VitisGen2

Mapping the Way to the Next Generation of Grapes

grape breeder Bruce Reisch working with grape seedlings in the greenhouse

About VitisGen2

Robot phenotyping powdery mildew resistance

Major Accomplishments

VitisGen2 project team at team meeting in 2018

Team Members

A scientist emasculating a grape flower with a pair of tweezers

Videos

Image of a webinar screenshot

Webinars

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Articles in popular press


 

 In The News

 

    • New Technology for Next-gen DNA Sequencing Validated by the VitisGen2 Project

      Illumina DNA processing cell, which looks similar to a computer chip, being held up for the camera.A new technology called rhAmpSeq™ is allowing grape
      geneticists and breeders to rapidly find and validate 2000 markers in diverse grape varieties and species.  These ‘core genome markers’ provide a new set of mileposts that were used during a pilot study by the USDA-funded VitisGen2 project to map traits in six unrelated ‘mapping populations’ representing the diversity of U.S. grape breeding programs, including numerous Vitis species.
      The rhAmpSeq technology, developed by Integrated DNA Technologies (IDT) and commercialized in March 2019, allows researchers to mix and amplify DNA from up to 4,000 individual samples and simultaneously sequence thousands of different markers of each sample.  This dramatically reduces the cost of DNA sequencing across the 19 grape chromosomes – and offers a detailed map of the entire genome for each of the 4000 individuals in one batch.

      Complicated workflow schematic for rhAmpSeq process: activation of primers, amplification, and indexing. The rhAmpSeq technology uses normal DNA primers followed by an RNA base and a PCR blocker in PCR 1. After these primers bind specifically to the target DNA, the RNA and blocker are removed and PCR amplification continues. This improved specificity enables thousands of markers to be amplified simultaneously for a given sample. Then ‘barcoding’ primers are used in PCR 2 to label each sample uniquely prior to pooling all samples for sequencing. This allows amplification and sequencing of 2000 DNA markers in up to 4000 samples.

       

      The VitisGen2 project team, a multi-institutional research collaboration funded by the USDA-National Institute of Food and Agriculture Specialty Crops Research Initiative, played a key role in adapting the rhAmpSeq process to plant breeding platforms. Unlike single nucleotide markers that provide binary information (reference allele or alternative allele), the larger 250 base pair sequences employed by VitisGen2’s rhAmpSeq strategy generates high information content per marker.

      Professor Bruce Reisch commented, “As early testers of the rhAmpSeq system from IDT, we were really pleased to see how we were able to rapidly accelerate the VitisGen2 program by using a nearly 2,000 marker rhAmpSeq panel to analyze 19 Vitis linkage groups. The core marker set was useful across six unrelated populations representing the diversity of the genus, and the workflow was very easy to use and allowed high-throughput processing.”

      Allen Nguyen, IDT’s director of vertical market development, added, “We’re delighted to bring to market a more efficient molecular genotyping method that can help accelerate plant and animal improvement programs as demonstrated in the VitisGen2 project. IDT’s rhAmpSeq system makes it easy to simultaneously investigate thousands of targets or a few with only 2 PCR amplification steps. Though our target was to provide better data, faster for researchers, we also designed the system to be cost-effective.”

      Although the VitisGen2 project team helped pioneer this use of the technology, other scientists and plant breeders see the technology as being broadly applicable to a wide variety of crops.

      For more information, you can read the March 6 news release from IDT: https://idtb.io/38tvsg

      The VitisGen2 project is supported by the USDA-NIFA Specialty Crop Research Initiative (Award No. 2017- 51181-26829).

 

    • Upcoming VitisGen webinar on computer vision

      The VitisGen2 team is excited to announce that our 2019 webinar series will be kicking off next month!

      Headshot of Dani MartinezOur first webinar will be with panelist Dani Martinez, talking about “Advanced computer vision techniques: New technologies to streamline grape breeding”.

      This webinar will present a brief but thorough overview to the general public of what computer vision is, including its different techniques and the technology behind it. In addition, it will detail the methodology implemented in the powdery mildew phenotyping robots of the VitisGen2 project, as a case study.

 

    • Will Europe Embrace Hybrid Wine Grapes?

      In this Wines and Vines article, Tim Martinson and Bruce Reisch discuss new disease-resistant hybrids and how attitudes and regulations about hybrids are changing in the European Union.  This article is based on Bruce’s February VitisGen2 webinar: