Source: PENNSYLVANIA STATE UNIVERSITY submitted to
MOLECULAR MAPPING AND MARKER-ASSISTED SELECTION AND BREEDING FOR DISEASE RESISTANCE AND IMPROVED FRUIT QUALITY IN TOMATO
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
Reporting Frequency
Annual
Accession No.
0203928
Grant No.
(N/A)
Project No.
PEN04090
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Jul 1, 2005
Project End Date
Sep 30, 2008
Grant Year
(N/A)
Project Director
Foolad, M. R.
Recipient Organization
PENNSYLVANIA STATE UNIVERSITY
208 MUELLER LABORATORY
UNIVERSITY PARK,PA 16802
Performing Department
HORTICULTURE
Non Technical Summary
Most commercial cultivars of tomato are susceptible to early blight and late blight and have low fruit lycopene content. This project will identify sources of disease resistance, discern genetic bases of early and late blight resistance and high fruit lycopene content, and develop tomato lines with improved characteristics using a combination of marker-assisted selection and traditional breeding.
Animal Health Component
40%
Research Effort Categories
Basic
40%
Applied
40%
Developmental
20%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011460104010%
2011460108020%
2011460116010%
2021460108010%
2021460116010%
2041460108020%
2121460108020%
Goals / Objectives
Previously we have identified and verified several QTLs for resistance to tomato early blight (EB) in the related wild species Lycopersicon hirsutum. Most of these QTLs, however, were identified within interval size of 25-30 cM each. Considering the wild nature of the donor parent, there is little doubt that transfer of such large-interval QTLs would result in significant linkage drag. A high rate of unfavorable allele fixation at QTL locations can make marker-assisted selection (MAS) less desirable. A solution is to fine-map the QTLs to reduce the interval size to a few cM and validate their individual effects in uniform genetic backgrounds and in multiple target environments. We will develop several near-isogenic lines (NILs) and sub-NILs, each containing one QTL interval in an otherwise uniform cultivated tomato genetic background. Such NILs and sub-NILs will not only facilitate clean transfer of QTLs, but also provide several other opportunities, including increasing the efficiency of background selection, validating individual and interactive effects of QTLs, examining QTL effects in different environments, marker-assisted transferring of QTLs to different elite genetic backgrounds without having to use the wild species, determining the presence and nature of association (linkage or pleiotropy) between the trait of interest and undesirable horticultural characteristics, and ultimately physical mapping, cloning and characterization of underlying genes. In this project, we also will be identifying new QTLs for EB resistance in populations derived from crosses between the cultivated tomato, L. esculentum, and the closely-related red-fruited species L. pimpinellifolium. Following the identification of QTLs and their verification in different populations and by different mapping strategies, we will develop new NILs and sub-NILs to fine map the QTLs for future marker-assisted breeding for EB resistance. To facilitate development of tomato lines with durable resistance to late blight (LB), we will screen additional tomato germplasm to identify new sources of LB resistance. We will then develop segregating populations and use them to identify new genes and/or QTLs for LB resistance. The new resistance genes or QTLs will be fine-mapped by developing NILs and sub-NILs, similar to that for EB resistance QTLs. A major goal of this project is to develop commercial lines of tomato with EB and LB resistance and with improved fruit quality (in particular high fruit lycopene content). We will use a combination of traditional protocols of plant genetics and breeding and contemporary techniques of molecular markers and MAS.
Project Methods
In this research, integrative approaches involving tools of traditional genetics and breeding, plant pathology and plant molecular biology will be employed. Screening of tomato germplasm or breeding populations for disease resistance will be carried out under field, high-tunnel, greenhouse and growth chamber conditions. We have developed efficient methods of screening tomato plants for early blight (EB) and late blight (LB) under different conditions using detached-leaflets, detached leaves or whole plants. A combination of methods will be used to complement each other. In case of LB, we will be screening populations against different isolates of Phytophthora infestans with the goal of identifying sources of genetic resistance and developing tomato lines with resistance to multiple isolates. To discern genetic bases of different traits of interest, interspecific segregating populations will be developed from crosses between the cultivated tomato, Lycopersicon esculentum, and the related wild species L. pimpinellifolium and L. hirsutum. In particular, we will be using inbred backcross (IBC), recombinant inbred line (RIL) and near-isogenic line (NIL) populations for QTL/gene mapping. For fine mapping and validation of QTLs, we will develop and use sub-NILs. Different molecular markers, including, Restriction Fragment Length Polymorphisms (RFLPs), Cleaved Amplified Polymorphic Sequences (CAPS), Resistance Gene Analogs (RGAs) and Expressed Sequence Tags (ESTs), will be used for genetic mapping. Different QTL mapping strategies, including marker-based analysis (MBA) and trait-based analysis (TBA; also known as selective genotyping or extreme distributional analysis) will be used to identify and QTLs. QTLs will be verified in different populations and under different environmental conditions before attempts are made to develop NILs and sub-NILs. Only QTLs with large effects, and which exhibit little or no genotype by environment interactions, will be selected for development of NILs and sub-NIls and for MAS transfer. The procedure for development of NILs using MAS will start in BC1 or BC1S1 population and will end in BC5S2 generation. For the development of NILs and sub-NILs, all markers will be PCR-based. Each selected QTL will be fine-mapped within 5-cm interval. Following the development of sub-NILs, individual or combinations of QTLs will be transferred to different genetic backgrounds by marker-assisted breeding. The procedure will be the same for both EB and LB QTLs. In case of LB, in addition to QTLs, we expect to identify new resistance genes (other than Ph1, Ph2 and Ph3) within resistant L. pimpinellifolium accessions. We will attempt to pyramid resistance genes and QTLs via marker-assisted breeding. In addition to MAS, traditional protocols of phenotypic selection and backcross breeding will be used to transfer disease resistance (in particular EB and LB) and improved fruit quality (in particular high fruit lycopene content).

Progress 07/01/05 to 09/30/08

Outputs
OUTPUTS: Basic genetic and applied breeding research were conducted on tomato resistance to early blight (EB), caused by fungi Alternaria solani and A. tomatophila, and late blight (LB), caused by oomycete Phytophthora infestans, and tomato fruit quality in particular fruit lycopene content. We developed a new RIL population of tomato from a cross between a Solanum lycopersicum breeding line and a desirable accession of S. pimpinellifolium. This population was evaluated for EB resistance and several other important traits under field conditions in multiple years. We also developed a molecular linkage map of this population using 294 co-dominant DNA markers, including RFLPs, ESTs, CAPS and SSRs. The map and the field data were employed to identify QTLs for several traits, including EB resistance for which 5 QTLs were identified, 3 of which consistent across years and generations. Co-localizations of EB-resistance QTLs with ESTs of candidate resistance genes were observed, suggesting potential involvement of such ESTs with EB resistance. Progress was made regarding the genetic basis of a new source of resistance to LB. We identified an accession of S. pimpinellifolium with resistance to at least 7 isolates of P. infestans. Experiments were conducted to identify and map genes or QTLs conferring resistance in this accession. Significant efforts resulted in identification of molecular markers polymorphic between this accession and a tomato breeding line. Using a selective genotyping approach and F2 and F3 populations, a new LB resistance gene, Ph-5, was identified and mapped. Efforts are underway to identify more polymorphic markers, develop near isogenic lines (NILs), and fine map and ultimately clone this gene. Resistance from this accession has been incorporated into our tomato breeding germplasm using traditional breeding protocols and marker-assisted selection technology. Inbred lines of cherry and grape tomatoes have been developed with this resistance. Research was conducted to explore the genetic basis of high fruit lycopene content in an accession of S. pimpinellifolium. Methods were improved to measure tomato fruit lycopene content accurately and efficiently. Using a RIL population, QTLs were identified for tomato fruit lycopene content, including 2 that were consistent across years and generations. Efforts are underway to develop NILs and to fine map and ultimately clone these QTLs. A patent was filed (currently pending) on the discovery of the new source of high fruit lycopene content and the new QTLs identified for this trait. Applied breeding research efforts were made to develop new tomato breeding lines and cultivars with commercial value using a combination of traditional breeding protocols and contemporary molecular techniques. Inbred lines of cherry, grape and plum fresh market tomatoes have been developed with improved disease resistance, exceptional fruit lycopene content and high yield, which are currently available for commercial trials. Experimental hybrids have been developed from crosses among these lines. Inbred lines and experimental hybrids of large-size fresh market and processing tomatoes are in the pipeline. PARTICIPANTS: Majid R. Foolad, Principal Investigator: Conceptualized the project, designed experiments and directed the research; conducted almost all of the field evaluations/screenings related to breeding activities; worked with graduate students in conducting greenhouse screening for disease resistance; contributed to gene mapping by statistical analyses; drafted and developed manuscripts, etc. Guoyang Lin, Sr. Res. Assistant (Technician): Grew and took care of plants in the field and greenhouse; made hybridizations among plants, harvested fruit and extracted seed; in charge of ordering laboratory chemicals and materials. Hamid Ashrafi, Graduate student and now postdoc: conducted molecular marker work in the lab and developed a genetic map; evaluated the RIL population for early blight resistance and fruit quality; conducted QTL mapping for traits of interest. Heather L. Merk, Graduate student: conducted molecular marker work in the lab, worked on late blight resistance project in the greenhouse and laboratory; identified and mapped a new LB resistance gene; assisted the PI in field evaluations. Matthew P. Kinkade, Graduate student: conducted molecular marker work in the lab, worked on fruit lycopene project, conducted genetic mapping and identified QTLs for fruit lycopene content; helped with the late blight resistance project. TARGET AUDIENCES: 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 RILs). 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. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
This research has resulted in identification of new sources of resistance to early blight (EB) and late blight (LB) as well as sources of high fruit lycopene content. These accessions have been useful for genetic characterization and mapping of desirable genes and QTLs in tomato. They also have been useful in our breeding program for development of tomatoes with improved desirable horticultural characteristics, including high yield, disease resistance and desirable fruit quality. It is anticipated that these accessions will also be useful to many other tomato researchers for both basic and applied breeding research. Using interspecific populations from crosses with these accessions we have developed a few new tomato genetic maps. These maps facilitate the utility of the identified wild accessions in genetic and breeding programs. We have employed the maps for the identification, mapping and characterization of desirable genes and QTLs, including those controlling disease resistance and high fruit quality characteristics. Such information has contributed to our better understanding of the genetic controls of the desirable traits and thus facilitated exploitation of the traits in our breeding program. For example, we have developed germplams carrying desirable genes and QTLs incorporated from the wild species. These include fresh-market and processing tomato inbred lines and experimental hybrids with improved yield, disease resistance and high fruit lycopene content. Some of these lines and hybrids will soon be shared with seed companies for commercial trials. Ultimately the release of these germplasms will provide benefits to growers, processors and consumers. The genetic maps as well as the genes and QTLs identified/characterized in this research will also be useful to other tomato researchers for various biological studies and breeding purposes. The identified genes and QTLs can be utilized for marker-assisted breeding of tomatoes with improved characteristics. Such genes and QTLs can also be used for basic research to decipher genetic and physiological mechanism underlying these traits. The improved germplasm will be useful to other tomato breeders for developing new and improved breeding lines and cultivars of tomatoes. The new inbred lines developed in this research will be useful for development of new and improved commercial cultivars. Our finding of a new gene for resistance to LB is particularly significant. Because it is different but complementary to other known genes for LB resistance in tomato, potentially it can be utilized for gene pyramiding and development of tomato breeding lines and cultivars with more durable LB resistance. Of similar importance is our identification of new sources of high fruit lycopene content and determination of QTLs controlling this trait. It is anticipated that these findings will facilitate development of tomatoes with higher levels of fruit lycopene content using contemporary techniques of molecular markers and marker-assisted selection.

Publications

  • Foolad, M. R. 2008. High Lycopene Content Tomato Plants and Markers for Use in Breeding for Same. 38 pages. (Pending).
  • Foolad, M. R. 2007. Genetics and breeding of disease resistance and improved fruit quality in tomato. In: Proc. Mid-Atlantic Fruit and Vegetable Convention, Hershey, PA. (Published as Supplement). p. 1.
  • Foolad, M. R., H. Ashrafi, A. Sharma, and G. Y. Lin. 2005. Genetics and breeding of early blight resistance in tomato. Proceeding of the 2005 EUCARPIA Tomato Meeting, Bari, Italy. Sept. 20-23. p. 7.
  • Foolad, M. R. 2005. Deployment of molecular markers and marker-assisted selection in tomato breeding. Proceeding of the 2005 EUCARPIA Tomato Meeting, Bari, Italy. Sept. 20-23. p. 31.
  • Ashrafi, H., A. Sharma, D. Nino-Liu, L. Zhang, and M. R. Foolad. 2005. Comparative mapping of early blight resistance QTLs and candidate resistance genes in F2, F3, F4 and a RIL population of tomato. Poster presented at Annual Conference of the American Society of Horticultural Science. Las Vegas, NV. July 18-21. p. 1040. (Abstract).
  • Ashrafi, M. and M. R. Foolad. 2005. Pre-sowing seed treatment - a shotgun approach to improve germination, plant growth and crop yield under saline and non-saline conditions. Advances in Agronomy. 88: 225-271.
  • Foolad, M. R., P. Subbiah, and L. Zhang. 2007. Common QTL affect the rate of tomato seed germination under different stress and non-stress conditions. Intl. J. Plant Genomics. vol. 2007. Article ID 97386. 10 pages. DOI: 10.1155/2007/97386.
  • Wahid, A., S. Gelani, A. Ashrafi, and M. R. Foolad. 2007. Heat tolerance in plants - A critical review. Env. Exp. Bot. 61 (2007) 199-223.
  • Foolad, M.R. 2007. Genome mapping and molecular breeding of tomato. International Journal of Plant Genomics. Vol. 2007. Article ID 64358. 52 pages. DOI: 10.1155/2007/64358.
  • Foolad, M. R., H. Merk, and H. Ashrafi. 2008. Genetics, genomics and breeding of late blight and early blight resistance in tomato. Cri. Rev. Plant Sci. 27: 75-107.
  • Sharma, A., L. Zhang, D. Nino-Liu, H. Ashrafi, and M. R. Foolad. 2008. A Solanum lycopersicum S. pimpinellifolium linkage map of tomato displaying genomic locations of R-genes, RGAs and candidate resistance/defense-response ESTs. Intl. J. Plant Genomics. (In Press).
  • Foolad, M. R. 2005. Recent development in stress tolerance breeding in tomato. In: Abiotic Stresses: Plant Resistance through Breeding and Molecular Approaches. M Ashraf and PJC Harris, eds. The Haworth Press Inc., New York, USA. pp. 613-684.
  • Foolad, M. R. 2007. Tolerance to abiotic stresses. In: Genetic Improvement of Solanaceous Crops, Vol. 2: Tomato. MK Razdan and AK Mattoo, eds. Science Publishers, Enfield, USA. pp. 521-592.
  • Foolad, M. R. 2007. Current status of breeding tomatoes for salt and drought tolerance. In: Advances in Molecular-Breeding Toward Drought and Salt Tolerant Crops. Jenks MA, Hasegawa PM and Jain M, eds. Springer, Heidelberg, Berlin, New York. pp. 669-700.
  • Foolad, M. R. 2008. Molecular markers and marker-assisted breeding in tomato. In: Genome Assisted Crop Improvement. Vol. II: Genome Applications in Crops. R. K. Varshney and R. Tuberosa, Eds., Springer, Dordrecht, The Netherlands. pp. 307-356.
  • Ashrafi, H., G. Y. Lin, and M. R. Foolad. 2006. Comparative mapping of early blight resistant QTLs and candidate resistance genes in early filial and a RIL population of tomato. Abstract in the Proceeding of the VI International Solanaceae Conference and Solanaceae Genomics Network, Madison, WI. July 23-27. (Abstract ID: 442).
  • Merk, H. L., H. Ashrafi, M. P. Kinkade, and M. R. Foolad. 2006. Identification and molecular mapping of a new dominant late blight resistance gene (Ph-5) in a Lycopersicon pimpinellifolium accession. Abstract in the Proceeding of the VI International Solanaceae Conference and Solanaceae Genomics Network, Madison, WI. July 23-27. (Abstract ID: 443).
  • Merk, H. L., M. P. Kinkade, H. Ashrafi, and M. R. Foolad. 2006. Identification and molecular mapping of a new dominant late blight resistance gene (Ph-5) in a Lycopersicon pimpinellifolium accession. In the Proceeding of Cross Over 2006, Exploring the Interface of the Life Sciences and Materials at Penn State, The Pennsylvania State University, University Park, PA. October 12. p. 50. (Abstract).
  • Ashrafi, H., A. Sharma, C. Kole, H. Merk, G. Y. Lin, and M. R. Foolad. 2006. Mapping of early blight resistance QTLs and candidate resistance genes in a RIL population of tomato. A poster presentation at The XIV International Conference on the Status of Plant and Animal Genome Research (PAG XIV). January 14-18, San Diego, CA. p. 218.


Progress 01/01/07 to 12/31/07

Outputs
OUTPUTS: Research was conducted on tomato resistance to early blight (EB), caused by fungi Alternaria solani and A. tomatophila, and late blight (LB), caused by oomycete Phytophthora infestans, and tomato fruit quality. A recombinant inbred line (RIL) population of tomato, which we developed during the past several years from a cross between a tomato (Solanum lycopersicum) breeding line and an accession of the tomato wild species S. pimpinellifolium, was evaluated for EB resistance and several other important traits under field condition. This study provided a fourth year field data on EB resistance in this population. We also expanded the molecular map of this population by adding more markers (total of 275). Five QTLs were identified for EB resistance, three of which located on chromosomes 5, 6 and 9 were consistent across years/ generations. Co-localizations of QTLs with candidate ESTs such as Mi-1, ethylene response factor-5, lipoxygenase B were also observed. Significant progress was made as to the identification and mapping of new LB resistance genes. Previously we had identified a new accession of S. pimpinellifolium with resistance to at least 7 isolates of P. infestans. Following screening of more than 450 molecular markers, we identified over 100 polymorphic markers for genetic mapping. Using a selective genotyping approach and F2 and F3 populations of a cross between the resistant accession and a susceptible tomato breeding line, a new LB resistance gene, Ph-5, has been identified and mapped. Currently, near isogenic lines (NILs) are being developed to fine map and ultimately clone Ph-5. This gene is also being incorporated into our tomato breeding lines using traditional breeding protocols as well as marker-assisted selection (MAS) technology. We have developed and utilized methods for accurate measurement of tomato fruit carotenoids content, which eliminate the cost and degradation issues inherent with HPLC-based assays. Using a RIL population of a cross between a lycopene-rich S. pimpinellifolium and a tomato breeding line we have identified QTLs for fruit lycopene content, including two that have been consistent across years and generations. Efforts are underway to develop NILs in order to fine map and ultimately clone these QTLs. Simultaneously efforts have been made to develop tomatoes with disease resistance, high fruit quality and high yield using traditional and contemporary breeding protocols. Desirable genes have been introgressed into our breeding germplasm, mainly from tomato wild species S. pimpinellifolium. We have developed new inbred lines of fresh-market plum, cherry and grape tomatoes. Inbred lines of large size fresh market as well as processing tomatoes are in the pipeline. In 2007, we developed and evaluated under field conditions a series of experimental hybrids, a subset of which was selected for industry review in 2008. Most of our inbred lines and hybrids are high yielding tomatoes with exceptional fruit lycopene content and good disease resistance. Efforts are underway to incorporate and pyramid LB resistance genes, including Ph-2, Ph-3 and Ph-5, into our fresh market and processing tomato lines and cultivars. PARTICIPANTS: Majid R. Foolad, Principal Investigator: Conceptualized the project, designed experiments and directed the research; conducted almost all of the field evaluations/screenings related to breeding activities; worked with graduate students in conducting greenhouse screening for disease resistance; contributed to gene mapping by statistical analyses; drafted and developed manuscripts; etc. Guoyang Lin, Sr. Res. Assistant (Technician): Grew and took care of plants in the field and greenhouse; made hybridizations among plants, harvested fruit and extracted seed; in charge of ordering laboratory chemicals and materials. Hamid Ashrafi, Graduate student and now postdoc: conducted molecular marker work in the lab and developed a genetic map; evaluated the RIL population for early blight resistance and fruit quality; conducted QTL mapping for traits of interest. Heather Merk, Graduate student: conducted molecular marker work in the lab, worked on late blight resistance project in the greenhouse and laboratory; identified and mapped a new LB resistance gene; assisted the PI in field evaluations. Matthew Kinkade, Graduate student: conducted molecular marker work in the lab, worked on fruit lycopene project, conducted genetic mapping and identified QTLs for fruit lycopene content; helped with the late blight resistance project. TARGET AUDIENCES: Scientific community: Through basic genetic discoveries, including identification and characterization of tomato germplams, 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 RILs). 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.

Impacts
This research has resulted in identification of new sources of resistance to early blight (EB) and late blight (LB) as well as sources of high fruit lycopene content. These accessions have been useful for genetic characterization and mapping of desirable genes and QTLs in tomato. The identified accessions have been extremely useful in our breeding program to develop tomatoes with improved desirable horticultural characteristics, including high fruit yield, disease resistance and improved fruit quality. We have developed new tomato genetic maps. The maps have been useful for the identification, mapping and characterization of desirable genes and QTLs, including those controlling disease resistance and high fruit quality characteristics. Such information has contributed to our better understanding of the genetic controls of the important horticultural characteristics studied in this research. The results also have contributed to the development of tomato germplams carrying the desirable genes incorporated from the wild species. As a result of this research, at Penn State we have developed fresh-market and processing tomatoes with improved yield, disease resistance and fruit lycopene content. It is expected that the release of these new tomatoes will provide benefits to growers, processors and consumers. The wild accessions, genetic maps, and the genes and QTLs identified/ characterized in this research are also useful to other tomato researchers for biological studies as well as breeding purposes. Specifically, the identified wild accessions and the improved germplasm are useful to tomato breeders for developing new and improved breeding lines and cultivars of tomatoes. The identified genes and QTLs can be utilized for marker-assisted breeding of tomatoes with improved characteristics. Such genes and QTLs can also be used for basic research to decipher genetic and physiological mechanism underlying the above mentioned traits. The new inbred lines developed in this research will be useful for development of new and improved commercial cultivars. In particular, our finding of new sources of resistance to LB is of paramount importance. As they are different but complementary to other source of LB resistance in tomato, they can be used for gene pyramiding and development of tomato breeding lines and cultivars with durable resistance. Furthermore, our identification of new sources of fruit lycopene content in tomato wild species and determination of QTLs controlling this trait will facilitate development of tomatoes with high level of fruit lycopene content using both traditional breeding protocols and contemporary molecular techniques.

Publications

  • Ashrafi, H. 2007. QTL mapping of early blight resistance and fruit quality related traits in a Lycopersicon esculentum x L. pimpinellifolium RIL population of tomato. Ph.D. Thesis. The Pennsylvania State University, University Park, PA. 221 pp.
  • Merk, H.L., H. Ashrafi, M.P. Kinkade and M.R. Foolad. 2007. Identification and mapping of new dominant gene conferring broad-spectrum resistance against late blight in tomato. Proceeding of The XV International Conference on the Status of Plant and Animal Genome Research (PAG XV). January 13-17, San Diego, CA. p. 210 (Abstract).
  • Ashrafi, H., M.P. Kinkade and M.R. Foolad. 2007. HPLC and spectrophotometer analyses of fruit carotenoids in a Lycopersicon esculentum, L. pimpinellifolium RIL population reveal several new QTLs for lycopene content. Proceeding of The XV International Conference on the Status of Plant and Animal Genome Research (PAG XV). January 13-17, San Diego, CA. p. 210 (Abstract).
  • Merk, H., H. Ashrafi, M. Kinkade and M.R. Foolad. 2007. Progress toward fine mapping of Ph5, a new late blight resistance gene in Tomato. Proceeding of the Tomato Breeders Roundtable, State College, PA. Nov. 4-7. p. 22 (Abstract).
  • Ashrafi, H., G.Y. Lin and M.R. Foolad. 2007. Mapping of early blight resistance QTLs in a RIL population of tomato. Proceeding of the Tomato Breeders Roundtable, State College, PA. Nov. 4-7. p. 23 (Abstract).
  • Foolad, M.R., G.Y. Lin and H. Merk. 2007. Development of fresh market and processing tomatoes at Penn State. Proceeding of the Tomato Breeders Roundtable, State College, PA. Nov. 4-7. p. 24 (Abstract).
  • Kinkade, M., H. Ashrafi and M.R. Foolad. 2007. Progress toward validation and isolation of novel genetic factors controlling lycopene content in a S. pimpinellifolium x S. lycopersicum RIL population. Proceeding of the Tomato Breeders Roundtable, State College, PA. Nov. 4-7. p. 31 (Abstract).


Progress 01/01/06 to 12/31/06

Outputs
Research was conducted on tomato resistance to early blight (EB), caused by fungi Alternaria solani and A. tomatophila, and late blight (LB), caused by oomycete Phytophthora infestans, and tomato fruit quality. A RIL population, which was developed from a cross between a Lycopersicon esculentum breeding line and an accession of L. pimpinellifolium, was evaluated in 2006 for resistance to EB under field condition. This study provided a third year field data on EB resistance in this population. The molecular map of this population was also expanded this year by adding more markers. Mapping analyses resulted in the identification of several QTLs for EB resistance in this population. Comparisons were made across the three years as to QTLs for EB resistance. As to the LB project, screening of wild tomato germplasm for resistance against new isolates of P. infestans was continued. Screenings were conducted using whole-plant and detached-leaflets under greenhouse and growth chamber conditions. Some new resistant accessions have been used for genetic mapping and breeding purposes. For example, a large F2 population (n = 1008) of a cross between a susceptible L. esculentum breeding line and a resistance accession of L. pimpinellifolium was developed and evaluated for LB resistance. The extreme resistant and susceptible individuals were selected for marker analysis. Extensive parental survey for marker polymorphism employing RFLPs, ESTs, CAPS, SSRs and RAPDs resulted in identification of about 90 polymorphic markers. A trait-based marker analysis (a.k.a. selective genotyping) resulted in identification and mapping of one major resistance gene. Research is underway to fine map this gene and possibly identify other resistance genes or QTLs in this population. The goal is to transfer resistance to our breeding lines via marker-assisted selection and to clone any major resistance gene(s) found in this population. Research was conducted to develop methods for fast and accurate measurement of fruit carotenoid content and to identify genetic components underlying high fruit lycopene content. While HPLC method provides accurate estimates of fruit carotenoid content, it requires specialized labor and the use of toxic solvents. We determined a fast and simple spectrophotometric method, which preserves the accuracy but eliminates the cost and degradation issues inherent with HPLC-based assays. Using interval mapping, we have identified several new QTLs, which collectively explain about 80% of the phenotypic variation for lycopene content in the RIL population. Alongside the basic research, efforts have been made to develop tomatoes with disease resistance, high fruit quality and high yield using traditional protocols of plant breeding. In 2006, thousands of crosses were made and hundreds of new populations developed. Tomato breeding materials of different generations and backgrounds were grown in 12 acres of land where they were evaluated for desirable characteristics and hundreds of selections were made. We have developed advanced breeding lines with desirable horticultural characteristics for production of commercial hybrid cultivars.

Impacts
This research has resulted in identification of new sources of resistance to EB and LB, and sources of high fruit lycopene content. These accessions will be useful for genetic characterization, mapping and cloning of desirable genes and QTLs in tomato. They also will be useful in breeding programs for developing improved cultivars. We have identified genes and QTLs for EB and LB resistance and for high fruit lycopene content. The identified QTLs for EB resistance can be used in marker-assisted breeding to develop tomatoes with improved EB resistance. We have developed fresh-market and processing tomato lines with improved EB resistance. These lines will be used to develop commercial hybrid cultivars. Our recent finding and mapping of major genes for LB resistance is of paramount importance. These genes are different from the previously-known LB-resistance genes; however, they are complementary. Pyramiding of resistance genes may lead to durable resistance against a broad spectrum of P. infestans isolates. Currently we are making efforts to combine different resistance genes in our breeding materials. The identification of genetic resources and QTLs for high fruit lycopene content will facilitate development of high-lycopene tomatoes using marker-assisted selection. Through our traditional breeding research we have developed tomato breeding liines with high fruit lycopene content which are being examined for development of commercial hybrid cultivars. The future release of these materials will be beneficial to the tomato industry as well as consumers.

Publications

  • Foolad, M. R. and Sharma, A. 2005. Molecular markers as selection tools in tomato breeding. Acta Hort 695: 225-240.
  • Foolad, M. R., Sharma, A., Ashrafi, H. and Lin, G. Y. 2005. Genetics of early blight resistance in tomato. Acta Hort 695: 397-406.
  • Foolad, M. R. 2006. Tolerance to abiotic stresses. In: Genetic Improvement of Solanaceous Crops, Vol. 2: Tomato. MK Razdan and AK Mattoo, eds. Science Publishers, Enfield, USA. pp. 509-578.
  • Foolad, M. R. and Lin, G. Y. 2006. Breeding tomatoes for early blight and late blight resistance, improved fruit quality, and adaptation to PA. Proc. of the 2006 Vegetable and Small Fruit Field Day. pp 7-10.
  • Ashrafi, H. and Foolad, M. R. 2006. Improving plant abiotic-stress resistance by exogenous application of osmoprotectants glycine betaine and proline. Environ. Exper. Bot. Accepted for Publication.
  • Foolad, M. R., Merk, H. L., Ashrafi, H. and Kinkade, M. P. 2006. Identification of new sources of late blight resistance in tomato and mapping of a new resistance gene. Proc. 21st Annual Tomato Disease Workshop, North Carolina State University, Fletcher NC, Nov. 9-10. Accepted for Publication.


Progress 01/01/05 to 12/31/05

Outputs
During the first six months of this project significant efforts were made to identify tomato wild accessions with resistance to oomycete Phytophthora infestans, the causal agent of tomato late blight (LB) disease. A few dozen tomato accessions, which we had previously identified with general disease resistance, were screened for resistance against 7 different isolates of the P. infestans. The evaluations were done at the whole-plant and detached-leaflet levels. Furthermore, whole plants were screened for LB resistance under both greenhouse and high-tunnel conditions. Extensive screenings resulted in the identification of a few accessions with exceptional resistance to LB. To identify and map resistance genes/QTLs, we have developed segregating populations from crosses between selected wild accessions and the cultivated tomato. Research is currently underway screening the segregating populations for LB resistance and developing a genetic linkage map using different molecular markers. During the past six months, we also continued our research on developing a new molecular linkage map of tomato based on an F8 RIL population of a cross between a cultivated tomato (Lycopersicon esculentum) line and an accession of L. pimpinellifolium. This population is segregating, and has been evaluated, for several agriculturally-important characteristics, including early blight (EB; caused by fungus Alternaria solani) and LB resistance, abiotic stress tolerance, and several fruit quality characteristics. We are investigating the genetic controls of several traits in this permanent mapping population, including the identification of contributing genes and/or QTLs. During the past six months, significant progress also has been made in our traditional breeding efforts to develop tomatoes with improved EB and LB resistance, high fruit quality, and tolerance to environmental stresses. During the summer of 2005, we grew and evaluated about 12 acres of tomato breeding materials and plants with desirable characteristics were selected and advanced.

Impacts
This research will identify new genetic resources which will be useful for both basic and applied research. The identified accessions will be used for genetic characterization, mapping and cloning of genes/QTLs controlling biologically and agriculturally important traits. They also will be utilized in breeding programs for transferring desirable characteristic to the cultivated tomato species. The identified wild accessions are currently being used in our genetics and breeding program to discern the genetic basis of important traits and to develop tomatoes with improved horticultural characteristics. Of particular significance is our findings of new resistance genes against aggressive isolates of P. infestans, the causal agent of tomato late blight. These genes will be combined with other known resistance genes to develop tomato cultivars with strong and durable resistance to late blight.

Publications

  • No publications reported this period