A rainy summer may be causing a pumpkin shortage this Thanksgiving, but diseases are the biggest threat to pumpkins, and other cucurbits including cucumber, squash, melon and watermelon; a problem that a new $6.5 million USDA grant hopes to fix.
A consortium of 20 researchers, led by Rebecca Grumet of Michigan State University, is using advanced genomic techniques to accelerate the development of disease-resistant varieties of cucurbit crops. The project is funded through the USDA National Institute of Food and Agriculture Specialty Crop Research Initiative. BTI Associate Professor Zhangjun Fei will lead the bioinformatics and genomics part of the initiative.
Fungal, bacterial and viral infections are the main threat to cucurbit crops. Often, wild relatives of these plants have genes that protect them from the infection, but which have been lost through the domestication process. By sequencing the genomes of thousands of cucurbit varieties, researchers can identify regions in the genomes that offer disease resistance and provide information to breeders so that they can generate more robust crops.
"We want to efficiently disseminate our information to the public, to breeders, especially," said Fei. "One of the main focuses of this project is to develop a breeder-friendly database, so they can use this information to facilitate breeding new cultivars."
Fei will receive up to 10,000 samples of watermelon, melon, cucumber, pumpkin and squash varieties from his colleagues. Then, using a process called genotyping-by-sequencing, he will sequence each genome and identify genetic markers that indicate disease-resistance in the plants. These genetic markers will reduce the need for field-testing and will enable breeders to save time, land and money while breeding new resistant crop varieties.
The genomic information will be publicly available through the Cucurbit Genomics Database. Fei began this website about 10 years ago, but the new grant will enable him to enlarge and reformat the database to include tools that are specially designed for breeders. Researchers at West Virginia State University will also collaborate on the bioinformatics and genomics portion of the project.
To educate breeders on how to use these genomics-assisted breeding tools, Fei and his colleagues plan to hold training sessions at upcoming Cucurbita meetings.
Ultimately, the project aims to provide improved crop varieties that will help farmers to avoid devastating outbreaks, so that more produce will end up on the dinner table.