California Ag Network

Tag: Science

  • 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.”

  • Trends We’re Watching In 2018: Experts Weigh In On Water, GM, Science Communication And More

    Sacramento, Calif., (January 10, 2018) – As we settle into 2018, it’s natural to wonder what the New Year may bring. There have been dozens of “trend pieces” discussing what’s in store. In this wrap, we consider possible 2018 trends in water, the GM debate, science communication, and food and nutrition.

    Water: After one of the driest Decembers on record, many Californians continue to worry about water supply. I turned to UC ANR water expert Faith Kearns. Faith is a scientist and communicator at the California Institute for Water Resources, a UC ANR-based “think-tank” that integrates California’s research, extension, and education programs to develop research-based solutions to water resource challenges. Faith writes about water issues for a number of publications, including UC’s Confluence blog. She was recently quoted in a Rolling Stone article about California’s “climate emergency,” penned by meteorologist/writer Eric Holthaus.

    Faith told me this: “Water quantity and human use tend to be the dominant lenses that we use to talk about water in California, but they’re not the only thing we need to be paying attention to. For example, water quality issues loom equally as large, and are of course related. But, even beyond that, there are also many non-use oriented ways that water impacts our lives – through recreation, aesthetics, and culture, just to name a few. A trend that I hope to see in 2018 is a broadening of the conversation on water, and an expansion of the kinds of knowledge that are brought to bear on water issues.”

    Editor’s note: The quality of American drinking water continues to be a point of local and national concern; it will undoubtedly be an important topic in the 2018 midterm elections in certain congressional districts. Learn more about this vital public health and social justice issue by visiting the National Drinking Water Alliance website (NDWA). NDWA is funded by the W.K. Kellogg Foundation and coordinated by UC ANR’s Nutrition Policy Institute.

    The debate over genetically modified food: Entering a new era?

    UC Davis associate professor and plant pathologist Neil McRoberts – who was recently named co-leader of UC ANR’s Strategic Initiative in Sustainable Food Systems – shared his ideas about where we might be headed in terms of framing the GM discussion.
    “…The GM debate is entering a new era with the growing use of gene editing – CRSPR-Cas9 – technology. Interestingly, this time around the ethics and socio-economics debate seems to be keeping pace with the science, as witnessed by the latest issue of the Journal of Responsible Innovation, which focuses on gene drive technologies and their uses. The special issue grew out of a workshop hosted at NCSU last year. The use of CRSPR has re-opened debates about how genetic modification should be regulated and labeled.”

    Editor’s note: You can learn more about Neil’s work here. He recently wrote a guest blog post for UC Food Observer about the importance of cash crops to smallholder farmers in Uganda and Malaysia. For more about the GM debate, read the text of Mark Lynas’ speech to the Oxford Farming Conference, in which he tries to “map out the contours of a potential peace treaty” between GM proponents and the technology’s opponents. h/t Nathanael Johnson.

    Will 2018 usher in an era of more civil communication around science-based topics?

    *It depends on us.

    Across the board, our public discourse took a dive in 2017 … and that’s a shame. Here’s to a New Year … and resolving to do a better job at communicating with clarity, integrity and with less judgment. The advancement of science (and perhaps the preservation of our sanity) depend upon it.

    I loved this piece by Tamar Haspel, which recently appeared in the Washington Post and specifically addresses science communication and agriculture/food issues. Shorter: If we want to persuade people, we have to be respectful. She writes:

    “Rudeness can increase polarization and entrench disagreements even further. Nasty begets nasty; it’s regression toward the mean …”

    As both a scientist and a communicator, UC ANR’s Faith Kearns also informed my thinking on where the communications trend line ought to go for 2018, telling me that:

    “One of the bigger challenges, and opportunities, facing the science communication community is how to really push ourselves to better incorporate more perspectives from the social sciences and humanities. This is particularly true on issues like food, agriculture, and the environment where so much of what is truly challenging is related to human behavior, decision-making, and psychology. It’s not just a matter of using research on science communication to inform practice, but also of responsibly integrating different forms of knowledge into communication efforts.”

    Food and nutrition trends

    There are an overwhelming number of food trend pieces out right now. The Hartman Group is a good account to follow to stay apprised of food trends throughout the year. Their Year in Review blog post is definitely worth a read. It identifies some trends from last year that will likely carry forward, including consumer demands for transparency, “conscious” consumerism, customized health and wellness, and the ways in which snacking is disrupting food culture. Bonus: you can access some of Hartman’s industry reports via links included in the blog post.

    For a largely culinary perspective of 2018 trends, check out the BBC’s Good Food piece. Nationally-known dietitian Christy Brissette has written an interesting piece about nutrition trends (think algae, Stevia, chicory root fiber and eating for “Diabetes 3” – aka Alzheimer’s).

    And if you’re having trouble keeping that New Year’s resolution to exercise more, consider reading this piece, which reports on a study indicating that exercise alters our microbiome – which could improve our health and metabolism. Gretchen Reynolds for the New York Times.