About

Matthew Clark is an Associate Professor and the Director of Research at the Minnesota Landscape Arboretum within the Department of Horticultural Science at the University of Minnesota. His research focuses on using traditional and molecular plant breeding approaches to develop improved fruit cultivars suitable for cold climate production. A key aspect of his work involves studying the genetics behind resistance to common pests and diseases, such as apple scab in 'Honeycrisp' apples and resistance to the insect pest phylloxera in grapevines. His goal is to develop new apple and other fruit varieties with multiple resistances to reduce pesticide use and enhance sustainability. Clark's research also emphasizes fruit quality, integrating sensory studies and metabolomics with genomics to understand flavor and aroma compounds that influence consumer enjoyment. His work aims to find solutions for growers through genetic improvement, impacting economic, environmental, and social aspects of sustainability. His background includes a B.A. in Psychology from Saint John's University, an M.S. and Ph.D. in Applied Plant Science from the University of Minnesota, with his research dedicated to disease resistance and fruit quality in horticultural crops.

Research topics

• Artificial Intelligence
• Genetics
• Computer Science
• Biology
• Computational biology
• Computer vision
• Botany

Selected publications

• Sensory Analysis to Inform Breeding Decisions in a Segregating Grapevine Population

  HortScience · 2025-05-30

  articleOpen accessSenior author

  In plant breeding settings, the flavor and aroma of new cultivars are traditionally evaluated based on the judgements of breeders or small technical groups without using data from sensory panels. A sensory descriptive analysis is one of the primary sensory evaluation techniques used to discriminate products. Because of time and monetary costs, descriptive analysis methodology has not been explored in grape breeding to advance the selection of target traits associated with the eating experience. We explored sensory evaluation methodology for screening grape ( Vitis spp.) seedlings of a mapping family and generating quality sensory data for further genetic studies. In 2018, we developed a lexicon with 29 sensory attributes, including five aroma attributes, three basic taste attributes, and 19 flavor attributes. Participants were able to characterize differences in 26 of the attributes among the genotypes tested. Malic acid (MA) and titratable acidity (TA) were positively correlated with sourness, citronella, lime, lemon, green apple, and kiwi flavors. Total soluble solids (°Brix) were positively correlated with sweetness, aroma intensity, flavor intensity, and floral flavor. Sweetness was positively correlated with overall aroma, taste, flavor intensities, floral and Concord aromas as well as floral, fruity, and Concord flavors. A hierarchical cluster analysis separated the genotypes into seven distinct groups, including cluster 1, which included most genotypes with low flavor and aroma intensities for all attributes, and cluster 7 with individuals with the herbaceous/green flavor and aroma. The most promising cluster genotypes for table grape breeding were included in cluster 6. They were characterized by fruity, floral, and labrusca (‘Concord’) attributes. The methodology developed for this study can be exploited in plant breeding research to characterize the variation of flavor and aroma traits in mapping families.

  PublisherOA PDFDOI

• 'Honeycrisp': the challenge of the apple crisp revolution

  Fruit Research · 2025-01-01 · 1 citations

  articleOpen access

  'Honeycrisp' apples are a crisp cultivar known for their unique texture and flavor. This cultivar is considered revolutionary in the world of crispy apples due to its high value and strong consumer preference. Many new cultivars have recently been developed using 'Honeycrisp' as a parent. However, growing, producing, storing, and marketing 'Honeycrisp' apples present significant challenges. A holistic approach to 'Honeycrisp' production will be discussed, covering aspects such as soil health, rootstocks, orchard management, environmental factors, physiological disorder development, storage protocols, and marketing strategies for sustainable production.

  PublisherOA PDFDOI

• Fine-mapping of the Vhc1 QTL for apple scab resistance on linkage group 1 of ‘Honeycrisp’

  Research Square · 2025-06-18

  preprintOpen access
  PublisherOA PDFDOI

• Red star rust (<i>Gymnosporangium yamadae</i>) on <i>Malus</i> spp. in United States public gardens

  Acta Horticulturae · 2025-06-01

  article
  PublisherDOI

• Consumer Preference for Novel Local Food: A Case Study on Cold-hardy Table Grape Cultivars

  HortTechnology · 2025-07-11

  articleOpen accessSenior author

  This study investigates consumer preferences and willingness to pay (WTP) for novel local food, specifically focusing on cold-hardy table grape cultivars. We conducted the second-price auction with 99 Minnesota participants to compare their preferences and WTP for five newly developed cold-hardy table grapes and three existing warm-climate table grapes. Comparing participants’ bids for novel cold-hardy table grapes to existing warm-climate table grapes, we construct three segment groups: “like all new grapes,” “mixed,” and “dislike all new grapes.” The majority of participants (81%) belong to “like all new grapes” and “mixed” groups, indicating a potential market opportunity for the novel local cold-hardy grape cultivars. We also conduct WTP estimates for each table grape cultivar. In addition, by examining the differences in attribute ratings, sociodemographics, table grape purchasing behaviors, and attitudes toward novel foods among three groups, we provide valuable insights into factors that influence consumer WTP for these novel local cold-hardy table grapes and discuss corresponding strategies for promoting and expanding the market.

  PublisherDOI

• Willingness to Pay with Reference-dependent Preferences: A Comparative Analysis of Attribute-based and Alternative-based Approach

  Journal of Agricultural and Applied Economics · 2025-02-20 · 1 citations

  articleOpen accessSenior author

  Abstract Consumer preferences are often influenced by reference-dependent preferences. This study investigates the influence of reference-dependent preferences on the estimation of willingness to pay (WTP) for table grape attributes elicited by a second-price auction. We evaluate two models: the attribute-based reference dependence model, where individuals compare the target product’s attributes with their favorite ones, and the alternative-based reference dependence model, where comparisons are made with a reference product. Results show that including reference points impacts the WTP estimation for different attributes, with varying levels of loss aversion, suggesting the attribute-specific influence of reference points.

  PublisherOA PDFDOI

• A pan-generic marker panel for apples to enable genetic research and breeding across <i>Malus</i> species

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-09

  preprintOpen access

  Wild Malus species harbor untapped genetic diversity to advance apple breeding, particularly for disease resistance and stress tolerance. However, existing marker panels, developed mainly using Malus domestica accessions, introduce ascertainment bias and limit detecting rare variants in wild species. We developed and validated a medium-density and cost-effective pan-generic 3K apple DArTag panel optimized to capture genome-wide variation across the Malus genus. The panel was constructed using conserved, syntenic, and collinear genomic blocks identified within the core genome of 13 Malus accessions for cross-species transferability. The panel was validated across three bi-parental mapping populations totaling 593 progeny. Across these populations, 2,461–3,234 SNP markers were polymorphic and 1,482–2,620 were informative. Each population contained over 900 multiallelic micro-haplotype loci, with several hundred loci exhibiting three or four distinct haplotypes. Markers were uniformly distributed across all 17 chromosomes, each containing between 60–230 informative SNPs. The panel was further evaluated on 174 diverse germplasm accessions from 20 Malus species. It exhibited strong cross-species transferability, exceptionally low rates of missing data (&lt;0.5%), and clear genetic differentiation between wild and domesticated accessions. Genome-wide association studies (GWAS) identified a major locus on chromosome 4 significantly linked to fruit length, weight, and width in addition to trait-specific associations on chromosomes 1, 6, 9, and 11. The cost-effectiveness of genotyping per sample (&lt;$15), combined with these results, underscore the panel′s broad utility for quantitative trait locus (QTL) mapping in bi-parental and diverse populations, marker-assisted selection in the breeding programs, and genetic diversity analysis across the Malus genus.

  PublisherOA PDFDOI

• Seasonal nonstructural carbohydrates in the crowns and rhizomes of in situ populations of Japanese knotweed (<i>Polygonum cuspidatum</i>) and the hybrid Bohemian knotweed (<i>Polygonum</i> ×<i>bohemicum</i>)

  Weed Science · 2025-01-01

  articleOpen accessSenior author

  Abstract Herbaceous perennials must annually rebuild the aboveground photosynthetic architecture from carbohydrates stored in crowns, rhizomes, and roots. Knowledge of carbohydrate utilization and storage can inform management decisions and improve control outcomes for invasive perennials. We monitored the nonstructural carbohydrates in a population of the hybrid Bohemian knotweed [ Polygonum × bohemicum (J. Chrtek &amp; Chrtková) Zika &amp; Jacobson [ cuspidatum × sachalinense ]; syn.: Fallopia × bohemica (Chrtek and Chrtková) J.P. Bailey] and in Japanese knotweed [ Polygonum cuspidatum Siebold &amp; Zucc.; syn.: Fallopia japonica (Houtt.) Ronse Decr.]. Carbohydrate storage in crowns followed seasonal patterns typical of perennial herbaceous dicots corresponding to key phenological events. Starch was consistently the highest nonstructural carbohydrate present. Sucrose levels did not show a consistent inverse relationship with starch levels. Lateral distribution of starch in rhizomes and, more broadly, total nonstructural carbohydrates sampled before dormancy break showed higher levels in rhizomes compared with crowns. Total nonstructural carbohydrate levels in crowns reached seasonal lows at an estimated 22.6% of crown dry weight after accumulating 1,453.8 growing degree days (GDD) by the end of June, mainly due to depleted levels of stored starch, with the estimated minimum of 12.3% reached by 1,220.3 GDD accumulated by mid-June. Depletion corresponded to rapid development of vegetative canopy before entering the reproductive phase in August. Maximum starch accumulation in crowns followed complete senescence of aboveground tissues by mid- to late October. Removal of aboveground shoot biomass in late June to early July with removal of vegetation regrowth in early September before senescence would optimize the use of time and labor to deplete carbohydrate reserves. Additionally, foliar-applied systemic herbicide translocation to belowground tissue should be maximized with applications in late August through early fall to optimize downward translocation with assimilate movement to rebuild underground storage reserves. Fall applications should be made before loss of healthy leaf tissue, with the window for control typically ending by late September in Minnesota.

  PublisherOA PDFDOI

• Willingness to Pay with Reference-dependent Preferences: A Comparative Analysis of Attribute-based and Alternative-based Approach – CORRIGENDUM

  Journal of Agricultural and Applied Economics · 2025-07-03

  erratumOpen accessSenior author
  PublisherOA PDFDOI

• Measuring air metagenomic diversity in an agricultural ecosystem

  Current Biology · 2024-08-01 · 18 citations

  articleOpen accessSenior authorCorresponding

  All species shed DNA during life or in death, providing an opportunity to monitor biodiversity via environmental DNA (eDNA). In recent years, combining eDNA, high-throughput sequencing technologies, bioinformatics, and increasingly complete sequence databases has promised a non-invasive and non-destructive environmental monitoring tool. Modern agricultural systems are often large monocultures and so are highly vulnerable to disease outbreaks. Pest and pathogen monitoring in agricultural ecosystems is key for efficient and early disease prevention, lower pesticide use, and better food security. Although the air is rich in biodiversity, it has the lowest DNA concentration of all environmental media and yet is the route for windborne spread of many damaging crop pathogens. Our work suggests that ecosystems can be monitored efficiently using airborne nucleic acid information. Here, we show that the airborne DNA of microbes can be recovered, shotgun sequenced, and taxonomically classified, including down to the species level. We show that by monitoring a field growing key crops we can identify the presence of agriculturally significant pathogens and quantify their changing abundance over a period of 1.5 months, often correlating with weather variables. We add to the evidence that aerial eDNA can be used as a source for biomonitoring in terrestrial ecosystems, specifically highlighting agriculturally relevant species and how pathogen levels correlate with weather conditions. Our ability to detect dynamically changing levels of species and strains highlights the value of airborne eDNA in agriculture, monitoring biodiversity changes, and tracking taxa of interest.

  PublisherDOI

Frequent coauthors

• Qi Sun

  Cornell University

  57 shared

• Amy Tabb

  Appalachian Fruit Research Laboratory

  56 shared

• Jason P. Londo

  55 shared

• Cheng Zou

  54 shared

• Hui-Ching Yang

  49 shared

• Alanna Burhans

  National Clonal Germplasm Repository

  49 shared

• Avi Karn

  Cornell University

  49 shared

• Laise de Sousa Moreira

  University of Minnesota

  49 shared

Education

• Ph.D., Horticultural Science

  University of Minnesota

  2005

• M.S., Horticultural Science

  University of Minnesota

  2001

• B.S., Horticultural Science

  University of Minnesota

  1998