About

Shelby Ellison is an Associate Professor in the Department of Plant and Agroecosystem Sciences at the University of Wisconsin–Madison. Her credentials include a Ph.D. Her research focuses on alternative crop genetics, contributing to the development and understanding of diverse agricultural options. As part of the Ellison Lab, she is involved in research and extension activities related to alternative crops, including Wisconsin hemp by hand. Her work aims to advance knowledge in plant genetics and support sustainable agricultural practices.

Research topics

• Botany
• Biology
• Horticulture
• Genetics
• Biochemistry
• Chemistry
• Food science

Selected publications

• Ancestry and Environmental Adaptation in North American Feral Cannabis

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-09

  articleOpen accessSenior author

  Abstract Understanding how different populations respond to environmental variation is fundamental to breeding climate resilient crops. In this study, we integrate three diverse georeferenced Cannabis datasets comprising North American feral populations and Eurasian samples (n=909) to resolve population structure, infer evolutionary relationships and quantify adaptive responses to climate across a broad environmental gradient. Phylogenetic analysis rooted to Humulus lupulus shows North American feral populations are more closely related to basal and hemp-type lineages than to drug-type or Iranian populations, a pattern supported by ancestry and PCA analyses. By combining these datasets, we capture a wider range of climatic variation and gain new insight into the adaptive potential of cannabis germplasm. Using environmental genomic selection (EGS), we identified nine bioclimatic traits with prediction accuracies exceeding 0.5 across the combined datasets (12,030 SNPs; 909 samples; training = 191). When analyzing the North American dataset alone, EGS revealed 14 traits with prediction accuracies greater than 0.85 (22,852 SNPs; 760 samples; training = 310). Genomic estimated adaptive values (GEAVs) revealed population specific climatic responses, particularly for precipitation related traits, with northeastern North American populations (Indiana and New York) showing signatures consistent with adaptation to wetter and cooler environments. Climate projections under a high emission scenario (SSP585) indicate that ∼34 % of sampled locations are expected to transition to different Köppen-Geiger climate classes by 2050, with distinct shifts observed among North American and Iranian populations. Genome environment association (GEA) analysis identified replicated temperature and precipitation associated loci across multiple chromosomes. Using genotype-phenotype data, genomic selection for cannabinoid traits revealed that only CBD achieved prediction accuracies exceeding 0.5, consistent with a polygenic architecture extending beyond the CBDAS locus. Collectively, these results demonstrate that feral and landrace Cannabis populations harbor substantial adaptive variation and represent an underutilized reservoir for climate resilient breeding and allele discovery, with relevance for pre-breeding efforts under future climate scenarios.

  PublisherDOI

• Structure and sequence evolution in the pennycress ( <i>Thlaspi arvense</i> ) pangenome

  New Phytologist · 2026-04-02

  articleOpen access

  Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. Harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and deploy genetic diversity. Here, we explore seven complete genomes of the emerging biofuel crop pennycress (Thlaspi arvense) drawn from across the species' current genetic diversity to catalog variation in genome structure and content. Across this new pangenome resource, we find contrasting evolutionary modes in different genomic zones. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. By contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions even in fast-evolving NOD-like receptor immune genes, where microsynteny breaks down across species, but gene cluster positioning macrosynteny is maintained. Our findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows repositioning and presence-absence variation on a local scale. This diversity is invisible to classical reference-based strategies and highlights the strength and utility of pangenomic resources. These results provide a valuable case study of rapid genomic structural evolution within a species and powerful resources for crop development in an emerging biofuel crop.

  PublisherDOI

• Anthocyanin accumulation, inflorescence dry weight and total cannabidiol content have different temperature optima in Cannabis sativa

  Journal of Cannabis Research · 2025-07-29

  articleOpen accessSenior author

  Limited information exists on how temperature affects phytocannabinoids and anthocyanin accumulation and inflorescence dry weight yield in Cannabis sativa. Understanding how temperature influences these traits is essential for refining cultivation practices, meeting market demands, and developing novel cannabis cultivars with improved agronomic, medicinal, and aesthetic attributes. In this study, a day-neutral inbred population with uniform expression of purple pigmentation on the leaves and flowers was used to explore how temperatures ranging from 0.5 to 22 °C impacts inflorescence dry weight, cannabidiol (CBD) percentage, and anthocyanin accumulation in cannabis. Data on inflorescence dry weight (g/plant), CBD (%), and anthocyanin concentration (mg∙L− 1) in the primary inflorescence of each plant were collected and analyzed. Total CBD concentration and inflorescence dry weight yield increased with increasing temperature– likely a result of plant maturity rather than temperature stimuli. Anthocyanin accumulation was significantly affected by temperature stimuli, exhibiting peak production levels at constant temperatures of 8 °C and 15 °C. CBD concentration and inflorescence dry weight predominantly correlate with plant maturity, whereas anthocyanin accumulation is responsive to variations in environmental temperature. Maximum anthocyanin levels at 8 °C and 15 °C, along with reduction at 0.5 °C and 22 °C, suggests distinct temperature-dependent regulatory pathways for anthocyanin biosynthesis in cannabis, separate from those influencing CBD biosynthesis and inflorescence dry weight. Modeling anthocyanin concentration, CBD concentration, and total inflorescence dry weight across various temperature treatments could optimize desired floral qualities and other traits associated with yield in cannabis.

  PublisherOA PDFDOI

• Structure and sequence evolution in the pennycress ( <i>Thlaspi arvense</i> ) pangenome

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-28 · 1 citations

  preprintOpen access

  Summary Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. However, harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and utilize genetic diversity. Here, we explore seven complete genomes of the emerging biofuel crop pennycress ( Thlaspi arvense ) drawn from across the species’s current genetic diversity to catalogue variation in genome structure and content. Across this new pangenome resource, we find contrasting evolutionary modes in different genomic regions. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. In contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions, even in fast-evolving immune genes where microsynteny breaks down across species but the macrosynteny of gene cluster positioning is maintained. Our findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows rearrangement and presence-absence variation on a local scale. This diversity is invisible to classical reference-based approaches and highlights the strength and utility of pangenomic resources. These results provide a valuable case study of rapid genomic structural evolution within a species and powerful resources for crop development in an emerging biofuel crop.

  PublisherOA PDFDOI

• First Report of <i>Fusarium graminearum</i> Causing Head Blight on Hemp ( <i>Cannabis sativa</i> ) in Wisconsin

  Plant Disease · 2025-12-22

  articleOpen accessSenior author

  In September 2024, blight symptoms were observed on hemp grain heads as part of a 0.5-acre grain cultivar trial at the University of Wisconsin-Madison, Arlington Agricultural research station (Latitude 43°18’9.47″N, Longitude 89°20’43.32″W). Grain threshed from infected heads was plated on Nash-Snyder media to isolate Fusarium species (Nash & Snyder 1962). Colonies from Nash-Snyder media were hyphal tip purified onto 1/4-strength potato dextrose agar. After approximately 5-7 days, isolated colonies produced white-pink mycelia, with some having dark red pigmented undersides. Macroconidia generated from Fusarium cultures were slightly hyaline and septate, with between 3 and 5 septa. Pollinated female flowers from the day-neutral cultivar “Pink Kush” were spray-inoculated with a 5 × 105 spores mL-1 suspension in 0.05% (v/v) Tween or mock-inoculated with Tween until runoff, then bagged in clear plastic bags (Yulfo-Soto et al. 2022). After 3 days, plants were uncovered and allowed to grow for an additional 6-9 days under greenhouse conditions (22-25°C with a 16-h photoperiod and 50% relative humidity). Visible mycelial growth was observed on test plants, but not on the mock-inoculated plants. Leaves from test plants were collected and disinfected in 10% bleach for 1 minute and rinsed in sterile DI water before plating on Nash-Snyder media with subsequent purification. Colony and macroconidia morphology were similar to the initial inoculum. Agar plugs taken from the hyphal tip-isolated colony were plated on carrot agar, which induced fertile and mature perithecia (Cavinder et al. 2012). Genomic DNA was extracted from mycelium using CTAB extractions (OPS Diagnostics, Lebanon, NJ, USA). The TEF1 (NCBI Accession Number: PX352985), RPB1 (PX352987), and RPB2 (PX352987) genomic loci were amplified using primers from O’Donnell et al. (2022) and sequenced on a PromethION (Oxford Nanopore Technologies, Oxford, UK). Alignment was performed using minimap2 (2.24-r1122). Variants were called using clair3 (1.0.9) to generate a VCF file that was subsequently used to generate the consensus read. Using polyphasic identification, a comparison of the generated consensus sequence with the Fusarium-ID database revealed significant similarity to Fusarium graminearum (LC13775, 97.89% similarity). Furthermore, the generated FASTA sequences were compared to available sequences in the Fusarium-ID database as follows: FASTA sequences were downloaded from the Fusarium-ID database and then parsed to retain only samples/sequences that possessed all three above loci and belonged to Fusarium. The sequences for each locus were then aligned using MUSCLE (3.8.31) and merged using FASconCAT-G (v1.06.1). Phylogenetic trees were generated using FastTree (2.2.0) and visualized using R packages ape (5.8-1) and ggtree (3.14.0). The consensus sequence grouped most closely with F. graminearum. Therefore, we conclude the isolated fungus likely causing disease is F. graminearum. This report contributes to the existing literature on Fusarium blight previously reported in North Carolina (Thiessen et al. 2020) and Kentucky (Yulfo-Soto et al. 2022). As F. graminearum is known to be a prolific mycotoxin producer, accumulation and concentration of these toxins should be carefully monitored, especially in the context of the recent approval of hemp grain for laying chickens by the Association of American Feed Control Officials.

  PublisherOA PDFDOI

• Comparing agronomic performance of industrial hemp varieties for suitable production in the United States

  Agronomy Journal · 2025-01-01 · 6 citations

  articleOpen access

  Abstract Industrial hemp ( Cannabis sativa L.) is an ancient crop used throughout history for fiber, oilseed, and therapeutic compounds. Hemp varieties were cultivated across diverse environments in the United States, but knowledge of those agronomic practices along with genetic resources was lost during a period in which cultivation of cannabis was prohibited. Therefore, regional performance evaluations of hemp varieties for crop performance coupled with scientific communication of outcomes to the public are crucial for hemp's development as an agricultural commodity. Objectives for this research were to evaluate relative yields of industrial hemp varieties grown across the United States and link their suitability for commercial production across locations. A national collaboration established variety trials containing seven industrial hemp varieties planted across 14 locations (36°–48° N latitude and 72°–110° W longitude) over a 3‐year period. Crop dry straw yield and seed yield increased from the averages of 1600 and 700 kg ha −1 in Year 1 to 2400 and 1150 kg ha −1 in Year 2, and 3050 and 815 kg ha −1 in Year 3, respectively. The varieties Anka and X‐59 performed best in Vermont and Virginia, where seed yields consistently exceeded 1100 kg ha −1 ; however, no single variety performed above average across all sites. Overall, this assessment identified two industrial hemp varieties suitable for commercial production in specific sites and highlighted the importance for hemp breeders to investigate variety × location × year interactions when developing improved varieties to best capture site‐specific productivity.

  PublisherOA PDFDOI

• Genetic diversity, population structure, and cannabinoid variation in feral Cannabis sativa germplasm from the United States

  Scientific Reports · 2025-07-01 · 6 citations

  articleOpen accessSenior author

  Cannabis sativa is one of the earliest plants to be domesticated for fiber, food and medicine. Seed from Cannabis grown for industrial purposes during the 18th through 20th centuries have escaped production and established feralized populations across the United States. To maximize the potential of feral Cannabis germplasm, determining the genetic structure and cannabinoid profile is crucial for selection and breeding of new compliant regionally adapted hemp cultivars. To resolve this, a collection of feral Cannabis, comprising 760 plants across twelve US states were sequenced using Genotyping-by-Sequencings (GBS), genotyped at the cannabinoid synthase (CBDAS) gene, and subject to gas chromatography-mass spectrometry (GC-MS) to assess cannabinoid profiles. Clustering analyses by ADMIXTURE and Principal Component Analysis (PCA) stratified the germplasm into five clusters (Mississippi-River, West North Central-b, West North Central-a, New York, and Indiana). The cannabinoid genotyping assay resolved the feral collections into Type I - B2/B2 (6%), Type II - B2/B1 (15%), and Type III - B1/B1 (78%). Total cannabinoid content ranged from 0.21 to 4.73%. The assessment of genetic diversity, population structure, and cannabinoid profile of the US feral Cannabis collection provides critical information and germplasm resources to develop new and improve existing hemp cultivars.

  PublisherOA PDFDOI

• Combining genome‐wide association and genomic prediction to unravel the genetic architecture of carotenoid accumulation in carrot

  The Plant Genome · 2025-01-30 · 6 citations

  articleOpen access

  Carrots (Daucus carota L.) are a rich source of provitamin A, namely, α- and β-carotene. Breeding programs prioritize increasing β-carotene content for improved color and nutrition. Understanding the genetic basis of carotenoid accumulation is crucial for implementing genomic-assisted selection to develop high-carotenoid lines. While previous studies identified loci (Y2, Y, Or, and REC) associated with carrot color and carotenoid content, this study employed genome-wide association (GWA) in a diverse panel of 738 carrot accessions. We discovered a novel locus with a candidate gene encoding phytoene synthase, a key enzyme in carotenoid biosynthesis. The Y2, Y, Or, and REC loci are mostly fixed in orange varieties, yet considerable variation in carotenoid concentration persists. This suggests a multigenic trait influenced by the environment. GWA of carotenoid concentration identified a quantitative trait locus for total carotenoids and α-carotene. We explored the accuracy of genomic prediction (GP) models to predict carotenoid concentration. We determined the optimal number of plants and plots required for accurate carotenoid phenotyping, finding ≥5 plants per plot and three plots per site as the minimum effective sample per accession. GP models achieved accuracies ranging from 0.06 to 0.40 depending on the carotenoid measured and environment the carrots were assayed. Additional studies in breeding programs will clarify the potential of genomic-assisted selection for high-carotenoid carrots.

  PublisherOA PDFDOI

• Survey of plant viruses in Wisconsin iris production demonstrates widespread prevalence of Potyvirus iriseverum

  Crop Protection · 2025-03-09 · 1 citations

  article
  PublisherDOI

• Crop Phenology and Genotypic Pool Impact the Occurrence of Six Viruses on Cannabis Sativa L

  SSRN Electronic Journal · 2025-01-01

  preprintOpen accessSenior author
  PublisherDOI

Recent grants

• NSF Postdoctoral Fellowship in Biology FY 2012

  NSF · $197k · 2012–2015

Frequent coauthors

• Philipp W. Simon

  68 shared

• Douglas Senalik

  51 shared

• Massimo Iorizzo

  29 shared

• Pablo F. Cavagnaro

  19 shared

• David M. Spooner

  University of Georgia

  19 shared

• Julie C. Dawson

  University of Wisconsin–Madison

  10 shared

• K. Corak

  University of Wisconsin–Madison

  8 shared

• Kevin Coe

  8 shared

Labs

• Ellison LabPI

  Alternative Crop Genetics

Education

• PhD/Genetics, Plant Sciences

  University of California Davis

  2012

• BS, Genetics

  University of Wisconsin Madison

  2006