California Ag Network

Tag: Genomics

  • Key Discovery on How a Plant-Parasitic Nematode Infects Such a Wide Range of Organisms

    UC Davis nematologists, including Valerie Williamson, professor emerita in the Department of Plant Pathology, and associate professor Shahid Siddique, Department of Entomology and Nematology, have long wondered how the plant-parasitic nematode, the Northern root-knot nematode, is able to infect such a wide range of organisms, from monocots and dicots to annual crops and woody plants.

    Now a 15-member research team of international nematologists and biotechnologists, led by UC Davis nematologists, have gained insight into how the DNA of this nematode species, Meloidogyne hapla, facilitates their success.

    The discovery, hailed by the team as groundbreaking, “is the most complete and contiguous genome assembly for a plant-parasitic nematode to date,” agreed Williamson and Siddique, co-authors of a newly published paper, “High-Resolution Genome Assembly and Linkage Mapping in Meloidogyne hapla Reveal Non-Canonical Telomere Repeats and Recombination Hotspots Associated with Effector Proteins,”  in the open-access medical journal, PLOS Pathogens

    The peer-reviewed research is online at https://tinyurl.com/44zx2eh2.

    “Interestingly, we discovered that Meloidogyne hapla uses an unusual DNA repeat at the ends of its chromosomes instead of typical telomeres, suggesting it may have an alternative way to protect its chromosomes end,” Siddique said.

    “Overall, our study integrates high-resolution structural genomics, genetic mapping, and functional inference to uncover links between genome architecture, recombination landscapes, and host–parasite interactions,” said first-author Pallavi Shakya, a doctoral candidate in the Siddique lab who received her master’s degree in plant biotechnology from Wageningen University, The Netherlands.

    Other co-authors include UC Davis doctoral candidate Alison Blundell and UC Davis postdoctoral researcher Dadong Dai, both of the Siddique lab, and scientists from The Netherlands, France, Indonesia, Australia, and Croatia.

    “Plant parasitic nematodes cause billions of dollars of damage annually to plant crops globally,” said Williamson, a Fellow of the Society of Nematologists.  “Root knot nematodes (RKN) are the most damaging species group in large part because they are able to infect diverse crops including both monocots and dicots, annual crops and woody plants.”

    “Over twenty years ago, my group and others decided to focus on a single species as a model to serve as a resource,” Williamson related. “We chose the species Meloidogyne hapla due to its relatively simple DNA genome, its genetic tractability, and the observation that isolates of the nematode differed in plants that they could infect. While considerable progress was made in analyzing the DNA, attempts to completely understand the genome structure were hindered by the tiny size of the organism and limitations in technology.”

    However, in recent years, dramatic improvements in biotechnology and bioinformatics developed. “Our international team of nematologists and biotechnologists worked together to produce a complete assembly of the genome that represents the DNA sequence of full-length chromosomes,” she said, pointing out that “As far as we are aware, this is the most complete genome for a plant-parasitic nematode.”

    has several novel features: Chromosome ends do not resemble those of most other animals or plants; the chromosome structure differs between isolates of this nematode with breaks, rejoining and recombination between chromosomes of different isolates,” Williamson said. “This genome flexibility may provide a clue as to how root-knot nematodes are able to change the spectrum of hosts that they can infect.  It will also provide a resource for studying the genome of other important RKN species and allow identification of nematode genes that contribute to successful parasitism. This information should inform best strategies for RKN control as well as development of plants with increased resistance.”

    The Northern root-knot nematode causes significant economic damage to many crops by causing root galls, stunting, reduced yield, and disfigurement, which makes infected produce like carrots unmarketable.  The damage affects a wide range of plants, including vegetables, fruit trees, and wine grapes in certain regions. Infections are most severe in young plants, which can lead to complete crop destruction, while established plants may sustain significant yield reduction.

    The abstract:

    “Root-knot nematodes (Meloidogyne spp.) are among the most destructive agricultural pests that cause significant yield losses across a wide range of crops. Meloidogyne hapla is a valuable model for studying root-knot nematodes due to its parasitic diversity, small diploid genome, and a reproductive strategy that facilitates genetic analysis. Here, we report the most contiguous genome assembly to date for any plant-parasitic nematode built using PacBio HiFi, Oxford Nanopore, Illumina, and Hi-C sequencing. Genetic linkage analysis of F2 populations derived from crosses between M. hapla strains validated the assembly but also revealed anomalies indicating chromosome structure differences between parental isolates such as fissions, fusions, and rearrangements. Strikingly, we identified sharply delimited zones with extraordinarily high recombination on most chromosomes. Notably, several of these high recombination zones were significantly enriched for genes encoding secreted proteins, many of which contribute to parasitism.

    These findings suggest that meiotic recombination facilitates effector diversification and offer insight into how these parasites diversify their effector protein repertoire to change or expand their extraordinary host range. We further report the discovery of a novel 16-nucleotide tandem repeat and lack of canonical telomere repeats at chromosome ends. The localization of this 16-nt repeat at chromosome ends highlights a potentially divergent mechanism of chromosome-end maintenance in this nematode group. Overall, our study integrates high-resolution structural genomics, genetic mapping, and functional inference to uncover links between genome architecture, recombination landscapes, and host–parasite interactions.”

  • UC Davis Nematologists Share International Spotlight

    UC Davis nematologists shared the international spotlight at the 64th annual meeting of the Society of Nematologists (SON), held recently in Victoria, British Columbia.

    Doctoral candidate Alison Blundell of the laboratory of associate professor Shahid Siddique, UC Davis Department of Entomology and Nematology, received the 2025 John M. Webster Outstanding Student Award from the Society of Nematologists at its recent meeting in Victoria, British Columbia. As the recipient of the $1500 prize, she presented a 30-minute talk on her research,   “Overcoming Resistance: Unraveling The Mechanisms Behind Root-knot Nematode Evasion of Tomato Mi-1 Gene.”

    Siddique delivered a keynote address, “Biotechnology and Genomics for Sustainable Nematode Management” in the international symposium series, which was sponsored by a grant received from the Organization for Economic Co-Operation and Development (OECD) and Co-Operative Research Programme: Sustainable Agricultural and Food Systems. It centered on the SON conference theme,  “Nematodes on the Move: Building Resilience and Sustainability through International Collaboration and Better Policies.”

    Siddique presented his keynote address under the realm of the symposium, “Reducing the Global Movement of Plant-Parasitic Nematodes and Rethinking Control Strategies,” Part 2.  Part 1 focused on “Understanding the Impact of Plant-Parasitic Nematodes on Global Food Security and Trade in a Changing World.”

    Siddique was one of 14 keynote speakers from 11 countries across 5 continents participating in the discussion, which consisted of three plenary sessions.

    Two doctoral candidates in the Siddique lab, Veronica Casey and Alison Blundell each won a travel award to attend the conference. Casey received the Hubbard Ag Science Award, and Blundell, the Bayer Award.

    Presenting talks were UC Davis Distinguished Professor Steve Nadler, former chair of the Department of Entomology and Nemtology; Amanda Hodson, assistant professor, and two postdoctoral researchers in the Siddique lab, Vera Putker and Bardo Castro.

    Nadler discussed “Phylogenetic Inference and the Diversity of Animal-Parasitic Nematodes”;  Hodson,  “The Relationship Between Nematode Indicators and Soil Carbon Pools across Managed and Unmanaged Landscapes in California”; Putker, “GPA2-Induced Selection Pressure Does Not Select for 187S Allele of the Effector GPRBP-1 in Virulent Globodera Pallida Populations,” and Bardo, “Biotechnology Approaches Against Root-Knot and Root Lesion Nematodes.”

    Blundell is the first UC Davis student to win the Webster award, launched in 2007 to recognize “a graduate student who has demonstrated outstanding accomplishments in his/her thesis research in nematology as well as other skills necessary to be a well-rounded scholar.”

    Blundell, who anticipates receiving her doctorate in 2026, joined the UC Davis doctoral program in 2020. She is completing her dissertation on “Trade-Offs Between Virulence and Evading Resistance in Root-Knot Nematodes.”  She investigates how root-knot nematodes overcome Mi-1 in tomatoes and is testing for susceptibility associated with resistance breaking. Mi-1 is a crucial gene in tomato plants that confers resistance against root-knot nematodes, which are parasitic nematodes that can and do severely damage crops.

    In addition to her scientific contributions, Blundell is involved in professional services with SON, including oral and poster presentations and as vice chair of the SON Graduate Student Committee. She engages in teaching, mentoring, and public outreach on the UC Davis campus. She promotes science education and agricultural awareness by volunteering at the annual UC Davis Picnic Day and the UC Davis Biodiversity Museum Day.

    Blundell, formerly Alison Coomer, holds a  bachelor of science degree in biology and a bachelor of arts in chemistry (2020) from Concordia University, Seward, Neb., where she received the Outstanding Graduate Student in Biology Award.

    The conference drew 179 attendees. The group experienced “a slightly lower attendance due to Visa concerns among foreign students attending U.S. universities,” a spokesman said. SON was formed in 1962 to advance the science of nematology in both its fundamental and economic aspects. Its membership stands at 356.

  • Dairy Producer Considerations for Genomic Testing

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    Genomic Testing was a big topic of discussion at the World Ag Expo dairy seminars this year. Genomic Testing is a new technology that is becoming more available and affordable to dairy producers; however, there are still many questions as to how it all fits in to individual dairy operations. Watch this brief video interview with Genetic Programs Manager at CRV, Sophie Eaglen, as she addresses several key points for dairy producers considering taking advantage of this technology. Read the full story in the March issue of California Dairy Magazine Digital.

     

  • Arabica Coffee Genome Sequenced

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    Davis, Calif., (January 17, 2017) – The first public genome sequence for Coffea arabica, the species responsible for more than 70 percent of global coffee production, was released today by researchers at the University of California, Davis.

    Funding for the sequencing was provided by Suntory group, an international food and beverage company based in Tokyo.

    Now available for immediate use by scientists and plant breeders around the world, the new genome sequence has been posted to Phytozome.net, the public database for comparative plant genomics coordinated by the U.S. Department of Energy’s Joint Genome Institute.

    Details of the sequence will be presented Sunday, Jan. 15, at the Plant and Animal Genome Conference in San Diego.

    Sequencing of the C. arabica genome is particularly meaningful for California, where coffee plants are being grown commercially for the first time in the continental United States and a specialty-coffee industry is emerging.

    “This new genome sequence for Coffea arabica contains information crucial for developing high-quality, disease-resistant coffee varieties that can adapt to the climate changes that are expected to threaten global coffee production in the next 30 years,” said Juan Medrano, a geneticist in the UC Davis College of Agricultural and Environmental Sciences and co-researcher on the sequencing effort.

    “We hope that the C. arabica sequence will eventually benefit everyone involved with coffee — from coffee farmers, whose livelihoods are threatened by devastating diseases like coffee leaf rust, to coffee processors and consumers around the world,” he said.

    The sequencing was conducted through a collaboration between Medrano, plant scientists Allen Van Deynze and Dario Cantu, and postdoctoral research scholar Amanda Hulse-Kemp, all from UC Davis.

    (A press kit, including video b-roll and high-resolution still images, is available.)

    Friendly challenge leads to C. arabica sequencing

    A few years ago, Medrano — born and raised in coffee-producing Guatemala — was urged by colleagues in Central America to consider introducing genomic technologies to improve C. arabica.

    In 2014, researchers elsewhere sequenced the genome of Coffea canephora — commonly known as robusta coffee and used for making coffee blends and instant coffee. There has been, however, no publicly accessible genome sequence for the higher-value and more genetically complex C. arabica.

    Medrano was intrigued with the challenge to sequence C. arabica, but as an animal geneticist was experienced in the genomics of livestock — not crops.

    Undeterred, he quickly tapped the expertise of molecular breeder Van Deynze, director of research at the UC Davis Seed Biotechnology Center and associate director of the UC Davis Plant Breeding Center, as well as Cantu, a plant geneticist in the UC Davis Department of Viticulture and Enology.

    Sequencing intersects birth of California coffee farming

    Coincidentally, the UC Davis research team was introduced to farmer Jay Ruskey, who with the help of University of California Cooperative Extension farm advisor Mark Gaskell, was growing the first commercial coffee plants in the continental United States at his Good Land Organics farm north of Santa Barbara.

    Coffee is a tropical crop, traditionally grown around the world in a geographic belt that extends no more than 25 degrees north or south of the equator. But at Ruskey’s Central Coast farm, coffee trees are producing high-quality coffee beans at a latitude about 19 degrees north of any other commercial coffee plantations.

    Ruskey also has planted coffee trees on some 20 other farms stretching from San Luis Obispo south to San Diego, launching what he believes will become a new specialty-coffee industry for California.

    Working with Ruskey, the UC Davis researchers collected genetic material — DNA and RNA samples — from different tissues and developmental stages of 23 Geisha coffee trees growing at Good Land Organics. Geisha, known for its unique aromatic qualities, is a high-value C. arabica variety that originated in the mountains of western Ethiopia.

    Plant material from one of the trees — UCG-17 Geisha — was used for developing the C. arabica genome sequence.