Mapping the Way to the Next Generation of Grapes
Staff spotlight with Noam Reshef
Noam Reshef works as a postdoctoral researcher in the Sacks lab at Cornell and is excited to help lead the way for the next generation of grape cultivars.
Staff spotlight with Dilmini Alahakoon
Dilmini Alahakoon started working on her PhD with the VitisGen2 project in 2016 in the Fennell lab at SDSU. Her primary interest is in grapevine phenology and she has worked in several QTL mapping populations
Staff spotlight with Research Technician, Heather Scott
Heather Scott manages the chemical analysis of the VitisGen fruit samples that come into the Sack’s lab. She particularly enjoys working with grapes, both in the field and in the lab.
Anna Underhill started on the Powdery Mildew Team in February and took the time to tell us a little bit about her background, her inspiration, and her role in the VitisGen project!
The VitisGen and VitisGen2 projects represent major investments in understanding grapevine genetics – and particularly in identifying markers associated with desirable traits for use in ‘marker-assisted selection’. DNA markers identified by geneticists and breeders are now incorporated into several selections and mapping populations by grape breeding programs in California, Minnesota, New York, and Missouri.We asked VitisGen2 breeders to provide photos and brief descriptions of a few of their selections and mapping populations and the traits they incorporate.Read the full article: Grape Selections from the VitisGen and VitisGen2 Projects.
The effectiveness of a collaboration between two research teams can be greater than the sum of its parts. This was part of the incentive for German scientist Daniel Zendler, a leading expert on the Ren3 and Ren9 genes for powdery mildew resistance, to spend the summer working with the VitisGen2 team at Cornell AgriTech’s campus.Daniel, Lance Cadle-Davidson and David Gadoury teamed up to combine equipment, manpower and expertise from each team, to move forward on targeting the location on the genome of these resistance markers, as well as determining how broadly effective they are against different strains of powdery mildew. You can read more about their research goals and findings in our article: “International collaboration advances research into grape disease resistance“.
We recently mentioned that VitisGen2 has a new project manager, Ugo Ikeogu. We’re very excited to have him on board! We’ve asked him a few questions about his background, extensive experience with genetics and phenotyping, what he’s looking forward to most in joining the project, and what advice he would give to another young scientist in the field. I hope you enjoy reading our Staff Spotlight on Ugo Ikeogu!
Olena Sambucci, a postdoctoral researcher at UC Davis, focuses her research on the economic trade-offs between grape traits, including disease resistance, wine varietal name, flavor profiles, and many other factors. She is part of VitisGen2’s economics team, under the guidance of Julian Alston.Learn more about VitisGen2’s economics team by reading the new “Research in Plain English” article summarizing research conducted by Olena, Julian and collaborators Kate Fuller and Jayson Lusk: The pecuniary and non-pecuniary costs of powdery mildew and the potential value of resistant varieties in California grapes. Olena also talked more about her current responsibilities, her background, and which podcasts help get her through long days in the most recent Staff Spotlight on Olena Sambucci.
New “Research In Plain English” article on foliar phylloxera resistanceThe VitisGen2 team members at the University of Minnesota have been studying the genetic underpinnings of foliar phylloxera resistance. Rootstocks resistant to this important grape pest have been available for some time — and a new article by Matthew Clark et al. explains how their research helps breeders come closer to breeding resistance to foliar phylloxera as well. The RIPE article provides a “plain English” explanation of the research described in the full article, linked below.Quantitative trait loci identified for foliar phylloxera resistance in a hybrid grape population. Authors: Matthew D. Clark, Soon L. Teh, Eric Burkness, Laise Moreira, Grace Watson, Lu Yin, William D. Hutchison and James J. Luby. Australian Journal of Grape and Wine Research, 24 (3), pages 292-300.
VitisGen2 scientists train neural networks to identify Powdery Mildew‘Practice makes perfect’ is undeniably cliché, but its truth is evident to everyone who has ever tried to learn a new skill. Whether it’s hitting baseballs, pushing piano keys, or pipetting off supernatant, this inevitable cycle of trial and error eventually yields to increasing expertise. What’s true for humans is also true for computer systems.Learn more about machine learning in article by Anna Underhill: “VitisGen2 scientists train neural networks to identify Powdery Mildew”
Mélanie Massonnet, postdoctoral researcher in Dario Cantu’s lab at UC Davis, explains how she uses genome-wide transcriptional analyses of grape breeding populations for powdery mildew resistance gene stacking and improving wine grape quality, along with telling us how her background growing up in France influenced her decision to work with wine and much more.
VitisGen2 team member Cheng Zou, postdoctoral researcher in Qi Sun’s lab at Cornell University, talks about finding a core-genome markers for comparing genotypic data across all grape species, and the applications for marker assisted selection and quantitative trait mapping! Don’t be intimidated though, she explains it in plain English.She also tells us what she enjoys about working with grapes, explains the amazing technology they use for finding genetic markers, and gives advice for someone beginning a career in genetics.
Our VitisGen2 teams are doing a lot of great work learning about the genetic underpinnings of downy mildew resistance in native American grape species. You can read about some of the work coming out of Dr. Hwang’s lab at the University of Missouri in our RIPE summary of their recent publication.
“American Vineyard” article on table grape breedingTim Martinson, Craig Ledbetter and Rachel Naegele wrote an article for “American Vineyard” magazine about how VitisGen2 is using marker assisted selection to breed new table grape varieties with deeper coloration. You can read the full article!
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.