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Mapping Grapevine Genomes: a Tool to Manage Quality and Sustainability

by Ted Rieger
October 14, 2020

Understanding grapevine genomes and genetics provides knowledge to understand differences in grape and wine color, aroma and flavor, and can be used to identify genes for disease resistance that allow for breeding grape varieties with resistance to diseases and pathogens such as Pierce’s Disease and powdery mildew. This understanding can assist with future vineyard sustainability, enabling development of grapevine materials and varieties to adapt to climate change, and that are best suited for quality production in the different environments found in the world’s grapegrowing regions. Researchers studying and mapping grape genomes believe this knowledge also has potential to provide tools to monitor gene expression in the vineyard and help guide viticultural practices to enhance fruit quality.

Two researchers discussed current projects and the future potential of grapevine genetics during an online forum October 8th presented by the University of California, Davis (UCD) Robert Mondavi Institute (RMI) for Wine and Food Science, “The Future of Winegrowing: Mapping Grapevine Genomes.”

Dr. Dario Cantu, a plant biologist and professor in the UCD Department of Viticulture and Enology is considered one of the leading researchers on grapevine genetics and genomics. His research program integrates bioinformatics and biochemistry with the application of genetics and genomics to study plant and microbial activities related to disease resistance, fruit ripening and flavor development. He has been a member of research teams that have mapped the genomes of Cabernet Sauvignon and Chardonnay.

Cantu defined genome as, “the complete set of genetic information in an organism.” A genome can provide a blueprint for building an organism.

Genome sequencing provides information on the genetic diversity that exists between grape varieties and grape species. “There is a lot of (mostly unexplored) variation between species, varieties and even clones,” Cantu said. Comparing diversity between two varieties, Cantu said, “About 20 percent of the genome of Zinfandel is different from the genome of Cabernet Sauvignon.” He noted that one gene can make a big difference in grape characteristics. Just one gene accounts for the color difference between Pinot Noir and Pinot Blanc that are actually two selections of the same variety, but produce different varietal wines.

There is also significant diversity between cultivated grape species compared with wild, uncultivated grape species. Researchers are analyzing and comparing genomes to understand domestication of grape species and varieties. Cantu calls this “an exercise that allows us to understand the characteristics of cultivated grapes and how they became more suitable for cultivation.” Cantu said, “Plant domestication is the process whereby wild plants have been evolved into crop plants through human selection.”

He pointed out that cultivated grapes commonly have larger berries and clusters, and different flavors than wild grapes. In addition, flowers on cultivated grapes have both male and female parts, enabling cultivated grapes to be self-pollinating. In contrast, in wild grape populations, male flowers and female flowers are found on separate plants. “We think domestication started about 20,000 years ago, and the use of Vitis vinifera for cultivated grapes began about 8,000 years ago,” Cantu said. 

Cantu’s lab has established a web portal (www.grapegenomics.com) as a central repository for information on grape genomes mapped to date and published papers. The website allows free access to anyone to this information, but it is generally of more interest to geneticists and researchers.  

Reference genomes found on the website for Vitis vinifera varieties include:  Black Corinth, Cabernet Sauvignon, Carmenere, Chardonnay, Merlot, Semillon and Zinfandel.  Genomes available for other grape species are: V. arizonica, and Muscadinia rotundifolia. Genomes are also mapped for four varieties of V. sylvestris, a wild subspecies of V. vinifera that provides an understanding of genetic differences between wild and cultivated grapes. The site also has information on genomes mapped for several common grape fungal pathogens such as Botrytis cinerea, Erysiphe necator (powdery milder), and Eutypa lata. 

Gene Expression as a Vineyard Management Tool

Dr. Marianna Fasoli is a senior manager in the Department of Winegrowing Research with E & J Gallo Winery.  She earned a Ph.D in applied biotechnology in 2012 from the University of Verona in Italy, where she studied grapevine plant molecular mechanisms. She discussed her studies of the molecular basis of grape quality.

At Gallo, she has studied gene expression over several vintages for Cabernet Sauvignon and for Pinot Noir in vineyards during grape development and ripening as a way to track and monitor key quality constituents and pathways. Grape berry samples were collected every ten days starting at pea-size through veraison and up to harvest at standard Brix levels.

Fasoli said this study identified three main “waves of gene expression.” The first wave expressed a gene during early grape development. The second wave showed gene expression near and right after veraison associated with early ripening, fruit softening and beginning of color change. The third wave of gene expression was associated with the completion of ripening and grape maturation. The study identified a specific gene that regulates anthocyanin accumulation.

Fasoli explained: “By tracking gene expression early, we can use this to predict fruit quality. If gene expression can be analyzed early enough, we may be able to use management practices to improve fruit quality at harvest.”  Fasoli suggested that at some point in the future, gene monitoring and analysis tools will be available to employ molecular viticulture in the field during the growing season to monitor and manage fruit quality, much like lab testing is done today to analyze grape and wine chemistry.

Fasoli summarized why we need information about grapevine genomes:

  • Varietal specific genomes are crucial to understanding typicity and varietal traits and their regulation.
  • Available genomes allow a deeper understanding of quality pathways and the effects of the environment and cultural practices.
  • Genomic information facilitates the discovery of new quality marker genes to be employed in “marker assisted breeding” that enables more efficient breeding of new varieties with desired characteristics.

 


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