Grape mapping populations reveal genetic variation in bloom and fruit development

by Tim Martinson, Al Kovaleski, and Bruce Reisch

On June 29, I photographed clusters from Bruce Reisch’s three Vitisgen mapping populations. Parents are Cornell hybrid cultivar Horizon (with perfect flowers), Illinois 547-1 (a male vine),  Vitis cinerea (late blooming male vine) and Vitis rupestris (early blooming, a female vine).  Note that ‘Horizon’ and V. rupestris had pea-sized berries and V. cinerea had not yet started to bloom.  Illinois 547-1 blooms earlier than V. cinerea and later than V. rupestris, but produces  no fruit.

Parents of three grape mapping populations


Mapping population #1:
Vitis rupestris x Horizon (planted in 2010).  Progeny of this cross bloomed early and fruit on these vines were uniformly at the ‘pea-sized’ berry stage.
Pictures of progeny of V. rupestris x Horizon


Mapping population #2:
 Horizon x Vitis cinerea (planted in 2011).  Progeny of this cross exhibited delayed bloom and cluster development -clusters were at prebloom to early fruit set, generally earlier blooming than the V. cinerea parent.
Horizon x Vitis cinerea progeny


Mapping population #3:
Horizon x Illinois 547-1 was established in 1990 and 1998.  Illinois 547-1 is the progeny of two wild parents used in mapping populations 1 and 2, Vitis cinerea and Vitis rupestris.  Fruit development on the ~150 siblings ranged from bloom to ‘pea-sized’ berries.  This family of sibling vines flowered over a long period of time, from early June to early July.
Photos of 4 sibling progeny of Horizon x Illinois 547-1

 

I went back and collected more clusters of both the parents and the progeny on July 6.

The parents: By July 6, the rachises of the male flowers (Ill. 547-1 and V. cinerea) were starting to wither away. The female V. rupestris B38 and the ‘perfect-flowered’ cultivar Horizon had fully-formed clusters with ‘pea-sized’ fruit.
Clusters of four parents of mapping populations, "Horizon", V. rupestris, V. cinerea, and Ill. 547-1


The progeny from three mapping populations: 
On July 6, I selected clusters from 5 siblings of the V. rupestris x Horizon population (left, pea-sized berries), the Horizon x Ill. 547-1 population (center, a range of sizes and male inflorescences) and the Horizon x V. cinerea population (right, flowering to BB-sized berries).

Clusters of 4-5 siblings of Horizon x Ill. 547, V. rupestris x Horizon, and Horizon x V. cinerea

The three mapping populations illustrate clear differences in the timing of bloom and subsequent fruit development.  Horizon crossed with V. rupestris showed advanced bloom and fruit development phenology, while Horizon crossed with V. cinerea showed delayed bloom and fruit development.  The Horizon x Ill. 547-1 population (with both V. cinerea and V. rupestris grandparents)  exhibited a whole range of bloom and berry development phenotypes.

Tracking bloom progression: Students from the Cornell AgriTech summer scholar program (Abe Steinberger and Hannah Levengood) and former graduate student Al Kovaleski collected observations every few days on the three mapping populations.  They recorded floral development on 171 V. rupestris x Horizon, 314 Horizon x Ill. 547-1 and 141 Horizon x V. cinerea vines, using the well-known “Eichhorn-Lorenz” (E-L) grapevine phenology index.  Dr. Al Kovaleski plotted curves derived from these observations from Stage 18, when floral caps start changing color prior to bloom, to Stage 26, when 100% of the flowers are open.  The bloom progression is plotted against cumulative growing degree-days (GDD).

Graph showing progression of bloom in V. rupestrisxHorizon, Horizonx Ill. 547, and Horizon x V. cinerea

The individual lines show the segregation of these F1 siblings both within each mapping population and clear differences between the three mapping populations.  The V. rupestris x Horizon vines bloom early and fast (with 50% bloom occurring over 25 GDD or approximately 1-2 d),  the Horizon x V. cinerea vines bloom late, and over a more extended time period, and the Horizon x Ill. 547-1 siblings are right in the middle.

Based on 2-3 years of flowering time data in these populations, the VitisGen2 project is  developing information on the locations in the grape genome that are responsible for controlling flowering time.  Note that Ill. 547-1 is itself a hybrid of two wild vines:  V. cinerea and V. rupestris, while “Horizon” is a commercial variety with ‘Seyval blanc’ and ‘Schuyler’ in its background.

Tim Martinson is senior extension associate and Bruce Reisch is professor in the horticulture section, based at Cornell Agritech in Geneva, NY.  Al Kovaleski is currently completing a  post-doctoral fellowship at the Arnold Arboretum of Harvard University.

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Getting the Perfect Cluster Shape: Defining Table & Wine Grape Traits with DNA Markers

Two parents MN1246 and MN1264 used to make mapping populations for cluster architecture and colorGetting the Perfect Cluster Shape: Defining Table & Wine Grape Traits with DNA Markers
USDA Scientist Rachel Naegele,  UM professor Matt Clark, and Cornell Extension Associate Tim Martinson describe how image analysis is being used in the VitisGen2 project on mapping populations of table grape selections in California and wine grape accessions in Minnesota to find genetic markers for cluster architecture and color attributes.

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“Research in Plain English” Article on Grape Color

The new “Research In Plain English” is available now : “Quantifying grape color

VitisGen2 team member Anna Underhill researched a digital image analysis technique to quantify the color of grapes and then found the associated genetic regions. Working with an F1 population parented by both a noir and a non-noir grape, Anna had a well-segregated population on which to conduct her investigation.

Evaluating and mapping grape color using image-based phenotyping. Authors: Anna Underhill, Cory Hirsch, Matthew Clark
Plant Phenomics, 2020, Article ID 8086309.

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Anne Fennell named Distinguished Professor!

Dr. Anne Fennell recognized for numerous research contributions Professor Anne Fennell's headshot

A primary investigator and member of the VitisGen2 breeding and genetics teams, Anne was named as a distinguished professor at the SDSU’s annual Celebration of Faculty Excellence.

Read more about the event and Anne’s accomplishments here

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Grape Selections from the VitisGen and VitisGen2 Projects

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.

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International collaboration advances research into grape disease resistance

Daniel Zendler

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“.

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Staff spotlight with new project manager, Ugo Ikeogu

Ugo IkeoguWe 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!

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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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