Progress 10/01/13 to 09/30/18
Outputs
Target Audience:Scientific community: Through basic genetic discoveries, including identification and characterization of tomato germplasm, genetic characterization of important traits in tomato, identification and mapping of new genetic markers, genes and QTLs, development of new breeding methodologies, and development of genetic populations for basic genetic studies [(e.g. development of new mapping populations such as recombinant inbred lines (RILs) and near-isogenic lines (NILs)], and publication of research results. Tomato industry: Through development of new tomato germplasm (breeding lines and hybrid cultivars) with disease resistance, high fruit quality and high yield; it is expected that both fresh-market and processing tomato industries will benefit from the products of this program. Public: Through development of tomatoes with improved disease resistance (thus less use of pesticides) and high fruit lycopene content (thus healthier fruit). Also, production of high yielding tomatoes will lead to lower consumer cost for the products. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Graduate and undergraduate students were involved in all aspects of basic and applied research conducted in the tomato program, including growing and maintaining plants in the greenhouse, cross hybridization, development of genetic and breeding populations, maintaining pathogen isolates in the laboratory, evaluation of plants for disease resistance, development of genetic markers and maps, QTL mapping, etc. In addition, during summer 2017, a senior undergraduate student from the University of Puerto Rico joined the tomato program through the Summer Research Opportunity Program (SROP), and he was trained in tomato breeding during an 8-week period. How have the results been disseminated to communities of interest?Research results are disseminated in different ways, including publications in refereed and non-refereed journals, and presentations at meetings. Further, the resulting breeding lines and experimental hybrid cultivars were released to tomato growers and seed companies for evaluation and commercialization. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Basic Genetic Research:During this period, research was focused on the identification and characterization of genetic sources of resistance to tomato (Solanum lycopersicum) late blight (LB), caused by the oomycetePhytophthora infestans. Screening of a large core collection of tomato accessions (~70), mainly from the wild speciesSolanum pimpinellifolium, for LB resistance resulted in the identification of 12 accessions with strong resistance to LB. Subsequently, we characterized the genetic basis of resistance, including determining the inheritance of resistance and identification of QTLs/genes conferring LB resistance, in five selected highly-resistant accessions. Briefly, the inheritance studies, employing different techniques, including variance components analysis, generation means analysis, parent-offspring regression/correlation analysis, and analysis of response to directional selection, indicated that in all these accessions resistance was heritable with moderately high heritability. We developed numerous genetic mapping populations, derived from crosses between each of these five resistant accessions and some elite tomato breeding lines with LB susceptibility. Populations included early filial (e.g. F2, F3 and F4) and backcross generations (e.g., BC1, BC1S1, BC2 and BC2S1) as well as a recombinant inbred line (RIL) population. Molecular markers (mainly SNPs) were developed for the various mapping populations using different techniques, including genotyping by sequencing (GBS) approach and the use of commercially available SolCAP Illumina Infinium Array. Thousands of polymorphic SNP markers were identified, subsets of which were used to develop six different genetic linkage maps (for the various interspecific populations). The mapping populations were also screened for LB resistance in numerous experiments. The various mapping populations, genetic maps and disease screening data were used to identify and map QTLs for resistance to LB resistance coming from each of the five accessions. In each mapping population, we identified between two and six LB-resistance QTLs, some of which were common across the resistant accessions (e.g., one on chromosome 10 shared in all accessions) and several QTLs were specific to specific accessions. A few QTLs were determined as being major QTLs, which could be more useful for breeding purposes. The identification of different resistance QTLs from the different accessions provides opportunity for combining/pyramiding resistance genes/QTLs in the cultivated tomato to produce stronger and potentially more durable resistance to LB. To validate and quantify individual effects of LB resistance QTLs, various projects have been undertaken. For example, one has been the development and examination of a RIL population (F10 generation) and others include development of near-isogenic lines (NILs), currently underway. Some resistance QTLs have been validated and others are being further investigated. Furthermore, gene expression analysis using RNA-seq approach is currently been employed to identify and characterize resistance genes underlying the identified LB-resistance QTLs. In a different collaborative research project, we developed a super high-density genetic linkage map of tomato based on an F10 RIL population, previously developed at Penn State from an interspecific cross between an elite tomato breeding line andS. pimpinellifoliumaccession with exceptional fruit quality characteristics (including high lycopene content). Through a genotyping-by-sequencing (GBS) approach, a total of 176,454 SNPs were detected, of which 144,520 were confirmed and 141,083 SNPs were mapped onto the 12 tomato chromosomes. The saturated map was used to verify the genomic locations of QTLs for fruit weight and lycopene content in this RIL population. The map was further used to validate the causative gene underlying a major lycopene QTL (lyc12.1), which we had previously fine-mapped using NILs derived from the same interspecific cross. The development of this highly-saturated genetic linkage map of tomato, along with the release of the RIL population and methodologies used for construction of the map, will facilitate wide use of the information and material for further genetic characterization in tomato by researchers and breeders throughout the world. Applied Genetic and Breeding Research:In addition to basic research, we conducted research to develop new breeding lines and hybrid cultivars of fresh-market (FM) and processing tomato with improved characteristics, including disease resistance, high fruit quality (in particular high lycopene content), high yield, and adaptation to PA and NE USA. Briefly, research was conducted to transfer the previously-known LB-resistance genes (Ph-2 and Ph-3) as well as new resistance genes we identified in our research at Penn State (described above) to our tomato breeding germplasm. Previously, we had developed tomato inbred lines with other desirable characteristics, including resistance to early blight (EB), caused by fungiAlternaria solaniandA. tomatophila, improved fruit quality (in particular high fruit lycopene content), high yield, early maturity, and adaptation to PA and U.S. Northeast conditions. During the past five years, we incorporated resistance to LB (from different resources) into our elite tomato breeding lines. Specifically, we transfer one or a combination of three LB-resistance genes, Ph-2, Ph-3 and Ph-5 into our breeding lines. We were able to develop many FM and processing tomato elite lines with resistance to EB and LB diseases and with other desirable horticultural characteristics. A final step of a tomato breeding program is to develop experimental F1hybrids from crosses among elite inbred lines for commercial evaluation. During the past five years, we shared many elite breeding lines (with various combinations of disease resistance and other desirable characteristics) with seed companies for production of commercial cultivars. Seed companies have developed co-hybrids using PSU tomato breeding lines and evaluated them for commercial production. Collaborations with several seed companies have resulted in successful production of several competitive hybrid cultivars. A notable impact of our research has been the development and commercialization of a fresh-market tomato hybrid variety (namedValentine), which was developed in collaboration with Johnny's Selected Seed (JSS), which is on the market and commercially available. This variety won an All-American Selection (AAS) award in 2018. Currently, several other co-hybrids are being evaluated for commercialization. In addition to co-hybrids developed in collaboration with seed companies, during the past few years we developed at Penn State over 300 new experimental hybrids of FM (large, plum, grape) and processing tomatoes. In addition to evaluating these hybrids at Penn State research farms, many of these hybrids have been grown in other locations in PA and across the country in collaboration with several growers and seed companies. We expect a number of these hybrids to be commercialized within the next few years.
Publications
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2018
Citation:
Gonda I, H Ashrafi, DA Lyon, SR Strickler, AM Hulse-Kemp, Q Ma, H Sun, K Stoffel, S Futrell, TW Thannhauser, Z Fei, AE Van Deynze, LA Mueller, JJ Giovannoni and MR Foolad. 2018. Development of a GBS-based high-density genetic map of a tomato RIL population, useful for high-resolution QTL mapping. The Plant Genome (in press)
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Burzynski EA, I Ryona, BI. Reisch, I Gonda, MR Foolad, JJ Giovannoni, GL Sacks. 2018. Quantifying compound � individual matrix effects in HS-SPME-GC-MS of plant populations. Molecules 23: 2436 (12 pages); https://doi.org/10.3390/molecules23102436
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Foolad, MR, M. Sullenberger, E. Ohlson and BC Gugino. 2014. Response of Accessions within Tomato Wild Species, Solanum pimpinellifolium to Late Blight. Plant Breeding 133:401-411; DOI:10.1111/pbr.12172
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Kinkade MP, MR Foolad. 2013. Validation and fine mapping of lyc12.1, a QTL for increased tomato fruit lycopene content. Theor Appl Genet 126:21632175; DOI:10.1007/s00122-013-2126-5
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Ashraf M and MR Foolad. 2013. Crop breeding for salt tolerance in the era of molecular markers and marker-assisted selection. Plant Breeding 132, 1020. doi:10.1111/pbr.12000
- Type:
Book Chapters
Status:
Published
Year Published:
2013
Citation:
Nowicki M, EU Kozik and MR Foolad. 2013. The tomato late blight. In: Translational Genomics for Crop Breeding: Vol. I, Biotic Stress, First Edition. RK Varshney and R Tuberosa, eds., John Wiley & Sons, Inc., USA. pp. 241-265.
- Type:
Book Chapters
Status:
Published
Year Published:
2013
Citation:
Kinkade MP and MR Foolad. 2013. Genomics-assisted breeding for tomato fruit quality in the next-generation omics age. In: Translational Genomics for Crop Breeding: Vol. II, Abiotic Stress, Yield, and Quality, First Edition. RK Varshney and R Tuberosa, eds., John Wiley & Sons, Inc., USA. pp. 193-210.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Foolad MR. 2014. Tomato breeding at Penn State. In: Proc. Mid-Atlantic Fruit and Vegetable Convention, January 28 30, Hershey, PA, pp 110-115.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Gugino, BK, IA Huerta, Foolad MR and Fry B. 2014. The integrated management of late blight on tomato. In: Proc. Mid-Atlantic Fruit and Vegetable Convention, January 28 30, Hershey, PA, pp 118-121.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
Gugino BK and MR Foolad 2013. Update on late blight and use of host resistance for disease management. In: Proc. Mid-Atlantic Fruit and Vegetable Convention, January 29-31, Hershey, PA, pp 95-97.
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2019
Citation:
Jia, M., Ashsrafi H., and Foolad M.R. 2018. Identification and characterization of late blight resistance QTLs in a tomato RIL population using genotyping-by-sequencing and RNA-seq approaches. Poster abstract submitted to Plant and Animal Genome XXVII Conference, San Diego CA, January 12-16, 2019.
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2019
Citation:
Gao, S., Ashsrafi H., and Foolad M.R. 2018. Identification and mapping of late blight resistance QTLs in the wild tomato accession PI 224710 (Solanum pimpinellifolium). Poster abstract submitted to Plant and Animal Genome XXVII Conference, San Diego CA, January 12-16, 2019.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Burzynski E.A., Reisch B.I.; Gonda I., Foolad M.R., Giovannoni J.J., Sacks G.L. 2018. Internal standards roulette: best practices for HS-SPME-GC-MS volatile analyses in plant populations. Proceeding of the Plant and Animal Genome XXVI Conference, San Diego CA, January 13-17; P0638
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Ford, R., Jia M. and Foolad M.R. 2018. Development and Evaluation of Experimental Hybrids of Tomato with Late Blight Resistance. Poster presented at the 21st Annual College of Agricultural Sciences Graduate and Undergraduate Research Expo, The Pennsylvania State University, March 27, University Park, PA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
Ohlson, EW, MT Sullenberger and MR Foolad. 2016. Characterization of Late Blight Resistance in Solanum pimpinellifolium Accessions PI 163245 and PI 224710. Poster presented at the Mid-Atlantic Fruit and Vegetable Convention, February 2 5, Hershey, PA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Ohlson, EW, MT Sullenberger and MR Foolad. 2015. Characterization of Late Blight Resistance in Solanum pimpinellifolium Accessions PI 163245 and PI 224710. Poster presented at the 18th Annual College of Agricultural Sciences Graduate and Undergraduate Research Expo, The Pennsylvania State University, March 24, University Park, PA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Smith JD, MR Foolad and TW McNellis. 2015. Exploring the Genetics of Clavibacter michiganensis Resistance in Wild Tomato Accessions. Poster presented at the 18th Annual College of Agricultural Sciences Graduate and Undergraduate Research Expo, The Pennsylvania State University, March 24, University Park, PA.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2013
Citation:
Reibson, AD. 2013. Transfer of late blight resistance genes in tomato via marker-assisted selection and phenotypic selection. MSc Thesis. The Pennsylvania State University, University Park, PA. 73 pp. (Thesis advisor: MR Foolad)
|
Progress 10/01/16 to 09/30/17
Outputs
Target Audience:Scientific community: Through basic genetic discoveries, including identification and characterization of tomato germplasm, genetic characterization of important traits in tomato, identification and mapping of new genetic markers, genes and QTLs, development of new breeding methodologies, and development of genetic populations for basic genetic studies [(e.g. development of new mapping populations such as recombinant inbred lines (RILs) and near-isogenic lines (NILs)], and publication of research results. Tomato industry: Through development of new tomato germplasm (breeding lines and hybrid cultivars) with disease resistance, high fruit quality and high yield; it is expected that both fresh-market and processing tomato industries will benefit from the products of this program. Public: Through development of tomatoes with improved disease resistance (thus less use of pesticides) and high fruit lycopene content (thus healthier fruit). Also, production of high yielding tomatoes will lead to lower consumer cost for the products. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Graduate and undergraduate students were involved in all aspects of basic and applied research conducted in the tomato program, including growing and maintaining plants in the greenhouse, cross hybridization, development of genetic and breeding populations, maintaining pathogen isolates in the laboratory, evaluation of plants for disease resistance, development of genetic markers and maps, QTL mapping, etc. In addition, during summer 2017, a senior undergraduate student from the University of Puerto Rico joined the tomato program through the Summer Research Opportunity Program (SROP), and he was trained in tomato breeding during an 8-week period. How have the results been disseminated to communities of interest?Research results are disseminated in different ways, including publications in refereed and non-refereed journals, and presentations at meetings. Further, the resultant breeding lines and experimental hybrid cultivars are released to seed companies for evaluation and commercialization. Some varieties are also shared with growers. What do you plan to do during the next reporting period to accomplish the goals?Continue the basic and applied genetics and breeding research, including identification and mapping of new late blight resistance genes, incorporation of resistance genes into our tomato germplasm, developing new breeding lines and experimental hybrid cultivars, trialing our new inbred lines and experimental hybrids, cooperating with seed companies to commercialize our germplasm, and publication of research results in journals.
Impacts
What was accomplished under these goals?
Basic Genetic Research: In a collaborative research project, we developed a super high-density genetic linkage map of tomato based on a recombinant inbred line (RIL) population, previously developed at Penn State from an interspecific cross between Solanum lycopersicum breeding line NC EBR-1 and Solanum pimpinellifolium accession LA2093. Through a genotyping-by-sequencing (GBS) approach, a total of 176,454 SNPs (single nucleotide polymorphisms) were detected, of which 144,520 were confirmed and 141,083 SNPs were mapped onto the 12 tomato chromosomes. The saturated map was used to verify the genomic locations of QTLs (quantitative trait loci) for fruit weight and lycopene content in this RIL population, previously identified using an earlier molecular map of the population. The map was further used to validate the causative gene underlying a major lycopene QTL (lyc12.1), which we had previously fine-mapped using near-isogenic lines (NILs) derived from the same cross. A report of our findings in this research has been submitted for publication in a refereed journal. The development of this highly-saturated genetic linkage map of tomato, along with the release of the RIL population and methodologies used for construction of the map, will facilitate wide use of the information and material for further genetic characterization in tomato by researchers throughout the world. In other projects, we continued investigation of the genetic basis of late blight (LB) resistance in a few tomato accessions, which were previously identified at Penn State as sources of LB resistance for tomato breeding. In particular, for one accession we have developed a new RIL population, now at F10 generation, and evaluated the population for LB resistance a few times. Additionally, we have taken a GBS approach to identify and map SNP markers in this population, which will be used to identify and verify QTLs conferring LB resistance in this population. For other tomato accessions, we have developed various populations to characterize the genetic basis of LB resistance, including mapping of QTLs underlying resistance and determining the heritability of resistance. Applied Genetic and Breeding Research: A notable impact of our applied research was the development and commercialization of a fresh-market tomato hybrid variety (named Valentine), which was developed in collaboration with Johnny's Selected Seed and will be available to public for commercial production in 2018. This variety was recently awarded an All-American Selection (AAS) award. Because of this, it is expected that other seed companies would want to sell the seed of this variety as well. During this project period, we also continued our research towards development of other tomato breeding lines and experimental hybrid cultivars with improved characteristics, including high yield, disease resistance, and high fruit lycopene content. Of particular interest has been development and evaluation of new inbred lines of tomato with late blight (LB) resistance. These inbred lines have been used in cross hybridizations with other Penn State tomato breeding lines to develop experimental hybrids with resistance to LB and other tomato diseases, and also with improved fruit quality and high yield. Further, we developed and evaluated numerous experimental hybrids of fresh-market and processing tomatoes with resistance to EB and other desirable characteristics. In addition to evaluating our inbred lines and experimental hybrids at the Penn State research farm, we provided seed of some of our hybrids to other researcher in public and private institutions as well as university extension agents and farmers for field trials in many states across the country.
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2017
Citation:
Sullenberger, MT, M Jia, S Gao and MR Foolad. 2017. Genetics analysis of late blight resistance in Solanum pimpinellifolium accession PI 270441: heritability and response to selection.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2017
Citation:
Gonda I, H Ashrafi, DA Lyon, SR Strickler, AM Hulse-Kemp, Q Ma, H Sun, K Stoffel, S Futrell, TW Thannhauser, Z Fei, AE Van Deynze, LA Mueller, JJ Giovannoni and MR Foolad. 2017. From short reads to QTL: a pipeline for high-resolution QTL mapping in recombinant inbred line (RIL) populations using tomato as a model.
- Type:
Journal Articles
Status:
Submitted
Year Published:
2017
Citation:
Ohlson EW, H Ashrafi and MR Foolad. 2017. Identification and mapping of late blight resistance QTLs in tomato accession PI 163245.
- Type:
Journal Articles
Status:
Submitted
Year Published:
2017
Citation:
Sullenberger MT and MR Foolad. 2017. Genetic characterization of late blight resistance in Solanum pimpinellifolium accession PI 270442. Submitted.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Foolad MR. 2017. Tomato breeding at Penn State. In: Proc. Mid-Atlantic Fruit and Vegetable Convention, January 31 - February 2, Hershey, PA, pp 192-195.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
Gonda I., Ashrafi H., Strickler S.R., Mueller L.A., Sacks G.L., Klee H.J., Howe K., Thannhauser T.W., Alseekh S., Fernie A.R., Fei Z., Foolad M.R., Giovannoni J.J. 2016. Combined metabolic quantitative traits loci (mQTL) and expression QTL (eQTL) analysis in a recombinant inbred line population. Proceeding of the 13th Solanaceae Conference, UC Davis, Davis CA, Sept. 12-16; pp. 62-63 (Abstract of the oral presentation).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
Gonda I., Ashrafi H., Strickler S.R., Mueller L.A., Sacks G.L., Klee H.J., Howe K., Thannhauser T.W., Alseekh S., Fernie A.R., Fei Z., Foolad M.R., Giovannoni J.J. 2016. Combined metabolic quantitative traits loci (mQTL) and expression QTL (eQTL) analysis in a recombinant inbred line population. Proceeding of the 13th Solanaceae Conference, UC Davis, Davis CA, Sept. 12-16; pp. 127-128 (Abstract of the poster presentation).
|
Progress 10/01/15 to 09/30/16
Outputs
Target Audience:Scientific community: Through basic genetic discoveries, including identification and characterization of tomato germplasm, genetic characterization of important traits in tomato, identification and mapping of new genetic markers, genes and QTLs, development of new breeding methodologies, and development of genetic material for basic genetic studies (e.g. development of new mapping populations such as recombinant inbred lines (RILs) and near-isogenic lines (NILs). Tomato industry: Through development of new tomato germplasm (breeding lines and hybrid cultivars) with disease resistance, high fruit quality and high yield; it is expected that both the fresh-market and processing tomato industries will benefit from the products of this program. Public: Through development of tomatoes with improved disease resistance (thus less use of pesticides) and high fruit lycopene content (thus healthier fruit). Also production of high yielding tomatoes will lead to lower consumer cost for the products. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Graduate and undergraduate students were involved in conducting research, including growing and maintaining plants in the greenhouse, cross hybridization among genotypes, development of genetic and breeding populations, maintaining pathogen isolates in the laboratory and evaluation of plant populations for disease resistance, development of genetic markers and map, QTL mapping, etc. How have the results been disseminated to communities of interest?Research results are usually disseminated via different ways, including publication in refereed and non-refereed journals and books, and presentations at meetings. Further, the resultant breeding lines and experimental hybrid cultivars have been shared with seed companies for commercial evaluation and use. What do you plan to do during the next reporting period to accomplish the goals?Continue the basic and applied genetics and breeding research, including identification of new late blight resistance genes, incorporation of resistance genes into our tomato germplasm, developing new breeding lines, developing new experimental hybrid cultivars, trialing of our new inbred lines and experimental hybrids, cooperating with seed companies to commercialize our germplasm.
Impacts
What was accomplished under these goals?
Basic Genetic Research: Studied the genetic basis of resistance to late blight (LB), caused by oomycete Phytophthora infestans, in four tomato accessions, including one cultivated Solanum lycopersicum and three wild S. pimpinellifolium accessions. Investigations included examining the heritability of LB resistance and identifying QTLs controlling resistance. It was determined that LB resistance in each of the four accessions was heritable, with moderately high heritability. It was also determined that the resistance in each accession was controlled by more than one gene (quantitative trait locus, QTL). Across the four accessions, several QTLs were identified for LB resistance, some of which were common to two to more accessions and some were specific to individual accessions. A few QTLs were determined as being major QTLs, which could be more useful for breeding purposes. The presence of different QTLs suggested the possibility of combining/pyramiding resistance QTLs from different accessions in the cultivated tomato to develop stronger and more durable resistance to LB. Research projects were initiated to transfer LB resistance QTLs from these accessions to Penn State tomato breeding lines (described below). To validate and quantify individual effects of LB resistance QTLs, different projects have been initiated. For example, one has been the development of a recombinant inbred line (RIL) population from a cross between a LB-resistant S. pimpinellifolium accession and a LB-susceptible tomato breeding line; the population is currently at F7-F8 generation. Other projects include development of additional mapping populations from crosses with two other LB-resistant S. pimpinellifolium accessions. Currently two graduate students in the lab conduct LB resistance research as part of their PhD thesis projects. Applied Genetic and Breeding Research: During this period we continued our research towards development of breeding lines and experimental hybrid cultivars of tomato with improved characteristics, including high yield, disease resistance, and high fruit lycopene content. During the past several years, research has been underway to develop new tomato germplasm suitable for production in PA and the northeast. This included development of tomato germplasm for short to medium growing season with high yield and other desirable characteristics, including resistance to early blight (EB; caused by Alternaria solani) and LB, and improved fruit quality. Several years of breeding research has resulted in development of many inbred lines of fresh-market and processing tomatoes. To facilitate release of such germplasm, during this research period we developed over 180 new experimental hybrids from crosses among inbred lines and evaluated them under field conditions in 2016. Several of the experimental hybrids were also evaluated by a few seed companies in other locations. Evaluation of these hybrids indicated that many of them were superior and should be of interest to commercial growers. Currently, work is underway towards commercialization of some of these hybrids.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Ohlson, EW and Foolad, MR. 2016. Genetic analysis of resistance to tomato late blight in Solanum pimpinellifolium accession PI 163245. Plant Breeding 135: 391-398. doi: 10.1111/pbr.12366.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
Foolad MR. 2016. Tomato breeding at Penn State. In: Proc. Mid-Atlantic Fruit and Vegetable Convention, February 2 5, Hershey, PA, pp 78-81.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2015
Citation:
Ohlson, EW. 2015. Genetic characterization and mapping of late blight resistance genes in the wild tomato accessions PI 163245 and PI 224710. PhD Thesis. The Pennsylvania State University, University Park, PA. 192 pp. (Thesis advisor: MR Foolad)
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2016
Citation:
Sullenberger, MT. 2016. Identification and mapping of new late blight resistance genes in the tomato wild species Solanum pimpinellifolium. PhD Thesis. The Pennsylvania State University, University Park, PA. 151 pp. (Thesis advisor: MR Foolad)
|
Progress 10/01/14 to 09/30/15
Outputs
Target Audience:Scientific community: Through basic genetic discoveries, including identification and characterization of tomato germplasm, genetic characterization of important traits in tomato, identification and mapping of new genetic markers, genes and QTLs, development of new breeding methodologies, and development of genetic material for basic genetic studies (e.g. development of new mapping populations such as recombinant inbred lines (RILs) and near-isogenic lines (NILs). Tomato industry: Through development of new tomato germplasm (breeding lines and hybrid cultivars) with disease resistance, high fruit quality and high yield; it is expected that both the fresh-market and processing tomato industries will benefit from the products of this program. Public: Through development of tomatoes with improved disease resistance (thus less use of pesticides) and high fruit lycopene content (thus healthier fruit). Also production of high yielding tomatoes will lead to lower consumer cost for the products. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Graduate and undergraduate students were involved in conducting research, including growing and maintaining plants in the greenhouse, cross hybridization among genotypes, development of genetic and breeding populations, maintaining pathogen isolates in the laboratory and evaluation of plant populations for disease resistance, development of genetic markers and map, QTL mapping, etc. How have the results been disseminated to communities of interest?Research results are usually disseminated via different ways, including publication in refereed and non-refereed journals and books, presentations at the scientific meetings (e.g. Tomato Breeders Round Table 2014) and growers conferences (e.g., 2013, 2014 and upcoming 2016 Mid-Atlantic Fruit and Vegetable Conventions). The breeding lines and experimental hybrid cultivars have been shared with seed companies for commercial evaluation. What do you plan to do during the next reporting period to accomplish the goals?Continue the basic and applied genetics and breeding research, including identification of new late blight resistance genes, incorporation of resistance genes into our tomato germplasm, developing new breeding lines, developing hundreds of new experimental hybrid cultivars, trialing of our new inbred lines and experimental hybrids, cooperating with seed companies to commercialize our breeding materials.
Impacts
What was accomplished under these goals?
A major accomplishment during this period was development of new breeding lines and experimental hybrid cultivars of tomato (Solanum lycopersicum) with improved characteristics, including high yield, disease resistance, and high fruit lycopene content. Briefly, during the past several years, research has been underway to develop new tomato germplasm suitable for production under PA and Northeast conditions. This included development of tomato germplasm for short to medium growing season with high yield and other desirable characteristics, including resistance to early blight (EB; caused by Alternaria solani) and late blight (LB; caused by Phytophthora infestans), and improved fruit quality. Several years of breeding research has resulted in development of many inbred lines of fresh-market tomatoes, including large round (beef type), plum shape, grape and cherry tomatoes. To facilitate release of such advanced germplasm to the market, during 2014-2015 we developed over 200 new experimental hybrids from crosses among inbred lines and evaluated them under field conditions in 2015. Several of the experimental hybrids were also evaluated by a few seed companies around the country. Evaluation of these hybrids indicated that many of them were superior to existing commercial cultivars of tomato and should be of interest for commercial production. While more experimental hybrids are being developed and evaluated, work is also underway towards commercialization of several of these hybrids. During the past few years, we also have been developing new inbred lines with resistance to LB, incorporating the previously known resistance genes (Ph-2 and Ph-3) as well as new resistance genes recently identified at Penn State. By the end of field season in 2015, several of these lines deemed advanced enough for making experimental commercial hybrid, a process that is currently underway. The basic research focused mainly on the identification and characterization of genetic resources for resistance to tomato late blight (LB). Screening of a core collection (approximately 70 accessions) of tomato wild species Solanum pimpinellifolium had resulted in identification of 12 new accessions with almost complete resistance to LB disease. Recently, we conducted research on four resistant accessions, characterizing their genetic basis of resistance, including inheritance studies and molecular mapping of resistance genes (QTLs). We determined that the LB resistance in each of these accessions was heritable with moderately high heritability. Further, we developed four separate molecular genetic maps, using SNP markers, and identified and mapped major and minor QTLs (genes) conferring resistance in each of these four accessions. We also initiated projects to transfer resistance from these accessions to the cultivated tomato. A major goal of these projects is to combine resistance genes from different sources to develop inbred lines and commercial hybrids with strong and durable resistance to LB.
Publications
- Type:
Journal Articles
Status:
Accepted
Year Published:
2015
Citation:
Foolad, MR and L. Zhang. 2015. A recombinant inbred line population of tomato and its genetic map constructed based on a Solanum lycopersicum � S. pimpinellifolium cross. Adv Studies Biol (accepted).
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Ohlson, EW and Foolad, MR. 2015. Heritability of late blight resistance conferred by Solanum pimpinellifolium accession PI 224710. Plant Breeding 134: 461467.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Foolad, MR, M. Sullenberger and H. Ashrafi. 2015. Detached-leaflets evaluation of tomato germplasm for late blight resistance and its correspondence with field and greenhouse screenings. Plant Disease 99:718-722.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Foolad, MR and H. Ashrafi. 2015. Characterization of early blight resistance in a recombinant inbred line population of tomato: I. Heritability and Trait Correlations. Adv Studies Biol 7: 131-148.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Ashrafi, H. and Foolad, MR. 2015. Characterization of early blight resistance in a recombinant inbred line population of tomato: II. Identification of QTLs and their co-localization with candidate resistance genes. Adv Studies Biol 7: 149-168.
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Progress 10/01/13 to 09/30/14
Outputs
Target Audience: Scientific community: Through basic genetic discoveries, including identification and characterization of tomato germplasm, identification and mapping of new genetic markers, genes and QTLs, development of new breeding methodologies, and development of genetic materials for basic genetic studies (e.g. development of new mapping populations such as recombinant inbred lines (RILs) and near-isogenic lines (NILs). Tomato industry: Through development of new tomato breeding lines and cultivars with disease resistance, high fruit quality and high yield; it is expected that both the fresh-market and processing tomato industries will benefit from the products of this program. Public: Through development of tomatoes with improved disease resistance (thus less use of pesticides) and high fruit lycopene content (thus healthier fruit). Also production of high yielding tomatoes may lead to lower consumer cost for the products. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Graduate and undergraduate students were involved in conducting research, including growing and maintaining plants in the greenhouse, cross hybridization among genotypes, development of genetic and breeding populations, evaluation of plants and populations for disease resistance, development of genetic markers, etc. How have the results been disseminated to communities of interest? Research results were disseminated via different ways, including publication in refereed and non-refereed journals and books, presentations at the scientific meetings (e.g. Tomato Breeders Round Table 2014) and growers conferences (e.g., 2013 and 2014 Mid-Atlantic Fruit and Vegetable Conventions). What do you plan to do during the next reporting period to accomplish the goals? Continue the basic and applied genetics and breeding research, including mapping of new late blight resistance genes, incorporation of resistance genes into our tomato germplasm, developing new breeding lines, developing hundreds of new experimental hybrid cultivars, trialing of our new inbred lines and experimental hybrids, cooperating with seed companies to commercialize our breeding materials.
Impacts
What was accomplished under these goals?
Major research focus was on the identification and characterization of genetic sources of resistance to tomato (Solanum lycopersicum) late blight (LB), caused by the oomycete Phytophthora infestans. Screening of a core collection of tomato wild species Solanum pimpinellifolium for LB resistance was completed. The core collection included approximated 70 wild accessions, which was screened for LB resistance along with several control genotypes with known resistance to susceptibility to LB. This collection has been screened over several years under different conditions and in response to different isolates of the pathogen P. infestans. The screening resulted in the identification of several S. pimpinellifolium accessions with strong resistance to LB. Previously we had characterized the genetic control of LB resistance in one accessions (PI 270443) and determined the inheritance of the resistance as well as two genes (QTLs) controlling the resistance. During 2013-2014 we have been characterizing the genetic control of resistance in four other resistant accessions, include inheritance studies and genetic mapping. We developed several genetic and mapping populations and sequenced the parental lines of the mapping population through a process known as genotyping by sequencing (GBS). This process has resulted in the identification of over 260,000 single nucleotide polymorphic (SNP) markers. A subset of these markers have further characterized for genetic mapping and identification of resistance genes/QTLs in these populations. The genetic/mapping populations have been screened for LB resistance in replicated trials. Currently, we are in the process of genotyping the mapping populations, so that we will be able to combine the phenotypic and genotypic data to identify and map the genes/QTLs contributing to resistance in the four resistant S. pimpinellifolium accessions. In addition to basic research, we have conducted research to develop new breeding lines and hybrid cultivars of tomato with improved characteristics, including disease resistance and high fruit lycopene content. Briefly, research has been underway to transfer LB resistance from the newly identified resistant accessions into our breeding germplasm. Inbred lines are being developed with LB resistance. Previously, we developed inbred lines with other desirable characteristics, including resistance to early blight, caused by fungi Alternaria solani and A. tomatophila, and improved fruit quality, in particular high fruit lycopene content. A final step of a tomato breeding program is to develop experimental F1 hybrids from crosses among advanced inbred lines for commercial evaluation. During this research period we have developed over 200 experimental F1 hybrids from crosses among different types of fresh-market tomato breeding lines, including large round (beef type), plum, grape and cherry tomatoes. Several of these experimental hybrids are being evaluated by seed companies for commercial utilization. Currently more hybrids are being developed, which will be evaluated in 2014 field season.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Foolad, MR, M. Sullenberger, E. Ohlson and BC Gugino. 2014. Response of Accessions within Tomato Wild Species, Solanum pimpinellifolium to Late Blight. Plant Breeding 133:401-411; doi:10.1111/pbr.12172
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Kinkade MP, MR Foolad. 2013. Validation and fine mapping of lyc12.1, a QTL for increased tomato fruit lycopene content. Theor Appl Genet 126:21632175; DOI:10.1007/s00122-013-2126-5
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Ashraf M and MR Foolad. 2013. Crop breeding for salt tolerance in the era of molecular markers and marker-assisted selection. Plant Breeding 132, 1020. doi:10.1111/pbr.12000
- Type:
Book Chapters
Status:
Published
Year Published:
2013
Citation:
Nowicki M, EU Kozik and MR Foolad. 2013. The tomato late blight. In: Translational Genomics for Crop Breeding: Vol. I, Biotic Stress, First Edition. RK Varshney and R Tuberosa, eds., John Wiley & Sons, Inc., USA. pp. 241-265.
- Type:
Book Chapters
Status:
Published
Year Published:
2013
Citation:
Kinkade MP and MR Foolad. 2013. Genomics-assisted breeding for tomato fruit quality in the next-generation omics age. In: Translational Genomics for Crop Breeding: Vol. II, Abiotic Stress, Yield, and Quality, First Edition. RK Varshney and R Tuberosa, eds., John Wiley & Sons, Inc., USA. pp. 193-210.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
Gugino BK and MR Foolad 2013. Update on late blight and use of host resistance for disease management. In: Proc. Mid-Atlantic Fruit and Vegetable Convention, January 29-31, Hershey, PA, pp 95-97.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Foolad MR. 2014. Tomato breeding at Penn State. In: Proc. Mid-Atlantic Fruit and Vegetable Convention, January 28 30, Hershey, PA, pp 110-115.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Gugino, BK, IA Huerta, Foolad MR and Fry B. 2014. The integrated management of late blight on tomato. In: Proc. Mid-Atlantic Fruit and Vegetable Convention, January 28 30, Hershey, PA, pp 118-121.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Ashrafi H, Ohlson EW, Sullenberger MT, Stoffel K, Massoudi M, Van Deynze A and Foolad MR. 2014. SNP marker discovery for tomato breeding using Genotyping-by-Sequencing (GBS). Proceeding of the Tomato Breeders Roundtable; p. 12, North Carolina State University, Mills River, NC, Sept. 14-17.
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