Volume 2, Issue 3 July 2010

SolCAP Workshop 1

Tomato Consortium 3

SGN-Breeders Portal 4

Interview with

Allen Van Deynze 6

“Spuds Unearthed!” 8

Calendar 13

Inside this issue:

SolCAP

Solanaceae Coordinated

Agricultural Project

Project Headquarters

Michigan State University

A372 Plant and Soil Science

East Lansing, Michigan 48824

SolCAP Newsletter Editor:

Kelly Zarka

Phone:

517-355-0271 Ext. 1-111

E-mail: solcap@msu.edu

Web site: http://solcap.msu.edu

SolCAP to Hold a Hands on Computer

Workshop at PAA Next Month!

In June I attended two conferences: a national eXtension Com-

munity of Practice (CoP) workshop in Austin, TX and the Euro-

pean Association for Potato Research (EAPR) Breeding and

Varietal Assessment section meeting in Wageningen, Nether-

lands. Both meetings intersected with SolCAP research, educa-

tion and extension objectives.

The national eXtension CoP workshop was held in Austin, TX. SolCAP is planning to

launch an eXtension website for our Plant Breeding and Genomics CoP. The workshop was

another timely event to meet and interact with extension people who are engaged in eXten-

sion. There were many valuable sessions such as eXtension Use Study, How to evaluate

and refresh content; Community Certification and Leadership, Engaging the Research

Community (presented by Alex Stone with input from myself on SolCAP); Learning Lessons

from a Pioneer Community of Practice; From Login to Launch, Beyond Text, Marketing,

and Evaluation; Use of Social Media. There was a meeting with (continued on page 2)

Dave D.’s Perspective:

Join us in Corvallis, Oregon, on August 15, 2010 for a free hands on workshop. The

workshop is being held in conjunction with the 94th annual meeting of the Potato Asso-

ciation of America, on the campus of Oregon State University.

Topics include:

1) Working with the Potato genome- C. Robin Buell

(Michigan State University)

2) Working with Infinium genotype data- Allen Van

Deynze (University of California, Davis)

3) Linkage analysis and QTL mapping in tetraploids-

Dr. Christine Hackett (Biomathematics and Statistics

Scotland, Dundee, UK).

Registration for the free SolCAP workshop and the PAA meetings can be found at this

website: http://oregonstate.edu/conferences/event/paa2010/

The tomato community should look forward to a similar workshop being held this year

during the Tomato Disease Workshop on Nov. 16th-18th 2010 at the University of

Florida/IFAS Gulf Coast Research and Education Center in Wimauma, Florida.

PAGE 2 VOLUME 2, I SSUE 3

Dave D.’s Perspective: (continued from page 1)

horticulture-related CoPs during the eXtension CoP Workshop. It was an opportunity for Alex Stone and I to

meet those from Consumer Horticulture, Grapes, Blueberries, Apples, Water Conservation in the Lawn and Land-

scape, and eOrganic. Getting the horticulture-related CoPs together gave us the chance to discuss the challenges to

launching, the long-term sustainability and managing a CoP for our projects.

The EAPR meeting was titled “Potato Breeding after the Completion of the DNA Sequence of the Potato Genome”.

There was a consensus that this meeting was very timely and highly valuable since the draft sequence of the potato

genome was completed this past winter. It brought together 127 scientists from many corners of the world to pre-

sent, listen and discuss current potato breeding and genomics research. Herman van Eck organized this meeting

with the intention of creating an interface of biology and breeding so that useful information flows across this inter-

face. The meeting created the format for the Potato Genome Sequencing Consortium (PGSC) to review and summa-

rize their advances and help the breeding community find ways to exploit this powerful resource. At this time we are

challenged to feed the world with the most important non-grain food crop and provide sustainable production with

less environmental impact. With the advances in sequencing technology and development of genome browsers,

breeders have a new tool to add to potato breeding efforts. With strong dialogue between the breeders (end users)

and the genomicists, we should find creative ways to use this information. One speaker from a private vegetable

seed company said we must become 3rd generation breeders. First generation breeders rely on phenotypic selection

in the field. Second generation breeders are applying marker technology to assist in selection. Many potato breeders

are at this stage or working to achieve this. Third generation breeding is a collaborative breeding by design team

approach that will take advantage of the genomic information, genotyping and phenotyping that bring about new

advances in potato breeding. The SolCAP Infinium 10K potato chip will play a part in bridging the gap between ge-

nomics and breeding.

The SolCAP team would like to extend a thank you to our fellow Solanaceae scientists for joining us in a consortium

through Illumina® to develop a potato array for the interrogation of SNPs in the genome. Approximately 10,000

SNPs are in the final content of a high density genotyping chip. Candidate SNPs were

validated for potato in elite germplasm. The SNPs were identified from Illumina tran-

scriptome sequencing of Atlantic (high solids chip-processor), Snowden (low reducing sugar

storage chip processor) and Premier Russet (low reducing sugar frozen processing) lines.

With the help of the Solanaceae community we have secured the $85 per sample price.

An amazing 3,000 samples were purchased during the time requirement. The next

tier of pricing would have required a 4,032 sample commitment.

In a letter from Cindy Taylor Lawley, the Agriculture Consortia Manager with

Illumina, she applauded SolCAP efforts by 1) providing an excellent characterization

of the potential market for this chip, 2) SolCAP and other sample contributors’ efforts resulted in securing a

24% discount per sample beyond what would have been possible without the consortia, 3) SolCAP was able to

lower the barrier to entry for many institutions, as they were able to access

this tool with only a 48 sample commitment and 4) Illumina saw orders from

each of the three major world regions as well as others from all over the world.

Through this collaborative effort the potato com-

munity is on the way to seeing significant ad-

vances in research. The SolCAP team is cur-

rently finalizing the details for Illumina tomato

bead chip consortium and we are looking for-

ward to working with the tomato community to

collaborate on another successful effort.

Corporate Headquarters

Illumina, Inc.

9865 Towne Centre Drive

San Diego, CA 92121-1975

800.809.4566

SolCAP’s Illumina Potato Bead Chip

Consortium a Huge Success!

PAGE 3 VOLUME 2, I SSUE 3

Invitation to join SolCAP’s Illumina Tomato Bead Chip

Consortium ! The SolCAP team would like to extend an invitation to our fellow Solanaceae scientists to join us in a consortium

through Illumina® to develop a tomato array for the interrogation of SNPs in the genome.

SolCAP's John Hamilton, under the supervision of Robin Buell, has completed SNP calling from the GAII tran-

scriptome sequence data. SolCAP generated sequence data for 4 cultivated varieties, an S. lycopersicum var Cera-

siformae accession and an S. pimpinellifolium accession. A total of 28,380 potential SNPs were identified. Not sur-

prisingly, many of these SNPs were identified between cultivated varieties and the wild accessions. We subse-

quently filtered the SNPs based on frequency of occurrence among the cultivated varieties, and then validated a

subset of the SNPs using highly parallel genotyping of a core collection of varieties and accessions. Our validation

rate was 97%, reflecting a combination of true polymorphisms and assay success. By comparing PM rates within

different market classes we have selected an optimized set of 9,200 SNPs. The number of SNPs expected to be poly-

morphic among cultivated varieties is 6,500; 5,600 among processing varieties; 4,000 among fresh market varieties;

and 3,500 among vintage varieties. At least 3750 of the markers are PM within S. pimpinellifolium and 2,760 are

PM between LA716 and M82. SolCAP is working with research teams in Europe and Illumina to finalize SNP con-

tent and develop a genotyping array that will be available to the tomato breeding and genetics community. Content

for the Tomato SNP array will be finalized over the next several weeks. A summary of the expected SNP content

follows:

Key benefits are offered to participants:

1. Early Access: An opportunity to access a genotyping tool unlike what has been available previously in the to-

mato community.

2. Technology Transfer Opportunity: Part of the mandate of SolCAP is to facilitate the transfer of technology

in the form of genotyping tools into the breeding effort in Solanaceae species. This consortium offers an opportu-

nity to work with experienced SolCAP members to learn the methods associated implementing genotyping methods

into characterizing genetic merit in tomato germplasm.

3. Reduced Pricing. The access to consortium members who participate will be at a consortium price that will be

below that available to contributors working alone. Per sample price of chips includes reagents necessary to run

chips on an iScan or Bead Array Reader. Specialists can facilitate your access to 3rd party service providers to

those participants who do not have immediate access to an Illumina genotyping instrument.

Responsibility of Participants:

Participants are expected to commit to using the chip either by purchasing directly or running samples through a

3rd party testing laboratory. The minimum kit size is suitable to run 48 sam-

ples. It is our experience from the potato consortium that investment of sam-

ples drives stronger and more productive participation in the process.

For further information contact your Illumina sales representative or Illu-

mina's Consortia Manager, Dr. Cindy Taylor Lawley:

llumina, Inc.

25861 Industrial Blvd

Hayward, CA 94545

Tel: 510.670.9478

Category % PM Total Number

Total Number 97% 9,200

Cultivated 70% 6,500

Processing 60% 5,600

Fresh-Market 43% 4,000

Vintage 34% 3,500

S. pimpinellifolium 40% 3,750

M82 x LA716 30% 2,760

PAGE 4 VOLUME 2, I SSUE 3

SGN – a portal to SolCAP data for

biologists and breeders The Sol Genomics Network (SGN, http://solgenomics.net/, figure 1) is a comprehensive database for genomic, genetic,

phenotypic, expression, and metabolic data for the Solanaceae and provides a number of bioinformatic tools to access

and work with these data. SGN is a primary bioinformatic resource for

Solanaceae molecular biologists; in the last couple of years, under the

auspices of the SolCAP project, an ongoing initiative was started to

make the database more attractive to breeders. The data resources on

SGN include genetic maps, markers, experimentally phenotyped loci,

traits, and mutants, and extensive sequence datasets such as BACs,

ESTs, annotated unigene sets, and whole genome sequences for the

tomato reference sequence, potato BACs, and the closest wild relative

of tomato, Solanum pimpinellifolium. Many other Solanaceae are cur-

rently being sequenced and will be available on SGN. Popular tools on

SGN includes homology searches based on BLAST, phylogenetic analy-

sis programs such as an interactive alignment and tree browser, and

genome browsers for accessing the sequence and annotations, and a

comparative map viewer for genetic comparative analyses.

In collaboration with SolCAP breeders, a dedicated portal has been

developed specific for breeders, that can be accessed at

http://solgenomics.net/breeders/ . The portal aims to serve as a one-

stop-shop for bioinformatic tools and datasets on SGN and external

links relevant to breeders. Currently, the portal links to SGN data-

bases describing the phenotypic and genotyping information on plant

lines and populations, marker and mapping data, and the new QTL

tool (http://solgenomics.net/qtl/). The SolCAP project has provided rich phenotypic data for tomato and potato, consisting

of ontology-based annotations and trait values and images of all accessions used. The new QTL tool both works on the

stored QTL populations that have complete phenotypic and genotypic datasets, and user-uploaded data.

The QTL tool is tightly linked with other datasets through

the comparative map viewer and genome browser, which

connects to other maps of the same and other species, and

genome locations on the sequenced genomes, facilitating

the identification of candidate genes responsible for the

QTL and more closely linked markers (Figure 2). The Sol-

CAP project is also generating a large number of SNP

markers and associated genotypic information, which will

be deposited in the SGN SNP database and available

through the breeders portal.

Unlike many other databases, SGN has a community cura-

tion system that allows users from the community to anno-

tate accessions and genes. Presently, over a hundred com-

munity members participate to submit information on

plant accessions and annotations of loci.

(continued on p.5)

Figure 1. The SGN homepage (http://

solgenomics.net/). The homepage was recently

re-designed to make the access to datasets and

tools more intuitive.

Figure 2. An example of mapping output from the

SGN QTL tool (solQTL). QTLs can be calculated on the

fly for data in the database or provided by the user.

This page shows the QTL data for the trait “fruit size”,

including population data, QTL scores on the twelve

chromosomes, and trait distribution data. Users can

upload their own populations and traits.

PAGE 5 VOLUME 2, I SSUE 3

This growing number of users can submit new plant accessions and add information to already stored accessions,

such as images, publications, and ontology descriptors. Community members have contributed to the annotation of

several hundred loci. Each locus can have so-called locus editors who can edit the information on the locus detail

page, add locus descriptions, ontology descriptors, as well as publications, figures and mutant images. Locus editors

are actively solicited by SGN curators by email or at conferences and are usually the world's leading experts with a

strong publication record on the locus in question, and their name is prominently displayed on the locus page; in fact,

the locus page can be understood as a continuously updated review article on that locus. This system helps to main-

tain up to date expert annotations for Solanaceae loci, with comparatively little overhead.

SGN also maintains pathway databases, called SolCyc, that describe the metabolism of Solanaceae plants. These da-

tabases are based on the Pathway Tools software from SRI International (http://bioinformatics.ai.sri.com/ptools/ ) and

are linked from the SGN tools menu or accessible at http://solcyc.solgenomics.net/ . Compounds, enzymes and path-

ways can be queried interactively, and expression and metabolomic data can be analyzed using the Omics viewer

tools.

We encourage you to visit SGN (http://solgenomics.net/ ) and to use the different data resources and tools. If you have

any questions or suggestions, please do not hesitate to email us at sgn-feedback@solgenomics.net , would love to hear

from you!

Wild Potato Germplasm Holds Key to Disease Resistance:

Looking for signs of resistance,

geneticists Dennis Halterman

(left) and Shelley Jansky examine

resistant (being held) and suscep-

tible potato plants that have been

inoculated with Phytophthora in-

festans, the causal agent of late

blight. Photo by Stephen Ausmus.

By Stephanie Yao

Wild potato germplasm that offers resistance to some major potato diseases

has been identified by Agricultural Research Service (ARS) scientists.

Geneticists Dennis Halterman and Shelley Jansky pinpointed the resistant

wild potato species in studies at the ARS Vegetable Crops Research Unit in

Madison, Wis.

Halterman has identified a wild potato species called Solanum verrucosum

that contains a gene with resistance to late blight, considered the most

destructive disease of potato. The wild species can be crossed with cultivated

potatoes, and efforts are under way to move the late-blight resistance gene

into the cultivated potato gene pool. But the scientists aren’t stopping there.

They are using S. verrucosum to create a potato that’s resistant to both late

blight and early blight, a fungal disease that primarily affects the potato

plant’s leaves and stems but, if left uncontrolled, can lead to considerable

reductions in yields.

To create the multi-disease-resistant cultivar, the scientists crossed S. ver-

rucosum with another wild potato species that is resistant to early blight,

and then crossed the wild potato hybrid with the cultivated potato. They

currently have seedlings in the greenhouse waiting to be tested in the field.

Halterman and Jansky are also looking for resistance to Verticillium wilt,

another fungal disease that can linger in the soil for up to 10 years. Halter-

man developed a molecular marker to screen potato germplasm for resis-

tance against this disease, saving the scientists time and effort. They found

resistance in the wild potato species S. chacoense and crossed it with the

cultivated potato. According to Halterman, this could be a good, durable

gene that may hold up over the long term.

The scientists’ studies have been published in Physiological and Molecular

Plant Pathology, Molecular Breeding and the American Journal of Potato

Research.

PAGE 6 VOLUME 2, I SSUE 3

In our last issue (SolCAP-March 2010) we highlighted The Seed Biotechnology Center (SBC). In this issue we would

like to continue with an interview with SolCAP’s co-Director and the director of research at SBC, Dr. Allen Van

Deynze.

This is an interview by DNA LandMarks and Dr. Allen Van Deynze,

Professional Researcher, University of California, Seed Biotechnol-

ogy Center for SeedQuest. DNA Landmarks is a world leader in

providing marker-assisted breeding services.

Dr. Allen Van Deynze is a molecular geneticist and a Profes-

sional Researcher at the Seed Biotechnology Center at the Uni-

versity of California Davis. We asked him for his thoughts on

the opportunities currently provided by marker-assisted breed-

ing technologies and where this field will take us in the future.

How long have you been in the field of molecular breed-

ing?

I’ve been doing it since 1989 with RFLPs

In that time what are some of the biggest changes you've

seen?

The biggest changes were conversion to PCR markers and now

beyond, RAPDs in early 1990s, Simple Sequence repeats in mid

1990s and SNPs in late 1990s. This still made technologies accessible only to major crops. The biggest change in the

last 3 years is sequencing technology that makes markers available to any organism, coupled with datapoints in the

pennies range.

Given the power of the genomic technology available today where do you see some of the most signifi-

cant applications of molecular breeding?

As mentioned above, sequencing technology has enabled us to sequence parents and in the near future populations

such that we are can truly use genome assisted breeding vs following simple marker associations to major loci. The

major change is that we can do denovo marker/quantitative trait loci (QTL) analysis on every population vs just the

most important ones. Breeders can have access to the full genotype of plants to combine with breeding value at the

phenotypic level. They can also understand the allelic makeup (heterozygous or homozygous at key loci) and begin to

understand what genes control complex traits. The current throughput of technologies allows breeders and geneticists

to accumulate data on 1000’s of individuals in days to weeks. The challenge is to handle the data.

For a long time, GMO technology has received the most attention (good and bad) in regards to crop bio-

technology while genomics has held a lower profile. Is this changing?

The media has amazing power regardless of how good or bad a technology is. Unfortunately, too often the flashy

alarming, yet scientifically not credible stories get promoted and published by groups with ulterior motives. Fortu-

nately, this is rarely the case with genomics and it is viewed very positively in media. Who doesn’t think it is cool that

a mass murderer can be instantly identified and convicted with a cheek swab, a small fragment of a hair on a crime

victim and a good database in less than 1 hour. Programs like CSI do it every week and have given the general public

a flavor of the benefits of technology like genomics. Ok it is not that fast, but the general methodology and capability

is correct. This is exactly what marker-assisted breeding does in plants---use DNA from plants to create and query

large databases of genetic data combined with trait data to decide which plants are likely to give us the best quality,

yield, resistances etc.

Given the significant investments by large, multinational ag biotech companies, where do academic in-

stitutions such as UC Davis fit into the R&D picture?

Highlight On: The Seed Biotechnology Center: Part 2

Dr. Allen Van Deynze, Director of Research, Seed

Biotechnology Center. Photo credit: Jeannette

Martins, Seed Biotechnology Center.

PAGE 7 VOLUME 2, I SSUE 3

Universities are very good at doing research and creating knowledge whereas large multinationals are very good at com-

mercializing products and implementing technologies. UC Davis is pioneering many of the applications and even the

genomics technologies themselves. Our strength comes in numbers. We have over 100 plant scientists on campus and

have access to the latest technologies through facilities such as our centralized Genome Center. I believe UC Davis plays

a central role in developing the biology to understand gene networks and what controls plant traits at the whole plant

level across dozens of crop species. Our capacity to analyze the huge volumes of data on comparative genomics – using

information from one species to understand others – is equal or larger than most multinationals. Basically, UC Davis

and many other public institutions are populating the biological databases across many organisms that enables marker

or genome assisted breeding. With over 200 plant commodities in California, we work closely with large and small

breeding companies to ensure we are working on the most relevant germplasm and that our research is integrated with

the seed industry.

What should medium-sized breeding companies be focusing on to

keep pace with their larger competitors?

As any seed company CEO will tell you, germplasm (plant varieties) is the

most important asset. Developing the best germplasm in most cost-effective

and efficient way is now even more important. There are few crop varieties

that last more than 3-5 years in most major crops anymore due to increased

investment in plant breeding. Furthermore the first company out with a

new trait, such as disease resistance, quality etc gets the lion’s share.

Marker assisted breeding can decrease breeding times from 8-10 years to 4-

5 years for a variety. Only in the last few years or so has it become cost

efficient for medium sized companies to fully use marker assisted selection

and whole genome selection on all their crosses vs just the few most impor-

tant ones. The challenge with marker-assisted selection is that there are

dozens of different technologies, with various, cost of reagents, throughput

and capital costs. Generally, cost per sample goes down with volume and

having a medium number of samples with a medium number of markers is

the most expensive. The best systems are flexible and allow one to choose a

different set of markers for every cross or population. This is critical as only

a small subset of the markers are informative in a given population. These

systems are becoming

more and more affordable. Another question for a traditional breeding com-

pany, is should I invest in my own lab and personnel to run markers, or

should out-source it. There are several service companies that have

decades of experience in applying markers to breeding. These are a great

choice to get started and establish marker assisted programs as the breed-

ing company does not need to make capital and personnel investments and accesses experienced personnel directly.

Most often the service companies either already have markers for your favorite crop or can develop them specifically for

a breeding company’s germplasm. As the service company must also make a profit, the cost of marker-assisted selection

is higher. As a company, one must weigh the cost of the capital investment, depreciation and experienced personnel with

the higher cost per data point through a service company. In my opinion, marker-assisted breeding is traditional breed-

ing now and is absolutely required to be in business, big or small. Breeders can now select on traits (phenotype) and

genotype and make more informed selections.

What will breeding with molecular markers look like 5 years from now? How about 10 years from now?

Hmm, 5 years, It will be integrated in all breeding programs, big and small at some level. We will shift from anonymous

markers to those controlling genes. We will be challenged with the huge volumes of data to analyze. In 10 years, we will

be using genome (as opposed to marker assisted breeding) assisted breeding and have the sequence of individuals in

every cross and have markers that represent the causative mutation for all major traits i.e. diagnostic. As breeders,

though, we still won’t be able to predict yield, but be very good at tracking it in every cross. Marker (genome)-assisted

selection is a powerful tool in breeding, but, we will always need breeding and breeders and always need to test varieties

in the field.

Copyright © SeedQuest - All rights reserved

DNA Landmarks is a world leader in providing marker-assisted breeding services.

Tomato Breeding; Seed Biotechnology Cen-

ter. Photo credit: Jeannette Martins.

PAGE 8 VOLUME 2, I SSUE 3

Spud’s Unearthed at the United States Botanic

Garden in Washington D.C.

The United States Botanic Garden’s East Garden is featuring an exhibition of special interest to us. It is called

“Spud’s Unearthed” and provides visitors an interesting tour of the 7,000 year history of the potato as well as

delving into potato science and research. The origins of this exhibit start with SolCAP’s very own Dr. C. Robin

Buell. She is one of the scientists involved in “The Potato Genome Sequencing Consortium” (PGSC). A compo-

nent of the PBSC grant, which supports 16 research groups from 13 countries, is education outreach. In an ef-

fort to enlighten the public on the importance of research funding not only for potatoes but agriculture in gen-

eral, Buell, along with Michigan State University

(MSU) potato breeder (our SolCAP co-director), Dr.

David Douches, collaborated with the United States

Botanic Garden. Visitors to the USBG, which is located

at 100 Maryland Ave., Washington D.C. just west of

the Capitol Building, will gain a wealth of knowledge

and be entertained as well.

The exhibit is focused with the general public in mind.

There are several sections of the exhibit ensuring that

there is something that will appeal to just about every-

one. Sections in the exhibit are named “Delicious”,

“Playful”, “Well Traveled”, “The Potato Genome Pro-

ject” and “Living and Growing”. The founders of the

privately owned “Potato Museum”, Tom and Meredith

Hughes generously collaborated with the USBG by

displaying some of their wide collection of artifacts and

entertaining memorabilia. The living and growing

section of the exhibit features an aeroponic potato

growing display which was designed and built by Jo-

seph Coombs and Greg Steere (scientists in Douches’

Potato Research Program). Visitors are able to see po-

tatoes forming right before there eyes. Kelly Zarka (SolCAP project assistant and scientist in Douches’ Re-

search Program) along with David Douches prepared a potato growing guide handout so visitors can “unearth”

their own spuds at home. The Delicious section provides information on the nutritional benefits of the potato

as well as showing the culinary point of view over the years.

(Continued on page 9)

The United States Botanic Garden is located just steps

from the Capitol Building. Photo credit: United States

Botanic Garden.

“Spuds Unearthed” exhibit at the United States Bo-

tanic Garden. Photo credit: United States Botanic

Garden.

The Delicious section of “Spud’s Unearthed”. Photo Credit:

United States Botanic Garden.

PAGE 9 VOLUME 2, I SSUE 3

The “Spuds Unearthed” exhibit features some demon-

strations both in indoor and outdoor settings as well

as having some guest scientists for a lecture series.

Currently lectures are scheduled for July 29 at

11:00am “CSI Dublin: Hunt for the Irish Potato Kil-

ler”, 1:30pm “Potatoes: Tasty and Healthy” and July

30 a pair of lectures including “U.S. Potato Gene-

bank: Service and Research for Potato Genetic Im-

provement” at 11:00am and Robin Buell will discuss

in language and concepts for a general audience, “The

Potato Genome Initiative” at 1:30pm. More events

will be scheduled for later this summer and fall.

The “Spuds Unearthed” exhibit runs from May 8th

through October 11, 2010. The exhibit as well as ad-

mission to the Botanic Garden is FREE and open

from 10:00am to 5:00pm. For more information on

the United States Botanic garden visit their website

at http://www.usbg.gov/

4th Annual National Plant Breeding Meeting

The annual meeting of the National Association of Plant Breeders (NAPB), an initiative of the Plant Breeding

Coordinating Committee (PBCC) will be held August 15-17, 2010, at Pioneer Hi-Bred’s headquarters in Johns-

ton, Iowa. The PBCC serves as a forum for issues and opportunities of na-

tional and global importance to the public and private sectors of the U.S.

national plant breeding effort. The meeting will begin at noon on Sunday,

August 15, and conclude Tuesday afternoon, August 17.

The meeting has three goals: 1) to discuss strategies to shape the future of

plant breeding, 2) to expose participants to state-of-the-art plant breeding

research through invited speakers, and 3) to exchange knowledge through

poster presentations by participants.

On the afternoon of August 17, there will be a career session available for

graduate/undergraduate students at the Pioneer facilities. More information about other post-conference ac-

tivities will be provided in future meeting announcements. Central Iowa, where Johnston is located, is home to

a number of other public and private plant breeding programs. Participants may wish to make independent

arrangements to visit these while they are in the area.

All plant breeders – student and professional, public sector and industry, U.S. and abroad – are encouraged to

attend. Please see the meeting web page at http://cuke.hort.ncsu.edu/gpb/meetings/pbccmeeting2010.html to

register on-line.

An information panel in the “Potato Genome Project” section

of “Spud’s Unearthed”. Photo Credit: Dr. C. Robin Buell

PAGE 10 VOLUME 2, I SSUE 3

The next best thing: Does Jay Scott hold the future

of decent store-bought tomatoes in his hands?

By Barry Estabrook

John "Jay" Scott, a horticulture professor and tomato breeder at the University of Florida's Gulf Coast Research and

Education Center outside Tampa, developed the Tasti-Lee, a tomato variety intended to be perfect for commercial pro-

duction.

In supermarket tomatodom, this is the Holy Grail: a fruit thick-skinned enough to shrug off the insults of modern agri-

business, but still tender at heart and tasting like, well, a tomato. And John "Jay" Scott might have discovered it.

Scott is a horticulture professor and tomato breeder at the University of Florida's Gulf Coast Research and Education

Center outside Tampa. For more than a decade, he has worked to perfect a tomato variety called Tasti-Lee. This

spring, Tasti-Lee left the rarefied confines of academic test plots and rigorously monitored consumer-tasting panels to

make its way in the competitive hurly-burly of Florida's $619 million tomato industry. The state produces about half of

the fresh tomatoes grown in the United States; between October and June, virtually all fresh, field-grown tomatoes

come from Florida. The high-stakes business is littered with once-

promising but now-forgotten tomato varieties.

If Tasti-Lee lives up to its early promise, Scott, who has bred between 30

and 40 new tomato varieties ("I haven't gone back and counted in a while")

over nearly four decades, will achieve a plant breeder's version of immor-

tality. And the rest of us finally will be able to head to the local supermar-

ket any day of the year and bring home a nutritious, decent-tasting to-

mato.

Scott, 61, is aware that mere mention of winter tomatoes being trucked

north from Florida is anathema to locavores, but he's also a realist.

"Consumers tend to be spoiled," he said. "They go into the grocery store

and they expect to see fresh tomatoes any time of year, even if they grum-

ble about the quality. I want people to buy Tasti-Lees because they like

them, not just because they are the only tomatoes there."

During the warmer months, large-scale fresh, field-grown tomato production

migrates north from southern Florida to the state's panhandle, through the

Carolinas and as far as New Jersey. In the depths of winter, Mexico supplies

fresh tomatoes to the United States.

These commodity fruits are the workhorses of the tomato trade, always in the local supermarket and a mainstay of

chain restaurants, where they are chopped into salsa, tossed into prepared salads and slipped between hamburger

buns. Increasingly, they find themselves sharing produce-counter space with branded, on-vine fruits grown in green-

houses in all parts of the country as well as new hybrids such as the trademarked UglyRipe, which looks (and, produc-

ers claim, tastes) like beloved heirloom varieties. These newcomers cost four times as much as commodity tomatoes.

Tasti-Lee is designed to give commodity farmers a tomato that can compete in this premium market.

Like many plant varieties, Tasti-Lee owes its existence to a combination of serendipity and the keen eye of an experi-

enced plant breeder. In Florida, the summer of 1998 was a terrible season for anyone trying to grow a tasty tomato,

Scott said. For some unknown reason -- too wet, too cloudy, too hot? -- Scott's tomato field tests, which included hun-

dreds of genetic lines, failed to produce fruits with any sweetness. Even varieties that had been sweet in previous

years tasted bland. But one morning while out in the field, Scott spotted a nice-looking tomato called Fla. 7907. He

picked a fruit, took out his pocket knife, cut off a wedge and popped it into his mouth. "Aha!" he said.

It was sweet, but Fla. 7907 had one big flaw that made it a non-starter for commercial production: It was almost per-

fectly spherical. The industry demands tomatoes with flattened tops and bottoms that can be picked green, sorted on a

conveyor belt, gassed with ethylene until they acquire the desired red-orange hue, and trucked for hundreds of miles,

the path a typical fresh Florida tomato takes to market.

John “Jay” Scott’s Tasti-Lee is being test

marketed. Photo: Courtesy of Tomato

Breeding Program at Florida State Uni-

versity.

PAGE 11 VOLUME 2, I SSUE 3

Not only do commercial tomatoes have to be the right shape, but they also have to be hard, and 7907 was softer than

most agribusiness tomatoes. To be successful, such varieties also must produce high yields of large, uniform fruit.

They have to be able to resist diseases and tolerate extremes of heat and cold. And they need to have a long shelf life,

according to Scott."Sometimes I wonder why we even bother with flavor," Scott said in an interview last month in his

office, a cramped space filled with all manner of tomato-related kitsch: tomato-shaped coffee mugs, framed antique

tomato-crate labels, a vintage advertisement for Campbell's tomato soup, a dog-eared stack of Tomato Magazines.

"There is no easy way to breed for taste. It's not like there's one genetic marker that tomatoes must have to taste

good," he said. Tomato flavor, Scott explained, is the result of the interplay of acids (primarily citric and malic),

sugars and the ephemeral scents of 15 to 20 volatiles, the term for chemicals that can be smelled.

The structure of a tomato makes breeding for both taste and toughness a difficult balancing act. The gooey part of a

tomato, called locular jelly, contains most of the all-important acidity, Scott said. The pericarp tissue, the walls of a

tomato, give it strength and sweetness, but no acidity. The harder a tomato is, the blander it is likely to taste.

Fortunately, Scott was also developing a line of what he calls "ultra-firm" tomatoes. Among those was one called Fla.

8059. It was hard, with the right shape and a perfectly acceptable flavor. Sensing a match made in heaven, Scott

crossbred the sweet but soft and spherical 7907 with the harder 8059, and in the fall of 2002, the first of what was

then referred to as Fla. 8153 ripened. Scott thought the new hybrid carried the best traits of both parents. At trials

conducted by the university, consumers on test panels agreed. Time after time, 8153 beat other tomatoes.

Subsequent chemical analyses showed that the fruit had a desirable balance of sugars, acids and volatiles. It also had

an unplanned-for bonus: Both of its parents possessed what Scott calls the crimson gene, giving 8153 a striking fire-

engine-red color and an extraordinarily high level of lycopene, an important antioxidant. "It sounds like magic,

doesn't it?" said Scott. "It really is, in a way."

Good-looking, good-tasting and good for you, Fla. 8153 had everything going for it except for a catchy, appetizing

name. Scott christened and trademarked his new baby Tasti-Lee, Lee being the first name of his mother-in-law, a

tomato lover who had encouraged and supported his research. After four seasons of field trials and consumer tests

confirmed that Tasti-Lee wasn't just a one-season

wonder, the variety was ready for its commercial

debut.

Four seed companies bid to buy the rights to

produce and distribute Tasti-Lee seeds. The

university chose Bejo Seeds. A large, family-

owned Dutch firm with offices around the world,

Bejo specializes in cabbage, carrots and other cool

-weather crops. "We felt that marketing would be

a key to Tasti-Lee's success," said Scott. "It

seemed like Bejo would be hungry to get into the

tomato market and that they would push Tasti-

Lee pretty hard." The job of giving Tasti-Lee that

push fell to Greg Styers, Bejo's sales and product

development manager for the southeastern

United States. "We had a vision to start with a

grass-roots movement," Styers said. He approached

Whitworth Farms, which grows vegetables on 700 acres near Boca Raton; it's a small player in the Florida tomato

business, which is dominated by a few huge companies. "Whitworth was big enough to deal with some large retailers

but small enough that they were willing to take a chance on Tasti-Lee," Styers said.

One of Whitworth's customers was Whole Foods Market. Glen Whitworth, who owns the farm along with his sister

and two brothers, approached one of the company's produce buyers, who agreed to test-market Tasti-Lee. In

February it began appearing in 16 Whole Foods stores in Florida. "With Tasti-Lee, we are trying to compete with

hothouse tomatoes," Whitworth said.

"Tasti-Lees are born to be sold as a premium tomato," said Styers. Instead of being picked "mature green" and gassed

with ethylene, Tasti-Lees are picked when they are first blushing pink and allowed to ripen naturally. In the produce

section, they have their own PLU code and bear stickers identifying them by name. They were selling for $3.99 a

pound at the Florida Whole Foods stores in March. At a competing supermarket, commodity tomatoes cost only 99

cents a pound.

Continued on page 12

Tasti-Lee tomato variety. Photo: Courtesy of Bejo seeds.

Like all retail chains, Whole Foods plays its cards close to its chest. Reached by telephone and then e-mail, the

company declined to comment on how Tasti-Lee was doing. But by late March, reorders were coming in faster

than Whitworth could grow Tasti-Lees, according to Styers. "I think the stars really lined up for Jay when he

developed this variety. It truly is remarkable."

Scott, who drawls his carefully chosen words with little inflection and almost no emotion, didn't go that far. "I

stand behind it," he said. "For a full-size tomato, it's better in my opinion than what's out there. Hopefully, it

goes."

If it doesn't, Scott has plenty to keep him busy. He's now developing heat-tolerant tomatoes, tomatoes with re-

sistance to a virulent leaf-curl virus, and tomatoes that can be grown on the ground and, theoretically, har-

vested by machine.

And he hasn't given up on flavor. "In some work we've done, there is this fruity-floral note that adds pique to

the sweetness," he said. "We've crossed a big, crimson tomato with that trait into one of Tasti-Lee's parents. The

result is even better-tasting. The trick now is to improve size, firmness and yields with further crossing."

Estabrook, former contributing editor at Gourmet magazine, lives in Vermont. He can be reached through his

Web site, http://www.politicsoftheplate.com.

PAGE 12 VOLUME 2, I SSUE 3

Bunol, Spain. Every year on the last Wednesday of August,

more then 40,000 people gather in the small town of Bunol,

Spain for a good-natured battle. The objective is to throw tons

of ripe tomatoes at each other filling the streets of this Span-

ish town with rivers of red pulp. In 2009, 100 tons of toma-

toes were used and people from as far away as Japan and

Australia, joined in on the food fight known as the "La To-

matina," now in its 64th year. The week-long festival features

music, parades, dancing, and fireworks. On the night before

the tomato fight, participants of the festival compete in a pa-

ella cooking contest. The tomatoes start to fly at 11am the

next morning and continue until 1pm. The cleaning process

involves the use of fire trucks to spray down the streets, with

water provided from a Roman aqueduct. Personally I would

rather eat tomatoes than wear them.

Fun Facts:

Tomatoes fly everywhere as people pelt each

other during the world's biggest tomato fight

at La Tomatina festival in Bunol, Spain.

Getty Images / Jasper Juinen

May 8 – October 11, 2010, “Spuds Unearthed”. East Gallery, United

States Botanic Garden. Washington D.C. Contributions to this ex-

hibit were made by SolCAP participants: Robin Buell, David Douches

and Kelly Zarka.

Aug. 2-5 2010, American Society of Horticultural Science Annual

Meeting, Desert Springs JW Marriott Resort & Spa Palm Desert,

California

August 15 - 19, 2010 Potato Association of America 94th Annual Meeting, Corvallis, Oregon.

http://potatoassociation.org Be sure to sign up for the SolCAP hands on computer workshop.

August 15-17, 2010 National Association of Plant Breeders (NAPB), an initiative of the

Plant Breeding Coordinating Committee (PBCC) at Pioneer Hi-Bred’s headquarters

in Johnston, Iowa.

Sept. 5-9th, 2010, The 7th Annual Solanaceae Conference, Dundee, Scotland. http://

www.sol2010.org/ (Note: SolCAP will be presenting)

Nov. 16th-18th 2010, The Tomato Disease Workshop, University of Florida/IFAS Gulf Coast

Research and Education Center, Wimauma, Florida. Be sure to sign up for a SolCAP work-

shop!

Jan. 15-19, 2011 Plant and Animal Genomics (PAG), Town and Country Resort, San Diego,

CA. SolCAP’s annual meeting will be scheduled soon in conjunction with this conference.

March 20-23, 2011, 43rd Tomato Breeders Roundtable, El Cid Resort, Mazatlan, Mexico. Be

sure to sign up for a SolCAP workshop.

Calendar of Events:

SolCAP

Solanaceae Coordinated Agricultural Project

Michigan State University

A372 Plant and Soil Science Building

East Lansing, Michigan 48824

SolCAP Newsletter Editor:

Kelly Zarka

Phone: 517-355-0271 Ext. 1-111

Visit us on the web:

http://solcap.msu.edu

PAGE 13 VOLUME 2, I SSUE 3

This project is supported by the Agriculture and Food Research Initia-

tive (AFRI) of USDA’s National Institute of Food and Agriculture

(NIFA)