California Ag Network

Tag: Agricultural Research Service

  • First Genome of Spotted Lanternfly Built from a Single Insect

    Agricultural Research Service (ARS) scientists, in cooperation with Pacific Biosciences and Penn State University, have published the first genome of the invasive Spotted Lanternfly (SLF) in the journal Gigascience and they did it from a single caught-in-the-wild specimen.

    Not only is it the first published genome for this pest, but no closely related species has had its genome sequenced, making the data even more important, according to entomologist Scott M. Geib with the ARS Daniel K Inouye U.S. Pacific Basin Agricultural Research Center.

    SLF, a native of China, Bangladesh and Vietnam, was first found in Pennsylvania in 2014 and has now spread to Virginia, Maryland and New York. This invasive pest has a taste for almonds, apples, apricots, grapes, peaches, blueberries and hops as well as hardwoods such as oak, walnut, and poplar. Various estimates put the potential economic damage in the billions of dollars, if the SLF becomes widely established in the United States.

    “Having the genome for this pest opens the door to a better understanding of its biology and behavior, and makes coming up with potential control methods much more likely to happen, such as developing a lure for a trap through understanding the insect’s olfactory genes, or exploring avenues such as gene editing or RNAi,” said Geib.

    While having the SLF genome is critical for the management and control of this invasive pest, the approach taken to obtain the genetic data is an achievement of remarkable note as well. For the first time, all of the DNA required to generate a whole genome sequence was taken from a single insect picked from a tree in the wild in Reading, Pennsylvania, across the street from the Reading Pagoda on Mt. Penn.

    One hurdle for deciphering this species’ genome is its relatively large genome size, at about 2.2 billion base pairs. Typically, with previous sequencing systems, many sequencing runs would have been needed to do the complete job, with each run using up the available DNA for the organism being sequenced.

    So often to have sufficient DNA for a complete genome sequence, many organisms would need to be pooled, introducing more opportunities for errors to be generated. To avoid such potential for errors, the subjects—especially insects—often have to be raised in colonies and inbred.

    “In cooperation with Pacific Biosciences and using their new sequencing platform—the PacBio Sequel II—that produces 10 times the data from a single sequencing run, we were able to generate sufficient coverage from just a single specimen. This allows for a very fast turn-around of data and assemblies as well as lowers cost, in this case under $2,000 in consumable supplies, not including the purchase price of the sequencing instrument of course,” explained Geib.

    For genome completeness, and since there aren’t many related genomes to compare that of the SLF to, the team checked a set of “core genes” that should be present exactly one time in all insects and verified how many of these were found in this genome project. In this case, they found about 97 percent of these single copy core genes, with a very low rate of duplication.

    “Sequencing such a large insect genome quickly and showing there is no need to pull the insect into a colony raises the feasibility that we can complete the Ag100Pest Project,” Geib said. The ARS Ag100Pest initiative is focused on deciphering the genomes of 100 insect species that are most destructive to crops and livestock and that are projected to have profound bioeconomic impacts to agriculture and the environment. “Now, with this system, doing 100 or even 1,000 genomes is not unrealistic,” he added.

    The ability to get a complete genome from a small amount of DNA also makes it practical to consider sequencing the genomes of physically tiny insects without having to catch or raise a large number of any one species. That expands the list of insects that may be genetically sequenced.

    By Kim Kaplan, USDA-ARS

    The Agricultural Research Service is the U.S. Department of Agriculture’s chief scientific in-house research agency. Daily, ARS focuses on solutions to agricultural problems affecting America. Each dollar invested in agricultural research results in $20 of economic impact.

  • Deciphering the Walnut Genome

    California produces 99 percent of the walnuts grown in the United States. New research could provide a major boost to the state’s growing $1.6 billion walnut industry by making it easier to breed walnut trees better equipped to combat the soil-borne pathogens that now plague many of California’s 4,800 growers.

    In a new study, a team of scientists at the University of California, Davis, and USDA’s Agricultural Research Service (ARS) used a unique approach to sequence the genomes of the English walnut and its wild North American relative by tapping into the capabilities of two state-of-the-art technologies: long-read DNA sequencing and optical genome mapping. The resulting genome sequences are believed to be of the highest quality ever assembled of any woody perennial.

    “By sequencing the genome of a walnut hybrid, we produced complete genome sequences for both parents in the time normally required to produce the sequence of one genome,” said Ming-Cheng Luo, leading genomics investigator on the project and a research geneticist in the Department of Plant Sciences at UC Davis.

    This approach could be applied to genome sequencing of trees and many other woody perennials, opening the door to a better understanding of the genetic blueprints of almonds, pecans, pistachios and grapes.

    “Like walnut, these other crops naturally cross-pollinate and are therefore highly variable,” said Jan Dvorak, co-principle investigator and genetics professor at the Department of Plant Sciences at UC Davis. “Variability has always greatly complicated our ability to produce a high-quality genome sequence for such crops, but these new technologies now make it possible,” Dvorak added.

    In California, walnuts are grown commercially using rootstocks chosen specifically for their ability to tolerate various soil-borne diseases.  “We chose to cross the widely used English walnut specifically with the wild Texas Black walnut because of its native resistance to several soil-borne diseases and root nematodes, which are serious pests of walnut in California” said Dan Kluepfel, a USDA-ARS scientist and principal investigator of the walnut-rootstock development project.

    The assembled genome sequences of the two walnut species also will now help researchers identify genetic markers that breeders can use to develop new varieties with improved pathogen and pest resistance.

    Major contributors to the project included UC Davis scientists Tingting Zhu, Le Wang, and Agriculture and Agri-Food Canada scientist Frank You.

    The study was published online today in Horticulture Research. The research was funded by the California Walnut Board and the USDA’s National Institute of Food and Agriculture Specialty Crop Research Initiative. The study can be found here.

    The Agricultural Research Service is the U.S. Department of Agriculture’s chief scientific in-house research agency. Daily, ARS focuses on solutions to agricultural problems affecting America. Each dollar invested in agricultural research results in $20 of economic impact.

  • Making Spinach with Low Oxalate Levels

    Featured Photo: ARS geneticist Beiquan Mou and colleagues analyzed hundreds of spinach plants to find ones with less oxalate, a compound linked to kidney stones.

    Salinas, Calif., (February 2, 2017) – Agricultural Research Service (ARS) scientists identified 8 spinach varieties that have low oxalate levels, which is sometimes linked to better health. Oxalic acid, or “oxalate,” is a naturally occurring plant chemical and in the human diet it’s been linked to kidney stone formation. It also can react with calcium, iron, and other minerals to inhibit mineral absorption.

    Scientists with the ARS’s Crop Improvement and Protection Research Unit in Salinas, California, and the University of Arkansas conducted a study to find genetic components related to oxalate concentrations in spinach. By analyzing the genetic code of 310 spinach varieties, ARS geneticist Beiquan Mou and his university colleagues identified 6 DNA markers linked to genes that contribute to oxalate levels and may be useful for breeders in reducing oxalate concentrations.

    The scientists analyzed oxalate concentrations in 300 USDA germplasm accessions and 10 commercial cultivars and found oxalate concentrations that ranged from 647.2 to 1,286.9 milligrams (mg) per 100 grams on fresh weight basis, according to Mou. They also found 8 accessions with less than 780 mg per 100 grams based on fresh weight that may be useful as sources of low oxalate concentration genes in breeding efforts.

    Spinach contains higher concentrations of oxalate than most crops, but it is an economically important vegetable crop worldwide and it’s considered healthful because of its high concentration of a number of key nutrients. Foods such as beets, rhubarb, strawberries, nuts, chocolate, tea, wheat bran, and almost all dry beans also are known to increase oxalate in the urine and may contribute to kidney stone formation.

    The results were published in November 2016, in the journal Euphytica.

    Read more about Mou’s research in the January issue of AgResearch.

    ARS is the U.S. Department of Agriculture‘s (USDA) in-house scientific research agency.