineyards highlights its potential to advance agricultural research and improve vineyard disease management practices.

  PublisherDOI

• Comparative genomics of &lt;i&gt;Rpv3&lt;/i&gt;, a multiallelic downy mildew resistance locus in grapevine (&lt;i&gt;Vitis&lt;/i&gt; sp.)

  OENO One · 2025-03-11 · 7 citations

  articleOpen accessSenior author

  Grapevine downy mildew, caused by the oomycete pathogen Plasmopara viticola, can lead to economically significant losses in humid climates. An ever-growing catalog of loci for resistance to P. viticola is available to breeders, including Rpv3 on the lower arm of chromosome 18. Widely used in French-American cultivars, Rpv3 is a complex TIR-NBS-LRR locus for which associated SSR markers have provided evidence of multiple alleles with varying degrees of resistance. However, SSRs lack the resolution to detect nuances between alleles and fully characterize the locus. PacBio long-read sequencing enables phased assembly of highly repetitive gene cluster regions, allowing for high resolution comparison among predicted alleles. Rpv3 haplotypes of eight Vitis genomes (‘Catawba’, ‘Chambourcin’, ‘Concord’, ‘Horizon’, MN1264, ‘Norton’, NY84.0101.03, and PN40024) were compared to identify differences in gene structure among Rpv3.1, Rpv3.2, Rpv3.3, co-located Rpv27, and susceptible SSR haplotypes. This region was extracted from each haplotype as delimited by their flanking SSR markers and ranged in length from 0.8 to 1.7 Mb. While there was strong consistency in gene structure within Rpv3.1, both Rpv3.2 and Rpv3.3 showed evidence of divergence between haplotypes. In addition to local alignments, the candidate genes identified in Rpv3.1 were tested for copy number and functional variation across haplotypes. The candidate gene region ranged in length from 85.3–220 kb from SSR UDV737. While the structure of this region and the TNL gene sequences were largely consistent within Rpv3.1 and Rpv3.2, the structure was variable among Rpv3.3 individuals. In spite of this structural variation among the Rpv3.3 SSR haplotype, their TNL gene sequences had strong similarity to Rpv27. The variation in gene structure shown in this study underscores the need for the refinement of allele naming, high-quality genome assemblies, as well as more informative, higher resolution marker systems for marker-assisted selection to improve resistance to grapevine downy mildew.

  PublisherOA PDFDOI