RIPE article and staff spotlight on Olena Sambucci

Olena SambucciOlena 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.

RIPE ARTICLE: 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.

STAFF SPOTLIGHT on Olena Sambucci.

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New “Research In Plain English” article on foliar phylloxera resistance

Our new “Research In Plain English” article is now available: “New resistance genes mapped for an important foliar insect pest of some hybrid grape cultivars

The 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.

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Using neural networks to identify Powdery Mildew

Leaf disk and 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

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New staff spotlight featuring Mélanie Massonnet from UC Davis

Melanie MassonetMélanie is a postdoctoral associate in Dario Cantu’s lab in the Department of Viticulture and Enology at the University of California in Davis.

She is in charge of the genome-wide transcriptional analyses of the breeding populations for powdery mildew resistance gene stacking and wine grape quality. Mélanie explains what this mouthful means, along with telling us how her background growing up in France influenced her decision to work with wine, and much more, in this Staff Spotlight on Mélanie Massonnet.

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Staff Spotlight on Cheng Zou

Cheng Zou 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.

Read Cheng Zou’s interview here.

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New RIPE article on genetic linkage mapping

Our new “Research In Plain English” article is now available: “A new locus associated with downy mildew resistance is found by creating a more accurate genetic linkage map

Our VitisGen2 teams are doing a lot of great work learning about the genetic underpinnings on 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:

Construction of a high-density linkage map and QTL detection of downy mildew resistance in Vitis aestivalis-derived ‘Norton’. Authors: Surya Sapkota, Li-Ling Chen, Shanshan Yang, Katie E. Hyma, Lance Cadle-Davidson and Chin-Feng Hwang. Theoretical and Applied Genetics, 132, pages 137-147.

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Qi Sun, Anne Fennell and Dario Cantu participate in INTEGRAPE meeting in Greece.

The Integrape meeting is focused on developing FAIR (Findable, Accesible, Interoperable and Reusable) standards to harmonize databases on Vitis genomics, genetics, and breeding.

COST Action INTEGRAPE logo

Report written by Qi Sun and Anne Fennell

Integrape (http://www.integrape.eu) is a cooperation network sponsored by European Cooperation in Science and Technology (COST, CA17111). The mission of INTEGRAPE is to bring together all stakeholders in the grapevine research community (academic, industry, policymakers and consumers) in an open, international, and representative network to develop minimal data standards and good practices in order to integrate data repositories and improve interoperability between datasets.

The first annual meeting of Integrape was held on March 25th-28th at the Conference Center of Mediterranean Agronomic Institute of Chania, Crete, Greece. Grape researchers from COST member countries of the Europe Union attended the meeting. United States is one of the COST International Partner Countries. Three VitisGen2 scientists, Dr. Anne Fennell of South Dakota State University, Dr. Qi Sun of Cornell University and Dr. Dario Cantu of UC Davis attended the meeting, and presented ongoing projects under VitisGen2.

FAIR (the principle that data should be Findable, Accessible, Interoperable, and Reusable) was the theme integrating the meeting. Grapevine research results in diverse dispersed datasets including repository collections, imaging, environmental biology, genomics, epigenomics, transcriptomics, proteomics, and metabolomics. Integrape’s meeting focus was to set up workable plans in the next four years to deliver FAIR data.

Action items being discussed at the meeting including data interoperability and data standards conventions, data analysis and best practices, interoperability of infrastructure and web services and dissemination of recommendations and guidelines. Integration of existing databases, e.g. Vitis International Variety Catalogue (VIVC) and the European Vitis Database; adoption of data and meta models like BrAPI and MIAPPE; establishing an international grape data registry to facilitate data findability; adoption of Vitis Ontology by the grape research community.

In recent year, VitisGen2 projects have been producing large amount of data associated with breeding activities in the US, with data types covering genomics, transcriptomics, metabolomics and phenomics. With the rapidly increasing mass of data, defining best practice in data management and enabling data interoperability are becoming more urgent issues for research and breeding programs in both US and European.

Collaborations between VitisGen2 and Integrape were discussed during the meeting. Initial action items including unifying the VitisGen2 Trait Ontology with the Vitis Ontology; establishment of globally unique germplasm identifiers; common models for data and meta data; participation in annual meetings by representatives of the two projects.

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“American Vineyard” article on table grape breeding

Two table grape clusters- on the left berries are green or pale pink, on the right berries are deep red

Tim 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!

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Lu Yin, PhD candidate at UMinn, featured in new Staff Spotlight

Lu Yin headshotLu Yin is a PhD candidate and research assistant at the University of Minnesota, working in Dr Matthew Clark’s lab to breed grapes that are more resistant to the insect pest foliar phylloxera. She answered our questions about her advice to someone just beginning their career (“Don’t be afraid to ask or speak!”), her research project (she grows over 1000 grape seedlings to find the best ones), and how listen to piano music and hymns helps keep her focused and engaged.

You can read more about Lu Yin, and view our previous staff spotlights!

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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.

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