CONSERVATION AND UTILIZATION OF GERMPLASM AT THE C.M. RICK TOMATO GENETICS RESOURCE CENTER

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1013392
• Project Start Date: Oct 1, 2017
• Project End Date: Sep 30, 2022
• Program Code: [(N/A)]- (N/A)

Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671

Performing Department
Plant Sciences

Non Technical Summary
This project supports the mission of the Agricultural Experiment Station by providing access to genetic resources needed for future improvement in the tomato crop. The TGRC is heavily used by plant breeders as a source of genetic traits. Examples of traits obtained from TGRC stocks that benefit the industry include resistance to diseases such as Fusarium wilt (race 3), Tomato Yellow Leafcurl Virus, and powdery mildew, as well as increased soluble solids content. In many growing regions tomatoes could not be grown economically without these and other disease resistances. Development of tomato varieties with improved drought tolerance would support water conservation goals. Genetic resistance supports agricultural sustainability by providing ecologically benign methods for controlling pests and diseases. Human nutrition is addressed by developing tomatoes with increased nutrient content and/or flavor. Molecular biology and biotechnology methods are used in this project to develop new sources of germplasm for tomato research and breeding, and to better understand crossing barriers that impede breeding efforts. For example, a better understanding of self-incompatibility mechanisms in tomato could be applied to potato where breeding of high yielding diploid cultivars is currently hampered by a lack of self-compatible inbred lines. Introgression of the previously inaccessible S. sitiens genome will provide access to novel traits not currently available in the genepool of cultivated tomato.

Animal Health Component

75%

Research Effort Categories

Basic

25%

Applied

75%

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1460	1080	15%
202	1460	1080	50%
206	1460	1040	15%
206	1460	1081	20%

Knowledge Area
206 - Basic Plant Biology; 202 - Plant Genetic Resources; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1460 - Tomato;

Field Of Science
1040 - Molecular biology; 1081 - Breeding; 1080 - Genetics;

Keywords

tomato

solanum lycopersicum

solanum sitiens

genetic resources

self-inompatibilty

interspecific incompatibilty

introgression

marker assisted selection

Goals / Objectives
Objectives:1. Acquire, maintain, evaluate, distribute and document tomato genetic resources. 2. Study the molecular genetic basis for interspecific reproductive barriers in Solanum and their relationship to self-incompatibility. 3. Develop a 'library' of S. sitiens introgression lines in cultivated tomato and evaluate these lines for novel traits.The primary goal of this project is to carry out the essential functions of the C.M. Rick Tomato Genetics Resource Center (TGRC), a genebank of tomato wild species, mutants, and other genetic stocks of tomato. The TGRC is a national and international resource for breeders, researchers and educators who use tomato. Many of it's ca. 4,500 accessions are unique and maintained nowhere else. The TGRC developed as a by-product of tomato research at UC Davis, and the genebank continues to be closely tied to active research research projects. One of these projects aims to decipher the molecular mechanisms of pollen rejection in inter- and intraspecific incompatibility. Using the tomato species as experimental tools, this research seeks to identify specific genes and molecular pathways controlling pollen-pistil interactions. Another research objective is to manipulate these reproductive barriers in order to transfer the genome of the previously inaccessible wild nightshade, Solanum sitiens, into cultivated tomato. This will be accomplished by synthesis of a series of introgression lines, each containing a single wild species chromosome segment, defined by markers, in tomato.

Project Methods
The methods used by the TGRC for the acquisition, maintenance, evaluation, distribution, and documentation of its germplasm are standard for genebanks. New stocks are acquired or developed through in-house research, transfers from other genebanks, or donations from other scientists. Germplasm maintenance involves seed germination testing, seed multiplication in field or greenhouse, and seed storage and backup. Refractory materials, such as lethal or sterile mutants, self-incompatible and/or photoperiod-sensitive wild species, etc., require appropriate treatments for satisfactory multiplication. Population sizes for reproduction of the wild species are based on their intrinsic genetic variability, as well as available space and resources. Careful and frequent plant observations are necessary to confirm trueness to type and purity, and to identify accidental outcrosses, mix-ups or other problems. New wild accessions are evaluated for key morphological traits, mating systems (outcrossing, facultative or inbreeding), and evidence of genetic variability. Certain prebred stocks require molecular marker analysis during each regeneration cycle. In addition, feedback from users of the collection is taken into account. The TGRC distributes seed samples upon request to interested scientists to facilitate research and breeding projects involving tomato. Each year, the TGRC distributes over 5,000 seed samples in response to ~300 requests from ~200 investigators in over 30 countries. In addition, many informational requests are answered each year. Documentation of the collection is via the TGRC website (http://tgrc.ucdavis.edu), which provides access to: lists of available stocks, our database of accessions, mutant genes, images and contacts, seed request submission procedures, horticultural guidelines and other resources. The reproductive barriers being studied are those that act prior to fertilization, and include self- and interspecific incompatibililty. Expression of these barriers is assessed by controlled crosses between species or genotypes, using fluorescence microscopy to visualize pollen tube growth within selective pistils. Genes are isolated by map-based cloning, homology search, and candidate gene methods. Transgene constructs -- CRISPR-Cas9, RNAi -- are used to assess gene function. Transgenic tomato plants are obtained by Agrobacterium transformation and are grown under isolation in the greenhouse.Synthesis of S. sitiens introgression lines in cultivated tomato involves standard hybridization methods combined with molecular genotyping and sequencing. Selected lines are self-pollinated to produce homozygous (stable) stocks.

Progress 10/01/19 to 09/30/20

Outputs
Target Audience:Our target audience includes academic and commercial researchers, plant breeders, biotechnologists, USDA staff (germplasm curators, research leaders, administrators), educators, and graduate and undergraduate students. We reach them through our publications, presentations, lectures, outreach, internships, and the TGRC website, https://tgrc.ucdavis.edu. In addition, we extend knowledge to the broader public through education and outreach efforts. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?One undergraduate student and a visiting researcher from Japan completed internships to gain knowledge and experience in tomato genetic resources, Mendelian genetics, and/or the use of molecular markers. Four undergraduate student employees gained training and experience in seed technology (germination testing, seed cleaning and packaging, etc) and horticultural practices in the field and greenhouse. How have the results been disseminated to communities of interest?Results were disseminated through publications, stock lists, the TGRC website (https://tgrc.ucdavis.edu), presentations, tours, lectures, interviews, and media coverage. Over 23 purely informational requests were answered. The PI gave presentations on the TGRC to lvisitors from academia and private industry, as well as guest lectures to courses on Plant Breeding, and Horticultural Research at UC Davis, In addition, Chetelat was interviewed for a high school student's research project. What do you plan to do during the next reporting period to accomplish the goals?The TGRC will continue the essential genebank activities summarized above, as well as pursue similar outreach opportunities. Our research program will expand to include a study of seed and pollen traits in the S. sitiens introgression lines.

Impacts
What was accomplished under these goals? Impact. By providing germplasm with desired traits such as disease resistance needed in breeding programs, the TGRC facilitates development of superior varieties that have the potential to benefit farmers, food processors, seed companies, the environment, and consumers. By providing genetic materials for basic and applied research, the TGRC enables new discoveries with potential practical applications that benefit society. Germplasm acquisition. No new accessions were acquired this year. Obsolete or redundant accessions were dropped, and some previously inactive accessions were 'rescued'. The current total of number of active accessions is 4,405. Germplasm maintenance and evaluation. 1000 cultures were grown for various purposes, of which 307 were for seed increase, including 55 wild species accessions. Germination tests were run on 697 seed lots. Progeny tests were performed on 44 stocks of male-steriles and other segregating genes, or accessions with unexpected phenotypes. 62 stocks of S. sitiens introgression lines were grown for marker assisted selection or for drought tolerance testing. Other stocks were grown for research on interspecific reproductive barriers and/or for wide crosses to S. ochranthum and S.juglandifolium. All plants grown for seed distribution were monitored in all stages of growthfor evidence of disease; TSWV was a big problem in our greenhouse this year. Newlyregenerated seed lots were split, with one sample stored at 5° C for filling seed requests, theother stored in sealed pouches at -18° C for long term preservation. 209 seed samples were sentto the USDA for backup storage. Seed distribution and utilization. A total of 4289 seed samples representing 2035 different accessions were distributed in response to 184 requests from 155 researchers and breeders in 28 countries; many purely informational requests were also answered. The overall utilization rate (the number of samples distributed relative to the number of accessions available) was 97%, which is lower than in previous years, likely due to the effects of Covid-19 restrictions. Information provided by requestors indicates our stocks continue to be used to support a wide variety of research and breeding projects. Our annual literature search uncovered 123 publications that mention use of TGRC stocks. Documentation of the collection. Updated stock lists were published on our website. New images of mutants and wild species were uploaded. Passport data on new accessions was added. Revised guidelines for seed germination were posted on our website. Seed request records and passport information on seed samples submitted for off-site back up were provided to the USDA for uploading to their GRIN-Global database. Research. The TGRC continued research on interspecific reproductive barriers and introgression of the S. sitiens genome. We isolated and characterized ui3.1, a gene expressed in pistils that is part of a novel mechanism of pollen rejection. We were awarded a grant from the Foundation for Food and Agriculture Research to study seed quality and pollination under heat stress.

Publications

• Type: Websites Status: Published Year Published: 2020 Citation: Chetelat, R. T. (2020) The tale of a wild tomatos discovery. Blog for American Society of Agronomy and Crop Science Society of America. https://sustainable-secure-food-blog.com/2020/09/22/the-tale-of-a-wild-tomatos-discovery/
• Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Chetelat, R. T. and X. Qin (2020) Accessing crop wild relatives: interspecific incompatibility mechanisms and introgression line breeding in tomato. Presentation to the California Plant and Soil Conference, Feb. 5, Fresno, California.

Progress 10/01/18 to 09/30/19

Outputs
Target Audience:Our target audience includes academic researchers, plant breeders, biotechnologists, USDA staff (germplasm curators, research leaders, administrators), educators, and graduate and undergraduate students. We reach them through our publications, presentations, and the TGRC website, https://tgrc.ucdavis.edu. In addition, we extend knowledge to the broader public through our education and outreach efforts. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Two high school students, one undergraduate student, and three visiting scientists (from Peru and China) completed internships of 1-12 months to gain knowledge and experience in tomato genetic resources, Mendelian genetics, and/or molecular biology. How have the results been disseminated to communities of interest?Results have been disseminated through publications, the TGRC website (https://tgrc.ucdavis.edu), presentations, tours, lectures, interviews, and media coverage. Over 41 purely informational requests were answered. PI Chetelat gave presentations on the TGRC to large numbers of visitors from academia and private industry, as well as guest lectures to the Plant Breeding Academy at UC Davis, and a graduate course on horticultural research. In addition, Chetelat was interviewed for a New York Times article on adapting crops to climate change. What do you plan to do during the next reporting period to accomplish the goals?The TGRC will continue to carry out its core functions and activities, outlined above, in the next reporting period.

Impacts
What was accomplished under these goals? Acquisitions. The TGRC accessioned a set of 56 introgression lines representing the genome of the wild nightshade S. sitiens in the background of cultivated tomato. Developed by the TGRC, these prebred lines capture ca. 93% of the donor genome and significantly expand the genepool of cultivated tomato. In addition, we rescued three accessions of S. ochranthum that had never been grown for seed increase. Obsolete or redundant accessions were dropped. The current total of number of accessions maintained by the TGRC is 4,398. Maintenance and Evaluation. Over 720 cultures were grown for various purposes, of which 412 were for seed increase, including 22 wild species accessions. Germination tests were run on 367 seed lots. Progeny tests were performed on 9 stocks of male-steriles and other segregating genes, or accessions with unexpected phenotypes. 174 stocks were grown for introgression of the S. sitiens genome. Other stocks were grown for research on interspecific reproductive barriers. All plants grown for seed distribution were tested for PSTVd; no positive plants were found. Eight lines were tested for the presence of transgenes; all were negative. Newly regenerated seed lots were split, with one sample stored at 5° C for filling seed requests, the other stored in sealed pouches at -18° C for long term preservation. 246 seed samples were sent to the USDA for backup storage. Distribution and Utilization. A total of 7,431 seed samples representing 2,444 different accessions were distributed in response to 291 requests from 232 researchers and breeders in 27 countries; over 41 purely informational requests were also answered. The overall utilization rate (i.e. the number of samples distributed relative to the number of accessions available) was 169%. Information provided by recipients indicates our stocks continue to be used to support a wide variety of research and breeding projects. Our annual literature search uncovered 98 publications that mention use of TGRC stocks. Documentation. New images of mutants and wild species were uploaded. Passport data on new accessions was added. Revised guidelines for seed germination, pollen collecting, and maintenance of wild species were posted on our website. Seed request records and passport information on seed samples submitted for off-site back up were provided to the USDA for uploading to their GRIN-Global database. Research.The TGRC continued research on interspecific reproductive barriers and introgression of the S. sitiens genome. We published a paper describing the S. sitiens introgression line population.

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: Chetelat, R. T., Qin, X., Tan, M., Burkart-Waco, D., Moritama, Y., Huo, X., Wills, T. and Pertuze, R. (2019) Introgression lines of Solanum sitiens, a wild nightshade of the Atacama Desert, in the genome of cultivated tomato. Plant J, 100, 836-850.
• Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Qin, X, X. Xiaomei, A. Mishra, and Chetelat, R. T. (2019) Deciphering the mechanisms of pollen rejection in wide crosses of tomato. Oral presentation to the XVI Solanaceae Conference, in Jerusalem, Israel.
• Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Chetelat, R. T., Qin, X., Tan, M., Burkart-Waco, D., Moritama, Y., Huo, X., Wills, T. and Pertuze, R. (2019) Introgression lines of Solanum sitiens, a wild nightshade of the Atacama Desert, in the genome of cultivated tomato. Poster presentation to the XVI Solanaceae Conference, in Jerusalem, Israel.

Progress 10/01/17 to 09/30/18

Outputs
Target Audience:Our target audience includes researchers, plant breeders, USDA staff (germplasm curators, research leaders, administrators), educators, and graduate and undergraduate students. We reach them through our publications, presentations, and the TGRC website, http://tgrc.ucdavis.edu. In addition, we extend knowledge to the broader public through our education and outreach efforts. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Several undergraduate students learned concepts of Mendelian and population genetics, plant breeding, and germplasm conservation. Two visiting scientists started one year internships in the lab for the purpose of improving their knowledge of tomato genetics, molecular biology, map-based cloning, and cytology. How have the results been disseminated to communities of interest?Results have been disseminated through publications, the TGRC website (http://tgrc.ucdavis.edu), presentations, tours, lectures, interviews, and media coverage. Over 32 requests for specific information on our stocks were answered by the TGRC. PI Chetelat gave presentations on the TGRC to large numbers of visitors from academia and private industry, as well as guest lectures to the Plant Breeding Academy, a graduate course on horticultural research (both at UC Davis), and an Intro to Plant Breeding course from the University of Nevada-Reno. Chetelat was interviewed for an online course on plant breeding prepared by Dr. Jeff Mitchell. What do you plan to do during the next reporting period to accomplish the goals?The core functions and activities of the TGRC outlined above will continue in the next reporting period.

Impacts
What was accomplished under these goals? Acquisitions. The TGRC acquired two new accessions this year, both long storage, delayed ripening varieties from Spain. In addition, we rescued three accessions of S. ochranthum that had never been successfully grown for seed increase. Obsolete or redundant accessions were dropped. The current total of number of accessions maintained by the TGRC is 4,344. Maintenance and Evaluation. Over 1,050 cultures were grown for various purposes, of which 561 were for seed increase, including 92 wild species accessions. Germination tests were run on 707 seed lots. Progeny tests were performed on 122 stocks of male-steriles, trisomics, and other segregating lines or accessions with unexpected phenotypes. 197 stocks were grown for introgression of the S. sitiens genome. Other stocks were grown for research on interspecific reproductive barriers. All plants grown for seed regeneration were tested for PSTVd; no positive plants were found. Newly regenerated seed lots were split, with one sample stored at 5° C to use for filling seed requests, the other stored in sealed pouches at -18° C to better maintain long term seed viability. 86 seed samples were sent to the USDA and 25 to the Svalbard Global Seed Vault for long term backup storage. Distribution and Utilization. A total of 6,946 seed samples representing 2,032 different accessions were distributed in response to 330 requests from 256 researchers and breeders in 31 countries; at least 32 purely informational requests were also answered. The overall utilization rate (i.e. the number of samples distributed relative to the number of accessions available) was 160%. Information provided by recipients indicates our stocks continue to be used to support a wide variety of research and breeding projects. Our annual literature search uncovered 90 publications that mention use of TGRC stocks. Documentation. New images of mutants and wild species were uploaded. Passport data on new accessions was added. Revised guidelines for seed germination, pollen collecting, and maintenance of wild species were posted on our website. Seed request records and passport information on seed samples submitted for off-site back up were provided to the USDA for uploading to their GRIN-Global database. Research. The TGRC continued research on the mechanisms of interspecific reproductive barriers and on introgression of the S. sitiens genome. We published a paper on a previously unknown mechanism for pollen recognition and rejection by flowers of the wild species S. pennellii. We completed development of a set of introgression lines that capture ca. 95% of the genome of S. sitiens in the background of cultivated tomato.

Publications

• Type: Journal Articles Status: Published Year Published: 2017 Citation: Qin, X. Q., Li, W. T., Liu, Y., Tan, M. L., Ganal, M. and Chetelat, R. T. (2018) A farnesyl pyrophosphate synthase gene expressed in pollen functions in S-RNase-independent unilateral incompatibility. Plant Journal, 93, 417-430.