About

Douglas R. Cook is a Professor of Plant Pathology at the College of Agricultural and Environmental Sciences at UC Davis. His research focuses on microbial community analysis in agricultural contexts, understanding the complex origins of plant disease, and exploring genomic diversity in crop wild relatives. His work includes genome-wide recombination studies, transcriptome divergence under drought stress, and population genomics of soil bacteria, contributing to advancements in plant pathology and agricultural innovation. Cook has authored numerous publications that investigate the genetic and microbial factors influencing plant health and disease, emphasizing the importance of genomics and microbial ecology in sustainable agriculture.

Research topics

• Biology
• Agronomy
• Computer Science
• Ecology
• Data science
• Agroforestry
• Engineering
• Genetics
• Biotechnology
• Business
• Botany

Selected publications

• Marker trait association analysis identified a novel quantitative trait loci (QTL) for Fusarium wilt resistance in chickpea (Cicer arietinum L.)

  Euphytica · 2025-07-31

  articleSenior author
  PublisherDOI

• Microbial Community Analysis Offers Insight into the Complex Origins of Plant Disease in a Smallholder Farm Context

  Phytobiomes Journal · 2024-07-08 · 2 citations

  articleOpen accessSenior author

  Classical approaches to plant disease diagnosis assume a single pathogen/single disease paradigm. Here, we revisit the presumed role of Fusarium oxysporum as the causal agent of wilting and yellowing of chickpea plants on smallholder farms in Ethiopia. Contrary to expectations, detection of Fusarium DNA using conserved PCR primers failed to associate the pathogen with symptomatic plants. Instead, culture-independent sequencing of microbial communities nominated unexpected pathogens and revealed patchiness in the assembly of common microbial consortia. Surprisingly, tests of differential enrichment identified Phytophthora as the most common disease-associated taxon. More generally, across all field sites, multilevel pattern analysis identified indicator taxa whose patterns of co-occurrence demarcate discrete microbial communities and are consistent with a range of specific interactions, including mutualism and antagonism. Taken together, these data indicate that soilborne chickpea disease in Ethiopia has heterogeneous origins and that despite decades of emphasis and disease resistance breeding, the role of Fusarium as the frequent agent of chickpea disease in Ethiopia remains enigmatic.

  PublisherDOI

• Viruses of nitrogen-fixing Mesorhizobium bacteria in globally distributed chickpea root nodules

  Research Square · 2023-06-05

  preprintOpen access
  PublisherOA PDFDOI

• Ecological Competence, Plant Growth Promoting and Symbiotic Characteristics of Different Mesorhizobium Strains Nodulating Chickpea (Cicer arietinum L.) from Ethiopia

  Zenodo (CERN European Organization for Nuclear Research) · 2023-08-17 · 3 citations

  articleOpen access

  Chickpea provide multiple benefits, due to high nutritive value as well as the ability of the crop to enrich nitrogen poor soils. In spite of its yield potential this legume depends on the rhizobial association. The objective of this study was to identify indigenous promising elite Mesorhizobium strains that impart variation eco-physiologically and symbiotically for enhancing nitrogen fixation in chickpea. 20 symbiont strains represented 64 genetically diverse indigenous Mesorhizobium species were tested at laboratory and greenhouse. Based on their eco-physiological competence (35%) of the strains grown at 1.5% NaCl, 25% of strain at pH4 and fewer strains (20%) tolerant to 40°C. Most strains (60%) able to utilize D-Sorbitol and D-Glucose carbon substrates and better utilized the amino acids Phenylanine (60%). Most of the Mesorhizobium strains exhibited (67%) resistance to antibiotics and up to (83%) heavy metal resistance. Three strains able to release available soluble phosphates from Ca3(PO4)2 (118.0 μg/ml) and FePO4 (93.3 μg/ml) after 8 days of incubation and all strains produced the phytohormone ranging from (7.7-28.4 μg/ml). The results highlighted more nodules were recorded from the Natoli variety (32-62 nodules) compared to fewer nodules (31-46) formed on Arerti variety. Moreover, 85% of the strains showed highly effective symbiosis on both Natoli and Arerti varieties. The data provided an important complement to select representative distinct symbiont strains to tested in multi-location field trials for enhance nitrogen fixation activities in chickpea production.

  PublisherDOI

• DMI1 gene encodes a protein that is required for the early steps of bacterial and fungal symbioses

  OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) · 2023-01-23

  articleOpen access1st authorCorresponding

  The invention relates to isolated DMI11 genes from Medicago truncatula which play a major role both in the early steps of Nod factor signaling that trigger several key developmental responses in the host plant and in the establishment of mycorrhizal symbiosis. The invention also relates to transgenic plants and plant cells expressing the DMI1 protein for increased root nodulation, and methods for transforming plants with a M. truncatula DMI1 gene.

  Publisher

• Viruses of Nitrogen-Fixing <i>Mesorhizobium</i> Bacteria in Globally Distributed Chickpea Root Nodules

  Phytobiomes Journal · 2023-09-12 · 4 citations

  articleOpen access

  Legume nodules are specialized environments on plant roots that are induced and dominated by nitrogen-fixing bacteria. Bacteriophages (phages) in these nodules could potentially provide top-down controls on the population size and, therefore, the function of nitrogen-fixing symbionts. Here we sought to characterize the diversity and biogeographical patterns of phages that infect nitrogen-fixing Mesorhizobium symbionts isolated from root nodules, leveraging 266 genomes of Mesorhizobium isolated from nodules and 648 nodule metagenomes collected from three species of chickpea plants ( Cicer spp.) under different agricultural management practices, spanning eight countries on five continents. We identified 106 phage populations (viral operational taxonomic units [vOTUs]) in Mesorhizobium draft genomes, 37% of which were confirmed as likely prophages. These vOTUs were detected in 64% of the Mesorhizobium-dominated nodule metagenomes and 58% of the Mesorhizobium isolates. Per metagenome, 1 to 16 putative Mesorhizobium vOTUs were detected, with more than half of the nodules containing only one such vOTU. The majority of vOTUs were detected exclusively in Ethiopia, followed by India and Morocco, with the lowest richness of putative Mesorhizobium phages in countries that applied industrial Mesorhizobium inoculants to crops. Two vOTUs were identified in five or more countries and in nodules dominated by different strains of Mesorhizobium, suggesting infection of diverse Mesorhizobium hosts and long-term interactions. Beta-diversity of these Mesorhizobium phage assemblages was significantly correlated with the dominant Mesorhizobium strain, but not with measured environmental parameters. Our findings indicate that nitrogen-fixing nodules in chickpea plants can contain distinct viral assemblages, with potential impacts on the nodule microbiome that bear further exploration.

  PublisherDOI

• Hiding in plain sight: Genome-wide recombination and a dynamic accessory genome drive diversity in <i>Fusarium oxysporum</i> f.sp. <i>ciceris</i>

  Proceedings of the National Academy of Sciences · 2023-06-26 · 29 citations

  articleOpen accessSenior author

  is among the most important of soil-borne pathogens, with a global distribution and an extensive host range. The pathogen is considered to be asexual, with horizontal transfer of chromosomes providing an analog of assortment by meiotic recombination. Here, we challenge those assumptions based on the results of population genomic analyses, describing the pathogen's diversity and inferring its origins and functional consequences in the context of a single, long-standing agricultural system. We identify simultaneously low nucleotide distance among strains, and unexpectedly high levels of genetic and genomic variability. We determine that these features arise from a combination of genome-scale recombination, best explained by widespread sexual reproduction, and presence-absence variation consistent with chromosomal rearrangement. Pangenome analyses document an accessory genome more than twice the size of the core genome, with contrasting evolutionary dynamics. The core genome is stable, with low diversity and high genetic differentiation across geographic space, while the accessory genome is paradoxically more diverse and unstable but with lower genetic differentiation and hallmarks of contemporary gene flow at local scales. We suggest a model in which episodic sexual reproduction generates haplotypes that are selected and then maintained through clone-like dynamics, followed by contemporary genomic rearrangements that reassort the accessory genome among sympatric strains. Taken together, these processes contribute unique genome content, including reassortment of virulence determinants that may explain observed variation in pathogenic potential.

  PublisherDOI

• Developing a Resource of Wild x Cultigen Introgression Lines for Crop Improvement of Chickpea

  Research Square · 2023-06-07 · 1 citations

  preprintOpen access
  PublisherOA PDFDOI

• Identification of Aluminum Tolerance in Ethiopian Chickpea (Cicer arietinum L.) Germplasm

  Agronomy · 2022-04-15 · 8 citations

  articleOpen access

  Aluminum (Al) toxicity is a major abiotic stress that negatively impacts plant growth and crop productivity. Al ions are released into soil solutions as a function of soil pH, which is in turn determined by a combination of factors, including local geology, historic vegetation and land-use patterns. Selection and use of Al-tolerant crops is a preferred method to address the problem of Al toxicity. The present study evaluated a combination of modern cultivars, advanced breeding lines and a local landrace for Al tolerance using a seedling-based hydroponic assay. Two sequential experiments were conducted to score root and shoot traits in the presence of aluminum. Initially, six Al concentrations (0, 50, 100, 120, 150 and 200 µM) were tested on six chickpea genotypes to identify the single Al concentration that best discriminates among genotypes. Subsequently, 31 chickpea genotypes were evaluated at 0 and 120 µM Al. Progressive declines in trait values were observed in all genotypes with increasing Al, although the degree of sensitivity varied significantly among genotypes. Genotypes were evaluated both for total root length under 120 µM Al and for relative root growth compared to a 0 µM Al control treatment. Considering both parameters, we identified four tolerant chickpea genotypes (DZ-2012-CK-0237, Wollega LV, DZ-2012-CK-0233 and Natoli) and two sensitive genotypes (Akaki and Fetenech). Wollega LV is a local landrace obtained from acidic soil regions of Western Ethiopia, presenting the possibility that historical selection during cultivation on acidic soils might underlie its unusual tolerance. The aluminum tolerance traits identified here are candidates for introgression breeding of new Ethiopian chickpea varieties with potential to increase yield and expand the area of cultivation.

  PublisherOA PDFDOI

• Towards the Development, Maintenance and Standardized Phenotypic Characterization of Single‐Seed‐Descent Genetic Resources for Chickpea

  Current Protocols · 2022-02-01 · 16 citations

  articleOpen access

  Abstract Here we present the approach used to develop the INCREASE “Intelligent Chickpea” Collections, from analysis of the information on the life history and population structure of chickpea germplasm, the availability of genomic and genetic resources, the identification of key phenotypic traits and methodologies to characterize chickpea. We present two phenotypic protocols within H2O20 Project INCREASE to characterize, develop, and maintain chickpea single‐seed‐descent (SSD) line collections. Such protocols and related genetic resource data from the project will be available for the legume community to apply the standardized approaches to develop Chickpea Intelligent Collections further or for multiplication/seed‐increase purposes. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. [Correction added on May 16, 2022, after first online publication: CRUI‐CARE funding statement has been added.] Basic Protocol 1 : Characterization of chickpea seeds for seed‐trait descriptors Basic Protocol 2 : Characterization of chickpea lines for plant‐trait descriptors specific for primary seed increase

  PublisherOA PDFDOI

Recent grants

• BREAD: Overcoming the Domestication Bottleneck for Symbiotic Nitrogen Fixation in Legumes

  NSF · $1.8M · 2010–2014

• Deducing the Genomic Footprint and Functional Impact of Chickpea Domestication on Nitrogen Fixation

  NSF · $3.3M · 2013–2018

• Towards the Complete Gene Inventory and Function of the Medicago Truncatula Genome

  NSF · $6.8M · 2001–2006

• Comparative Genomics of Legume Disease Resistance Gene Homologs

  NSF · $5.0M · 2006–2011

Frequent coauthors

• R. Varma Penmetsa

  Plant (United States)

  107 shared

• Jean Dénarié

  Interactions Arbres-Microorganismes

  73 shared

• Giles Oldroyd

  University of Cambridge

  71 shared

• Sharon R. Long

  University of South China

  69 shared

• Noelia Carrasquilla‐Garcia

  University of California, Davis

  55 shared

• Charles Rosenberg

  54 shared

• G. B. Kiss

  54 shared

• Brendan K. Riely

  University of California, Davis

  53 shared