Progress 10/01/10 to 09/30/15
Outputs
Target Audience:Our target audience includes California tomato growers, food processors, seed company plant breeders, tomato industry personnel, UC Cooperative Extension personnel, scientists, undergraduate and graduate students at UC Davis, and the public. PI St.Clair and colleagues have published journal articles from the results of this project and presented project results at scientific meetings and conferences attended by scientists, agricultural industry personnel, growers and seed company plant breeders. The PI has presented the project and research results at meetings of California tomato growers and California food processors. Some conferences and meetings are also attended by agricultural and seed industry personnel, plant breeders and UC Cooperative Extension personnel. The PI also teaches undergraduate and graduate classes in plant breeding at UC Davis. Fresh water for agricultural production is a limited resource in the arid western US. Cultivated tomato (Solanum lycopersicum) is a major crop in California and is sensitive to water stress. Breeding cultivated tomato for productivity under limited water would enhance agricultural sustainability by reducing crop production inputs. Wild tomato species such as S. habrochaites can grow with limited water and withstand drought episodes and chilling temperatures. Genes in wild tomato species that confer water stress tolerance can be identified and used to breed tolerance in cultivated tomato. We are using genetics and genomics to identify genes from wild tomato that confer tolerance to water stress. Tomato breeding lines derived from wild tomato via marker-assisted selection are used to determine the genetic basis of water stress. Breeding lines can also serve as a resource for breeding water stress-tolerant cultivars that will enhance agricultural productivity and conserve valuable fresh water supplies. Cultivated tomato is also susceptible to many diseases including late blight. We've created advanced generation tomato breeding lines derived from late blight (P. infestans) resistant wild tomato (S. habrochaites) and higher-resolution mapped resistance and horticultural trait QTLs. We discovered favorable alleles from wild tomato that could prove beneficial to breeding. Advanced breeding lines will enable plant breeders to perform marker-assisted transfer of the valuable wild species QTL alleles into their elite inbred breeding lines used as parents in commercial hybrid cultivars. Our project bridges the gap between discovery of valuable QTL alleles in wild relatives of crop species and deployment of the wild species QTL alleles in breeding to further advance development of improved cultivars. Changes/Problems:The short arm of chromosome 9 is a gene-rich euchromatic region containing little repetitive DNA in the cultivated tomato (S. lycopersicum) reference genome. However, our sequence data has revealed that this syntenic region in S. habrochaites is structurally complex, containing highly repetitive DNA regions interspersed with low and single copy DNA. This complex genome structure complicates obtaining a scaffold sequence for S. habrochaites and subsequent gene annotation to assist with identification of candidate genes/polymorphisms for QTLs mapped to this region. It will require additional BACs in this region to be sequenced and/or PacBio sequencing of genomic DNA from S. habrochaites to obtain scaffold sequence for our target region on the short arm of chromosome 9. What opportunities for training and professional development has the project provided?During the five years of this project, with the mentorship and supervision of PI St.Clair, four graduate students (Ph.D. graduates Erron Haggard and Erin Arms, Masters graduates Emily Johnson and Jared Lounsbery), postdoctoral researcher Dr. Oded Cohen, and eight undergraduate assistants have received training in plant genetics, genomics and breeding research. Project activities included field experiments with interspecific tomato lines to assess water stress tolerance, horticultural traits, and late blight disease resistance; sequencing of S. habrochaites BAC genomic clones and sequence data analysis; mRNA-Seq transcriptome experiments and data analyses; statistical analysis of data from field experiments for horticultural, water stress tolerance traits, and late blight disease resistance traits; and mapping of QTLs. Arms, Lounsbery, Johnson and Haggard conducted field experiments, field data analyses and QTL mapping. Arms and Cohen in collaboration with bioinformatics experts conducted analyses on sequence data for S. habrochaites BAC clones. Arms conducted mRNA-Seq transcriptome experiments and data analyses. Undergraduate assistants assisted with research and related tasks. Undergraduate assistants were trained in methods required for plant genetics, genomics and breeding research, including PCR-marker analysis, using genomics databases in research, greenhouse plant care methods, data collection and data management. PI St.Clair teaches an annual undergraduate class in plant breeding (PLS154) at UC Davis. Our research was used to illustrate marker-assisted breeding, use of wild germplasm for crop improvement and QTL mapping using marker genotype data and trait data from this project. The lab exercises provide computer-based experiences for undergraduates in designing polymorphic genetic markers, creating a linkage map and using it to map QTL for plant traits. PI St.Clair also teaches graduate classes in plant breeding. How have the results been disseminated to communities of interest?PI St.Clair and colleagues have published journal articles from the results of this project and presented project results at scientific meetings and conferences, including Crop Science Society of America, Plant and Animal Genome, Plant Genomics Congress, and the American Seed Trade Association. Graduate students have presented research posters at conferences including Crop Science Society of America, and Plant and Animal Genome. The PI has presented the project and research results to California tomato growers, California food processors, tomato industry personnel, seed company plant breeders and UC Cooperative Extension personnel. The PI has also discussed the project with UC Cooperative Extension specialists and farm advisors. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Cultivated tomato (Solanum lycopersicum) is sensitive to abiotic stress caused by limited water availability. In contrast, some wild tomato species can tolerate limited water and withstand drought episodes. Previously, we identified a region on chromosome 9 in wild tomato (Solanum habrochaites) which contains a major effect QTL (stm9) conferring resistance to rapid-onset water stress caused by root chilling. The basis of this response is the ability to rapidly respond to water stress via root signaling to the leaves to close their stomata, thereby preventing wilting (water loss). We used marker-assisted selection to obtain a set of sub-near-isogenic lines (sub-NILs) for the S. habrochaites chromosome 9 region containing QTL stm9. We used these sub-NILs to conduct high-resolution mapping of QTL stm9, localizing it to a 0.32 cM region. To analyze chromosome 9 sequence, we obtained PacBio long-read sequence for 30 clones from our S. habrochaites BAC genomic library and compared it to the contigs to our prior Illumina data on these BACs. We have discovered that this chromosome 9 region in S.habrochaites has highly repetitive DNA regions interspersed between low and single copy DNA, in contrast to the syntenic region in the cultivated tomato reference genome that is gene-rich with little repetitive DNA. To obtain scaffold for this region in S. habrochaites, it will require additional sequencing, preferably with PacBio. To facilitate candidate gene identification for QTL stm9, we conducted mRNA-Seq experiments with paired sub-NILs subjected to root chilling. We used this data to identify transcripts that may be associated with the tolerant phenotype for testing as candidate genes. We identified a number of potential candidates. Gene knock-out constructs are being created for four candidate genes in the QTL stm9 region. We conducted field experiments with sub-NILs to determine if the chromosome 9 region also confers tolerance to slow-onset water stress induced by restricted irrigation. Trait data from several years of replicated field experiments with chromosome 9 sub-NILs subjected to two levels of irrigation (full and one-third of evapotranspiration for tomato) revealed multiple QTLs for plant and fruit traits in a gene-rich region of chromosome 9, including QTLs for yield, maturity and plant biomass. In general, QTLs for most plant and fruit traits were closely linked to, but not coincident with, QTL stm9. The S. habrochaites genes conferring water stress tolerance would provide ideal targets for marker-assisted breeding to improve abiotic stress tolerance of cultivated tomato. In addition, we used marker-assisted selection to generate a new set of sub-NILs for chromosome 9 from S. habrochaites that extends proximally towards the centromere. These new sub-NILs will be used to further resolve the location of multiple QTLs for traits associated with water stress tolerance: delta-13 (water use efficiency), biomass and specific leaf area.The sub-NILs we produced are advanced generation tomato breeding lines that can serve as a genetic resource for breeding water-stress tolerant tomato cultivars. Cultivated tomato is susceptible to many pathogens, including Phytophthora infestans, causal agent of late blight disease. Some accessions of wild tomato have high levels of resistance to this pathogen. We investigated the genetic basis of this resistance in S. habrochaites. During this project we completed several years of replicated field experiments conducted with chromosome 5 and 11 sub-NILs derived from late blight resistant wild tomato S. habrochaites. All data analyses were completed and QTL mapped. Within each introgressed chromosome region, we mapped multiple QTLs for late blight resistance and horticultural traits, indicating complex genetic architecture. We also conducted combining ability studies and determined that disease resistance is expressed in F1 hybrid combinations between resistant sub-NILs and susceptible cultivated tomato. Sub-NIL breeding lines that would be suitable to use in subsequent breeding efforts were identified.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Lounsbery, J., E.M. Arms, A.J. Bloom, and D.A. St.Clair. 2015. QTL for water stress tolerance traits localize on chromosome 9 of wild tomato Solanum habrochaites. Crop Sci. doi:10.2135/cropsci2015.07.0432
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Haggard, J.E., E.B. Johnson, and D.A. St. Clair. 2015. Multiple QTL for horticultural traits and quantitative resistance to Phytophthora infestans linked on Solanum habrochaites chromosome 11. G3. 5:219-233. doi:10.1534/g3.114.014654
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Arms, E.M., A.J. Bloom, and D.A. St. Clair. 2015. High-resolution mapping of a major effect QTL from wild tomato Solanum habrochaites that influences water relations under root chilling. Theor. Appl. Genet. 128: 1713-1724. doi:10.1007/s00122-015-2540-y.
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Progress 10/01/13 to 09/30/14
Outputs
Target Audience: Our target audience includes California tomato growers, food processors, seed company plant breeders, UC Cooperative Extension personnel, our scientific peers, undergraduate and graduate students at UC Davis and the public. Fresh water for agricultural production is a limited resource in the arid western US. Cultivated tomato (Solanum lycopersicum) is a major crop in California and is sensitive to water stress. Breeding cultivated tomato for productivity under limited water would enhance agricultural sustainability by reducing crop production inputs. Wild tomato species such as S. habrochaites can grow with limited water and withstand drought episodes and chilling temperatures. Genes in wild tomato species that confer water stress tolerance can be identified and used to breed tolerance in cultivated tomato. We are using genetics and genomics methods to identify genes from wild tomato that confer tolerance to water stress. We created tomato breeding lines derived from wild tomato using marker-assisted selection. The breeding lines were evaluated in field experiments over several years, and multiple traits associated with tolerance to limited water were mapped to this region. These breeding lines can serve as a resource for breeding water stress-tolerant cultivars that will enhance agricultural productivity and conserve valuable fresh water supplies. We created advanced generation tomato breeding lines derived from late blight (P. infestans) resistant wild tomato (S. habrochaites) and higher-resolution mapped resistance and horticultural trait QTLs. We discovered favorable alleles from wild tomato that could prove beneficial to breeding. Advanced breeding lines will enable plant breeders to perform marker-assisted transfer of the valuable wild species QTL alleles into their elite inbred breeding lines used as parents in commercial hybrid cultivars. Our project bridges the gap between discovery of valuable QTL alleles in wild relatives of crop species and deployment of the wild species QTL alleles in breeding to further advance development of improved cultivars. Changes/Problems: The short arm of chromosome 9 is a gene-rich euchromatic region containing little repetitive DNA in the cultivated tomato (S. lycopersicum) reference genome. However, our sequence data has revealed that this syntenic region in S. habrochaites is structurally complex, containing highly repetitive DNA regions interspersed with low and single copy DNA. This complex genome structure complicates obtaining a scaffold sequence for S. habrochaites and subsequent gene annotation to assist with identification of candidate genes/polymorphisms for QTLs mapped to this region. It will require additional BACs in this region to be sequenced and/or PacBio sequencing of genomic DNA from S. habrochaites to obtain scaffold sequence for our target region on the short arm of chromosome 9. What opportunities for training and professional development has the project provided? Under the mentorship and supervision of PI St.Clair, several graduate students (Ph.D. graduate Erron Haggard, Ph.D. candidate Erin Arms, and Masters candidate Jared Lounsbery), postdoc Oded Cohen, and undergraduate assistants have received training in plant genetics, genomics and breeding research. Project activities included sequencing of S. habrochaites BAC genomic clones and sequence data analysis; obtaining mRNA-Seq transcriptome data for paired sub-NILs for chromosome 9 and data analyses; completion of data analysis from field experiments for horticultural, water stress tolerance traits, and late blight disease resistance traits and mapping of QTLs. Ms. Arms, Mr. Lounsbery and Mr. Haggard conducted the field experiments, field data analyses and QTL mapping. Ms. Arms and Mr. Cohen in collaboration with bioinformatics experts are conducting bioinformatics analyses on sequence data for S. habrochaites BAC clones and mRNA-Seq transcriptome data. Undergraduate assistants were supervised by the graduate students and postdoc, and assisted with research and related tasks. Undergraduate assistants were trained in methods required for plant genetics, genomics and breeding research, including PCR-marker analysis, using genomics databases in research, greenhouse plant care methods, data collection and data management. PI St.Clair teaches an annual undergraduate class in plant breeding (PLS154) at UC-Davis. This research project was used to illustrate marker-assisted breeding, use of wild germplasm for crop improvement and QTL mapping using marker genotype data and trait data from this project. The lab exercises provide computer-based experiences for undergraduates in designing polymorphic genetic markers, creating a linkage map and using it to map QTL for plant traits. How have the results been disseminated to communities of interest? PI St.Clair and colleagues have published journal articles from the results of this project and presented project results at scientific meetings and conferences, including the 2014 Crop Science Society of America conference, the Plant and Animal Genome conference, and the American Seed Trade Association meeting. The PI has presented the project and results to California tomato growers, tomato food processors and seed industry personnel. The PI has discussed the project with UC cooperative extension specialists and farm advisors. What do you plan to do during the next reporting period to accomplish the goals? We will continue our genetics and genomics analyses of the chromosome 9 region from S. habrochaites. This will include additional sequencing of S. habrochaites and bioinformatics analyses and mRNA-Seq data analyses. We will employ the results of these analyses towards the identification of QTL candidate genes for subsequent functional testing. We are also using marker-assisted selection to generate a new set of sub-NILs for chromosome 9 from S. habrochaites that extends towards the centromere. These new sub-NILs will be used to resolve the location of multiple QTLs for traits associated with water stress tolerance: delta-13 (water use efficiency) and specific leaf area.
Impacts
What was accomplished under these goals?
Cultivated tomato (Solanum lycopersicum) is sensitive to abiotic stress caused by limited water availability, while some wild tomato species can tolerate limited water and withstand drought episodes. Previously, we identified a region on chromosome 9 in wild tomato (Solanum habrochaites) which contains a major effect QTL (stm9) conferring resistance to rapid-onset water stress caused by root chilling. The basis of this response is the ability to rapidly respond to water stress via root signaling to the leaves to close their stomata, thereby preventing wilting (water loss). We used marker-assisted selection to obtain a set of sub-near-isogenic lines (sub-NILs) for the S. habrochaites chromosome 9 region containing QTL stm9. We used these sub-NILs to conduct high-resolution mapping of QTL stm9, localizing it to a 0.32 cM region. We obtained PacBio long-read sequence for 30 clones from our S. habrochaites BAC genomic library and are comparing the contigs to our prior Illumina data on these BACs. We have discovered that this chromosome 9 region in S.habrochaites has highly repetitive DNA regions interspersed between low and single copy DNA, in contrast to the syntenic region in the cultivated tomato reference genome that is gene-rich with little repetitive DNA. To obtain scaffold for this region in S. habrochaites, it will require additional sequencing, preferably with PacBio. To facilitate candidate gene identification, we conducted mRNA-Seq experiments with paired sub-NILs subjected to root chilling, and are analyzing this data to identify transcripts that may be associated with the tolerant phenotype for testing as candidate genes. Trait data from several years of replicated field experiments with chromosome 9 sub-NILs subjected to two levels of irrigation (full and one-third of evapotranspiration for tomato) revealed multiple QTLs for plant and fruit traits in a gene-rich region of chromosome 9, including QTLs for yield, maturity and plant biomass. In general, QTLs for most plant and fruit traits were closely linked to, but not coincident with, QTL stm9. The S. habrochaites genes conferring water stress tolerance would provide ideal targets for marker-assisted breeding to improve abiotic stress tolerance of cultivated tomato. The sub-NILs we produced are advanced generation tomato breeding lines that can serve as a genetic resource for breeding water-stress tolerant tomato cultivars. We also completed analyses of data obtained previously from replicated field experiments conducted with chromosome 5 and 11 sub-NILs derived from late blight resistant wild tomato S. habrochaites. Within each chromosome region, we mapped multiple QTLs for resistance and for horticultural traits. Breeding lines that would be suitable to use in subsequent breeding efforts were identified.
Publications
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2014
Citation:
Haggard, J.E., Johnson, E.B. and St.Clair, D.A. Multiple QTL for horticultural traits and quantitative resistance to Phytophthora infestans linked on Solanum habrochaites chromosome 11. G3: Genes, Genomes, Genetics (in press)
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Haggard J.E. and D.A. St.Clair. Combining ability for Phytophthora infestans quantitative resistance from wild tomato. Crop Science (doi: 10.2135/cropsci2014.04.0286).
|
Progress 01/01/13 to 09/30/13
Outputs
Target Audience: Target audiences include seed company breeders, tomato growers, consumers, tomato processing industry members and the public. Fresh water for agricultural production is a limited resource in the arid western US. Water stress decreases crop productivity and yield. Cultivated tomato (Solanum lycopersicum) is sensitive to water stress, causing reduced fruit yields. Breeding cultivated tomato for productivity under limited water would enhance agricultural sustainability by reducing crop production inputs. Some wild tomato species such as S. habrochaites have the ability to grow with limited water and withstand drought episodes and chilling temperatures. Genes in wild tomato species that confer water stress tolerance can be identified and used to breed tolerance in cultivated tomato. We are using genetics and genomics methods to identify the genes from wild tomato that confer tolerance to water stress. We created tomato breeding lines derived from wild tomato using marker-assisted selection. The breeding lines were evaluated in field experiments over several years, and multiple traits associated with tolerance to limited water mapped to this region. These breeding lines can serve as a resource for breeding water stress tolerant cultivars that will enhance agricultural productivity and conserve valuable fresh water supplies. We created advanced generation tomato breeding lines derived from late blight (P. infestans) resistant wild tomato (S. habrochaites) and higher-resolution mapped resistance and horticultural trait QTLs. We discovered favorable alleles from wild tomato that could prove beneficial to breeding. Advanced breeding lines will enable plant breeders to perform marker-assisted transfer of the valuable wild species QTL alleles into their elite inbred breeding lines used as parents in commercial hybrid cultivars. Our project bridges the gap between discovery of valuable QTL alleles in wild relatives of crop species and deployment of the wild species QTL alleles in breeding to further advance development of improved cultivars. Changes/Problems: The Illumina sequencing data (reads) for our 33 S. habrochaites BAC genomic clones for chromosome 9 has proven to be significantly more complex to analyze than anticipated. Our flow cytometry results from 2010 indicated that S. habrochaites has a genome size 1.5 x larger than S. lycopersicum, strongly suggesting the presence of additional repetitive sequences in the wild species. The initial analyses during winter/spring 2013 of our BAC read data by the UCD Genome Center Bioinformatics Core personnel did not lead to conclusive results. This was likely due to repeated sequences in the S. habrochaites genome that are not present in the reference genome sequence of cultivated tomato (S. lycopersicum cv. H1706, available on the SGN website). Repeated sequence complicates read alignment to a reference genome and complicates scaffolding. To address this issue, since summer 2013 we have been collaborating with UCD bioinformatics professor Dr. Ian Korf on the analysis of the BAC Illumina reads and creation of scaffold sequence for S. habrochaites chromosome 9. We will also obtain longer read data for our BACs using the PacBio platform that will assist in contig assembly and scaffolding. What opportunities for training and professional development has the project provided? Under the mentorship and supervision of PI St.Clair, several graduate students (Ph.D. candidates Erin Arms, Erron Haggard, Masters candidate Jared Lounsbery), and undergraduate assistants have received training in plant breeding, genetics and genomics research. Project activities included completing hydroponic tank experiments with chromosome 9 sub-NILs for high resolution QTL mapping; conducting replicated field experiments across two years with chromosome 9 sub-NILs under restricted irrigation to assess plant and fruit trait responses to water stress and map traits; statistically analyzing trait data and mapping trait QTLs on chromosome 9; sequencing of S. habrochaites BAC genomic clones and sequence data analysis; completion of data analysis for horticultural and late blight disease resistance traits for sub-NILs for chromosomes 5 and 11 and mapping of QTLs. Ms. Arms conducted the hydroponic tank experiments; Ms. Arms, Mr. Lounsbery and undergraduate assistants conducted the field experiments, Ms. Arms, Mr. Lounsbery and Mr. Haggard conducted data analyses and QTL mapping, and Ms. Arms is working with bioinformatics experts on analyzing sequence data for S. habrochaites BAC clones. Undergraduate assistants were supervised by the graduate students and assisted with lab, field and greenhouse research and related tasks. Undergraduate assistants were trained in methods required for plant genetics and breeding research, including PCR-marker analysis, using genomics databases in research, greenhouse plant care methods, field research methods, data collection from field experiments, and data management. PI St.Clair teaches an annual undergraduate class in plant breeding (PLS154) at UC-Davis. This research project was used to illustrate to the class marker-assisted breeding, use of wild germplasm for crop improvement and QTL mapping. The PI developed several new class laboratory exercises on linkage and QTL mapping using marker genotype data and trait data from this project. The new lab exercises provides computer-based experiences for undergraduates in designing polymorphic genetic markers, creating a linkage map and using it to map QTL for plant traits. How have the results been disseminated to communities of interest? PI St.Clair and colleagues have published journal articles from the results of this project and presented project results at scientific meetings and seminars. The PI has presented project results to California tomato growers, tomato food processors and seed industry personnel. The PI has discussed the project with UC cooperative extension specialists and farm advisors. What do you plan to do during the next reporting period to accomplish the goals? We will continue our genetics and genomics analyses of the chromosome 9 region from S. habrochaites. This will include further sequencing and bioinformatic analyses of S. habrochaites BAC clones, mRNA-Seq analysis of sub-NILs, and identification of QTL candidate genes for subsequent functional testing.
Impacts
What was accomplished under these goals?
Cultivated tomato (Solanum lycopersicum) is sensitive to abiotic stress caused by limited water availability. Breeding cultivated tomato for productivity under limited water would enhance agricultural sustainability. Some wild tomato species have the ability to tolerate limited water and withstand drought episodes. Genes in wild tomato species that confer water stress tolerance can be identified and used to breed tolerance in cultivated tomato. Previously, we identified a region on chromosome 9 in wild tomato (Solanum habrochaites) which contains a major effect QTL (stm9) conferring resistance to rapid-onset water stress caused by root chilling. The basis of this response is the ability to rapidly respond to water stress via root signaling to the leaves to close their stomata, thereby preventing wilting (water loss) and plant damage. We used marker-assisted selection to obtain a set of sub-near-isogenic lines (sub-NILs) for the S. habrochaites chromosome 9 region containing QTL stm9. We evaluated the sub-NILs in replicated hydroponic tank experiments and completed high-resolution mapping of QTL stm9, localizing it to a 0.32 cM region. We identified 33 clones from our S. habrochaites BAC genomic library for the stm9-containing region. The BACs were sequenced with Illumina and we are collaborating with bioinformatics experts to analyze this data and use it for candidate gene discovery. We completed several years of replicated field experiments with chromosome 9 sub-NILs subjected to two levels of irrigation (full and one-third of evapotranspiration for tomato) to map traits associated with water stress tolerance. Phenotypic data for fruit and plant traits was collected, statistically analyzed and used for QTL mapping. We detected multiple QTLs for plant and fruit traits in a gene-rich region of chromosome 9, including QTLs for yield, maturity and plant biomass. In general, QTL for most plant and fruit traits were closely linked to, but not coincident with, QTL stm9. To verify our results from 2012, we repeated the field experiment in 2013. Field trait data collection was completed in October 2013. All trait data is being statistically analyzed and results from 2012 and 2013 are being compared. Some traits exhibit genotype by year (and/or location) interactions, while others are relatively stable. Our research will determine the contribution of the chromosome 9 region from S. habrochaites to growth and productivity of tomato plants subjected to water stress. The S. habrochaites genes conferring water stress tolerance would provide ideal targets for marker-assisted breeding to improve abiotic stress tolerance of cultivated tomato. The sub-NILs we produced are advanced generation tomato breeding lines that can serve as a genetic resource for breeding water-stress tolerant tomato cultivars. We also completed analyses of data obtained previously from replicated field experiments conducted with chromosome 5 and 11 sub-NILs derived from late blight resistant wild tomato S. habrochaites. Within each chromosome region, we mapped multiple QTLs for resistance and for horticultural traits. Breeding lines that would be suitable to use in subsequent breeding efforts were identified.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Easlon, H.M., St.Clair, D.A., and Bloom, A.J. (2013) An introgression from wild tomato (Solanum habrochaites) affects tomato photosynthesis and water relations. Crop Science, doi: 10.2135/cropsci2013.06.0401; Posted online 27 Nov. 2013.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Easlon, H.M., Rubio Asensio, J.S., St.Clair, D.A. and Bloom, A.J. (2013) Chilling-induced water stress: variation in shoot turgor maintenance among wild tomato species from diverse habitats. American Journal of Botany 100: 1991-1999.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Haggard, J.E., Johnson, E.B. and St.Clair, D.A. (2013) Linkage relationships among multiple QTL for horticultural traits and late blight (P. infestans) resistance on chromosome 5 introgressed from wild tomato Solanum habrochaites. G3: Genes, Genomes, Genetics 3: 2131-2146.
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Progress 01/01/12 to 12/31/12
Outputs
OUTPUTS: California tomatoes for processing and fresh market uses have a farm-gate value of over $1 billion annually. The UC-Davis tomato breeding and genetics research program focuses on the use of wild tomato species diversity for the genetic improvement of quantitatively inherited traits of economic and agricultural importance. Advanced breeding lines (pre-bred lines) of cultivated tomato (Solanum lycopersicum) containing genes introgressed from wild tomato are created as a resource for tomato improvement efforts. We map traits and identify DNA markers tightly linked to target quantitative trait loci (QTLs) that are useful for marker-assisted breeding in tomato. The determination of causal gene(s) for QTLs will provide specific targets for marker-assisted selection (MAS) breeding efforts as well as for furthering understanding of basic trait biology. Our research demonstrates the value of marker-assisted gene introgression from wild species in applied crop breeding programs. Improvement of traits that would benefit California tomato production includes resistances to biotic stresses (e.g., diseases and pests) and abiotic stresses (e.g., temperature extremes and restricted water). We are investigating the genetic basis of quantitative resistance to late blight disease (caused by Phytophthora infestans) from wild tomato and are researching the genetic and genomic bases of tolerance to water stress from wild tomato. Rapid-onset water stress can be induced by chilling roots. Wild tomato (Solanum habrochaites) responds to root chilling by closing stomata and maintaining shoot turgor, while cultivated tomato (S. lycopersicum) does not close its stomata and the shoots wilt. Previously we identified a major QTL from wild S. habrochaites for shoot turgor maintenance under rapid-onset water stress via root chilling, and localized to a 2.7 cM region on chromosome 9 (i.e., QTL stm9). We recently high-resolution mapped and localized stm9 to a 0.32 cM region. Our current and longer term project objectives are to: sequence this chromosome 9 region from S. habrochaites and identify candidate genes for stm9; perform functional tests of gene candidates; perform comparative re-sequencing of wild species alleles at stm9 gene(s); conduct experiments with chromosome 9 sub-NILs to evaluate traits under water stress. The oomycete Phytophthora infestans, causal agent of late blight disease, is a major pathogen of tomato and causes extensive crop damage and losses. Cultivated tomato (S. lycopersicum) is susceptible, but wild S. habrochaites is highly resistant. Previously we mapped several major quantitative resistance QTLs from wild S. habrochaites, and fine-mapped QTLs on chromosomes 5 and 11 in sub-near-isogenic lines. Our project objectives included: higher-resolution mapping of two resistance QTLs on chromosomes 5 and 11 and horticultural trait QTLs for marker-assisted breeding; determine linkage relationships among trait QTLs in the introgressed regions from S. habrochaites; and assess combining ability of F1 hybrids between elite inbred lines and selected sub-NILs for late blight disease resistance. PARTICIPANTS: PI/PD Dr. Dina St.Clair leads the project, sets priorities, organizes tasks, and supervises project personnel, including plant breeding graduate students Erin Arms, J. Erron Haggard, Jared Lounsbery, Emily Johnson (former M.Sc. student, graduated March 2012), and undergraduate assistants. Dr. Arnold Bloom provides plant physiology expertise on water stress research. Activities for the water stress research included: greenhouse propagation of plants via seed and vegetative cuttings; conducting hydroponic tank experiments with sub-NIL seedlings to assess shoot turgor maintenance under root chilling; propagation via self-pollination of homozygous sub-NILs; conducting replicated field experiments to assess response to restricted drip irrigation. Ms. Arms conducted hydroponic tank experiments, and Ms. Arms and Mr. Lounsbery conducted replicated field experiments on the sub-NILs under normal and restricted drip irrigation, collected trait data and performed statistical and QTL mapping analyses. Activities for the late blight resistance research included: propagating marker-selected sub-NILs via seed and plants in the greenhouse; conducting replicated field experiments with sub-NILs and collecting plant and fruit trait data; maintaining P. infestans isolates and producing inoculum for experiments; statistically analyzing field data. Ms. Johnson and Mr. Haggard conducted the replicated field experiments with undergraduate assistants, collected plant and fruit data from the field experiments; Ms. Johnson assayed resistance of sub-NILs to P. infestans isolates in replicated growth chamber experiments; Ms. Johnson and Mr. Haggard analyzed trait data, mapped QTLs, and wrote (or are writing) manuscripts for publication. Undergraduate assistants helped with field, lab and greenhouse tasks, and were trained in plant genetics and breeding research methods, including pathogen isolate culturing, PCR-marker analysis, greenhouse plant care, propagation via seed and cuttings, and data collection. Dr. St.Clair teaches an annual undergraduate class in plant breeding (PLS154) at UC-Davis. Several computer-based laboratory exercises were developed for the class with the trait and genotype data from the water stress resistance project to illustrate linkage and QTL mapping. TARGET AUDIENCES: Fresh water for agricultural production is a limited resource in many parts of the US, particularly the arid west. Water stress decreases crop productivity and yield. Cultivated tomato (Solanum lycopersicum) is sensitive to stress caused by limited water availability, and fruit yields are reduced. Breeding cultivated tomato for productivity under limited water would enhance agricultural sustainability. Wild tomato species have the ability to grow with limited water and withstand drought episodes and chilling temperatures. Genes in wild tomato species that confer water stress tolerance can be identified and used to breed tolerance in cultivated tomato. Previously, we identified a region on chromosome 9 in wild tomato (Solanum habrochaites) that confers resistance to rapid onset water stress caused by root chilling. The basis of this response is the ability to rapidly respond to water stress via root signaling to the leaves to close their pores (stomata), thereby preventing wilting (water loss). In this project, we are using genetics and genomic techniques to identify the genes from wild tomato that confer tolerance to water stress. We have created tomato breeding lines containing the water stress tolerance genes from wild tomato using marker-assisted selection. The breeding lines were evaluated in field experiments, and multiple traits associated with tolerance to limited water availability mapped to this region. Breeding lines with wild tomato genes can serve as a resource for breeding water stress tolerant cultivars that will enhance agricultural productivity and conserve valuable fresh water supplies. We created advanced generation tomato breeding lines containing the P. infestans resistance QTLs from wild tomato (S. habrochaites) and identified markers tightly linked to the QTLs. Linked markers and advanced breeding lines will enable plant breeders to perform marker-assisted transfer of the valuable wild species resistance QTL alleles into their elite inbred breeding lines used as parents in commercial F1 hybrid cultivars. From the mapping of horticultural trait loci, we have discovered favorable alleles from wild tomato that could prove beneficial to breeding. Our project bridges the gap between discovery of valuable QTL alleles in wild relatives of crop species and the effective deployment of the wild species QTL alleles in breeding programs to enhance development of improved cultivars. Target audiences include seed company tomato breeders, tomato growers, consumers, and tomato industry members. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
For characterization of rapid onset water stress controlled by the chromosome 9 region containing QTL stm9, we used 18 unique sub-near-isogenic lines (sub-NILs) for this S. habrochaites introgressed region. Replicated phenotyping of the 18 sub-NILs for shoot turgor maintenance under root chilling was performed and trait data used to high-resolution map stm9 to a 0.32 cM region. During summer to fall 2012 we conducted replicated field experiments at two California field locations with the same set of 18 sub-NILs plus controls T5 and stm9 NIL under two drip irrigation treatments (normal and 1/3 evapotranspiration rate (ETo) for tomato). Significant differences for shoot biomass, fruit yield and other horticultural traits were detected among the sub-NILs for 1/3 ETo, indicating that the genotypes varied for tolerance to slower-onset water stress. Using the field data, horticultural trait QTLs were mapped in the introgressed region. Interestingly field horticultural trait QTLs did not overlap with the 0.32 cM region containing QTL stm9, suggesting different genes in this region control traits associated with water stress tolerance. Previously we identified a set of 33 S. habrochaites BAC clones from our genomic library for the stm9 region, and during fall 2012 these clones were sequenced on Illumina HiSeq. Bioinformatics analyses of the sequence reads are in progress to create assemblies and scaffolds of this chromosome 9 region from S. habrochaites. Our P. infestans resistance research employed marker-selected sub-NILs for resistance QTLs on chromosomes 5 and 11 introgressed from S. habrochaites. We completed replicated field experiments (two years and several locations) with the sub-NILs and obtained data on resistance to late blight and horticultural traits. We used the trait data and marker genotype data on the sub-NILs to higher-resolution map the QTLs for each trait. We determined that the resistance QTLs fractionated into multiple QTLs on both chromosomes 5 and 11, suggesting complex genetic architecture. Most horticultural traits also mapped to two or more QTLs per chromosome region, demonstrating complex inheritance and indicating multiple loci control each trait. Sub-NILs with resistance to P. infestans and acceptable horticultural traits were identified as pre-bred lines for breeding programs. A combining ability study was completed on F1 hybrids between selected sub-NILs and commercial inbred cultivars evaluated in replicated field experiments. F1 hybrids and their parents were phenotyped for P. infestans resistance and horticultural traits. Trait data analyses indicated that the sub-NILs contributed late blight disease resistance to their hybrid progeny, suggesting their potential usefulness in breeding cultivated tomato for increased disease resistance.
Publications
- Johnson, E.B., Haggard, J.E., St.Clair, D.A. (2012) Fractionation, stability, and isolate-specificity of QTL for resistance to Phytophthora infestans in cultivated tomato (Solanum lycopersicum). G3: Genes, Genomes, Genetics 3: 1145-1159.
- Haggard, J.E., Johnson, E.B., St.Clair, D.A. (2012) Combining ability of tomato lines with quantitative resistance to Phytophthora infestans introgressed from wild tomato. Proceedings, Plant and Animal Genome XX Conference, San Diego, CA.
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Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: Tomatoes grown in California for processing and fresh market uses have a farm-gate value of over $1 billion annually. The UC-Davis tomato breeding and genetics research program focuses on the use of wild tomato species diversity for the genetic improvement of quantitatively inherited traits of economic and agricultural importance. Advanced breeding lines (pre-bred lines) of cultivated tomato (Solanum lycopersicum) containing genes introgressed from wild tomato are created as a resource for tomato improvement efforts. We map traits to obtain DNA markers tightly linked to target quantitative trait loci (QTLs) that are useful for marker-assisted breeding in tomato. The determination of causal gene(s) for QTLs provides specific targets for marker-assisted selection (MAS) breeding efforts as well as for furthering understanding of basic trait biology. Our research demonstrates the value of marker-assisted gene introgression from wild species in applied crop breeding programs. Improvement of traits that would benefit California tomato production includes resistances to biotic stresses (e.g., diseases and pests) and abiotic stresses (e.g., temperature extremes and restricted water). We are investigating the genetic basis of quantitative resistance to late blight disease (caused by Phytophthora infestans) from wild tomato and are researching the genetic and genomic bases of tolerance to rapid-onset water stress in tomato. Rapid-onset water stress can be induced by chilling roots. Wild tomato (Solanum habrochaites) responds to root chilling by closing stomata and maintaining shoot turgor, while cultivated tomato (S. lycopersicum) does not close its stomata and the shoots wilt. Previously we identified a major QTL from wild S. habrochaites for shoot turgor maintenance under rapid-onset water stress via root chilling. This QTL localized to a 2.7 cM region on chromosome 9 (i.e., QTL stm9). Our current project objectives are to: perform high-resolution mapping of stm9 and identify candidate genes; perform functional tests for stm9 candidate genes; perform comparative re-sequencing of wild species alleles at stm9 gene(s); conduct experiments with stm9 recombinants to evaluate growth responses after drought episode(s). The oomycete Phytophthora infestans, causal agent of late blight disease, is a major pathogen of tomato and causes extensive crop damage and losses. Cultivated tomato (S. lycopersicum) is susceptible, but wild S. habrochaites is highly resistant. Previously we mapped several major quantitative resistance QTLs from wild S. habrochaites, and fine-mapped QTLs on chromosomes 5 (lb5) and 11 (lb11) in sub-near-isogenic lines. Our project objectives include: high-resolution mapping of two resistance QTLs on chromosomes 5 and 11 to obtain markers tightly linked to resistance gene(s) and favorable horticultural trait gene(s) for marker-assisted breeding; and assessing combining ability of F1 hybrids between elite inbred lines and selected homozygous sub-NILs for late blight resistance. PARTICIPANTS: PI/PD Dr. Dina St.Clair leads the project, sets priorities, organizes tasks, and supervises project personnel, including plant breeding graduate students Erin Arms, J. Erron Haggard, Emily Johnson, Jared Lounsbery, technician Rochelle Ng, and undergraduate assistants. Dr. Arnold Bloom provides plant physiology expertise on water stress research. Activities for the water stress research included: greenhouse propagation of plants via seed and vegetative cuttings; conducting hydroponic tank experiments with sub-NIL seedlings to assess shoot turgor maintenance under root chilling; marker genotyping, selection, and propagation via self-pollination of homozygous sub-NILs; conducting greenhouse pot experiments and replicated field experiments to assess response to water-restriction treatments. Ms. Ng performed marker genotyping of sub-NILs, Ms. Arms and Ms. Ng conducted hydroponic tank experiments, and Ms. Arms conducted greenhouse pot experiments and field experiments on the sub-NILs using water stress treatments. Activities for the late blight resistance QTL research included: propagating marker-selected sub-NILs for QTLs lb5 and lb11 via seed and plants in the greenhouse; transplanting sub-NIL plants to replicated field experiments; collecting plant and fruit trait data from replicated field experiments; maintaining P. infestans isolates on media and producing inoculum for experiments; conducting growth chamber experiments on sub-NILs with multiple P. infestans isolates; analyzing field and growth chamber data. Ms. Johnson and Mr. Haggard propagated sub-NIL via seed, planted field experiments, and collected plant and fruit data from the field experiments; Ms. Johnson assayed resistance of sub-NILs to P. infestans isolates in growth chamber experiments; Ms. Johnson and Mr. Haggard analyzed trait data and mapped QTLs. Undergraduate assistants helped with field, lab and greenhouse tasks, and were trained in plant genetics and breeding research methods, including pathogen isolate culturing, PCR-marker analysis, greenhouse plant care, propagation via seed and cuttings, and data collection. Dr. St.Clair teaches an annual undergraduate class in plant breeding (PLS154) at UC-Davis. A computer-based laboratory exercise was developed for the class with the trait and genotype data from the water stress resistance project to illustrate linkage and QTL mapping. TARGET AUDIENCES: Fresh water for agricultural production is a limited resource in many parts of the US, particularly the arid west. Water stress decreases crop productivity and yield. Cultivated tomato (Solanum lycopersicum) is sensitive to stress caused by limited water availability, and fruit yields are reduced. Breeding cultivated tomato for productivity under limited water would enhance agricultural sustainability. Wild tomato species have the ability to grow with limited water and withstand drought episodes. Genes in wild tomato species that confer water stress tolerance can be identified and used to breed tolerance in cultivated tomato. Previously, we identified a region on chromosome 9 in wild tomato (Solanum habrochaites) that confers resistance to rapid onset water stress caused by root chilling. The basis of this response is the ability to rapidly respond to water stress via root signaling to the leaves to close their pores (stomata), thereby preventing wilting (water loss). In this project, we are using genetics and genomic techniques to identify the gene(s) from wild tomato that confer tolerance to rapid-onset water stress. We have created tomato breeding lines containing the water stress tolerance gene(s) from wild tomato using marker-assisted selection. The breeding lines with the wild tomato gene(s) are being tested in field experiments to determine the role of these gene(s) in providing tolerance to limited water availability. Breeding lines with wild tomato gene(s) will also serve as a resource for breeding water stress tolerant cultivars that will enhance agricultural productivity and conserve valuable fresh water supplies. We have determined DNA markers tightly linked to late blight resistance QTLs from wild tomato (S. habrochaites) and created advanced generation tomato breeding lines containing the P. infestans resistance QTLs. Linked markers and advanced breeding lines will enable plant breeders to perform marker-assisted transfer of the valuable resistance QTL alleles from wild S. habrochaites into their elite inbred breeding lines used as parents in commercial F1 hybrid cultivars. From the mapping of horticultural trait loci, we have discovered favorable alleles from wild tomato that could prove beneficial to breeding. Our project bridges the gap between discovery of valuable QTL alleles in wild relatives of crop species and the effective deployment of the wild species QTL alleles in breeding programs to enhance development of improved cultivars. Target audiences include seed company tomato breeders, tomato growers, consumers, and tomato industry members. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
For genetic and genomic characterization of rapid onset water stress controlled by QTL stm9, we are using 18 unique sub-near-isogenic lines (sub-NILs) for this region that were previously marker-selected. During spring and fall 2011 we conducted replicated hydroponic tank experiments with the 18 sub-NILs and controls. Significant differences were detected for shoot turgor maintenance under rapid-onset water stress among the sub-NILs, indicating a smaller genomic region was responsible for this difference. Filters of an 8X genomic S. habrochaites bacterial artificial chromosome (BAC) library were used to identify a subset of BAC clones for the stm9 region. These clones are undergoing DNA fingerprinting and end-sequencing to define a minimal tiling path and identify BACs for genomic sequencing. In 2011, greenhouse pot experiments with two genotypes (a NIL for stm9 from S. habrochaites and cultivar T5) were used to assess responses to normal versus water-restriction treatments. Fresh and dry weights of shoots and roots were obtained at the 3-, 5- and 7- true leaf stages. Differences were not significant for the genotypes across water treatments, suggesting that these growth stages were too early in the life cycle to reveal differences in stress responses. A preliminary field experiment was conducted in 2011 with the 18 sub-NILs, T5 and stm9 NIL under three water treatments (normal, 2/3 evapotranspiration rate (ET) and 1/3 ET). Significant differences for total biomass and fruit yield were observed among the genotypes for 1/3 ET, indicating that the genotypes varied for tolerance to slow-onset water stress. In 2012, replicated field experiments will be expanded to two locations to obtain data on the sub-NILs and controls for total biomass, fruit yield, maturity, and other horticultural traits under two water treatments (normal and 1/3 ET). Late blight resistance research employed marker-selected sub-NILs for resistance QTLs on chromosomes 5 and 11 introgressed from S. habrochaites. The sub-NILs were evaluated in replicated field experiments over two years and several locations for resistance to late blight and horticultural traits. Data on resistance to P. infestans, plant and fruit horticultural traits, plus marker genotype data on the sub-NILs, were used to higher-resolution map the QTLs for each trait. Surprisingly, the resistance QTLs fractionated into multiple QTLs on both chromosomes 5 and 11, suggesting complex genetic architecture. Most horticultural traits mapped to two or more QTLs per chromosome region, demonstrating complex inheritance and indicating multiple loci control each trait. The sub-NILs were also evaluated for resistance to three different California P. infestans isolates in replicated growth chamber experiments. Data analyses revealed that some QTLs were detected with all three isolates, while others exhibited QTL x isolate interactions. Some resistance QTLs were detected with both field and growth chamber data, suggesting QTL stability across environments. Sub-NILs with resistance to P. infestans and acceptable horticultural traits were identified as pre-bred lines for breeding programs.
Publications
- St.Clair, D.A. (2010) Quantitative disease resistance and quantitative resistance loci (QRLs) in breeding. Annual Review Phytopathology 48: 247-268.
- Haggard, J.E., Johnson, E.B., St.Clair, D.A. (2011) Quantitative resistance to Phytophthora infestans introgressed from wild tomato: high resolution mapping and linkage with horticultural trait loci. Proceedings, Plant and Animal Genome XIX Conference, San Diego, CA.
- Johnson, E.B., Haggard, J.E., St.Clair, D.A. (2011) Phytophthora infestans resistance QTLs in tomato: high-resolution mapping using field and growth chamber experiments and testing of multiple isolates. Proceedings, Plant and Animal Genome XIX Conference, San Diego, CA.
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Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: The tomato industry in California, consisting of processing and fresh market tomatoes, has a farm-gate value of over $1 billion annually. Our tomato breeding and genetics research program focuses on genetic improvement of cultivated tomato (L. esculentum, syn. Solanum lycopersicum) for quantitatively inherited traits of major economic and agricultural importance. We create advanced breeding lines (pre-bred lines) containing introgressed genes from wild tomato, which serve as a resource for tomato improvement efforts. Our research on the genetic and genomic bases of agriculturally important quantitative traits reveals DNA markers tightly linked to target quantitative trait loci (QTLs) that are useful for marker-assisted breeding in tomato. Determination of the causal gene(s) for QTLs will provide specific targets for marker-assisted selection (MAS) breeding efforts. Our research demonstrates the value of marker-assisted gene introgression from wild species in applied breeding programs. Desirable traits for improvement of tomato for California production include tolerance or resistance to biotic stresses (e.g., diseases and pests) and abiotic stresses (e.g., temperature extremes and restricted water). Currently, we are investigating the genetic basis of quantitative resistance to late blight disease (caused by Phytophthora infestans) and the genetic and genomic bases of tolerance to rapid-onset water stress in tomato. Rapid-onset water stress can be induced by chilling roots. Wild tomato (Lycopersicon hirsutum, syn. Solanum habrochaites) responds to root chilling by closing stomata and maintaining shoot turgor, while cultivated tomato (S. lycopersicum) does not close its stomata and the shoots wilt. Previously we mapped a major QTL from wild S. habrochaites for shoot turgor maintenance under rapid-onset water stress via root chilling to a 2.7 cM region on chromosome 9 (i.e., QTL stm9). Our project objectives are: perform high-resolution mapping of stm9 and identify candidate genes; perform functional tests for stm9 candidate genes; perform comparative re-sequencing of wild species alleles at stm9 gene(s); conduct experiments (pots and field) with stm9 recombinants to evaluate growth responses after drought episode(s). The oomycete Phytophthora infestans, causal agent of late blight disease, is a major pathogen of tomato and causes extensive crop damage and losses. Cultivated tomato (S. lycopersicum) is susceptible, but wild S. habrochaites is resistant. Previously we mapped several major quantitative resistance QTLs from wild S. habrochaites, and fine-mapped QTLs on chromosomes 5 (lb5) and 11 (lb11) in sub-near-isogenic lines. Our project objectives include: high-resolution mapping of two resistance QTLs, lb5 and lb11, to obtain markers tightly linked to resistance gene(s) and favorable horticultural trait gene(s) for marker-assisted breeding; and assessing combining ability of F1 hybrids between elite inbred lines and selected homozygous sub-NILs for late blight resistance. PARTICIPANTS: PI/PD Dr. Dina St.Clair leads the project, sets priorities, organizes tasks, and supervises project personnel, including plant breeding graduate students Erin Arms, J. Erron Haggard, Emily Johnson, technician Rochelle Ng, and undergraduate assistants Rebecca Pelton, Loy Durham and Matt Dougherty. Dr. Arnold Bloom provides plant physiology expertise on the water stress research. Activities for the water stress research included: growing thousands of seedlings in the greenhouse; marker genotyping and selection of recombinant heterozygous sub-near-isogenic lines (sub-NILs) for QTL stm9; greenhouse propagation of plants via seed and vegetative cuttings; conducting hydroponic tank experiments with cuttings of heterozygous sub-NIL plants to assess shoot turgor maintenance under root chilling; marker genotyping, selection, and propagation via self-pollination of homozygous recombinant sub-NILs; conducting greenhouse pot experiments to assess response to water-restriction treatments. Ms. Ng performed marker genotyping of sub-NILs, Ms. Arms and Ms. Ng conducted hydroponic tank experiments, and Ms. Arms is conducting greenhouse pot experiments with NIL and control plants under water stress treatments. Activities for the late blight resistance QTL research included: propagating marker-selected sub-NILs for QTLs lb5 and lb11 via seed and plants in the greenhouse; transplanting sub-NIL plants to replicated field experiments; collecting plant and fruit trait data from replicated field experiments; maintaining P. infestans isolates on media and producing inoculum for experiments; conducting growth chamber experiments on sub-NILs with multiple P. infestans isolates; analyzing field and growth chamber data. Ms. Johnson performed marker genotyping on sub-NILs; Ms. Johnson and Mr. Haggard propagated sub-NIL via seed, planted field experiments, and collected plant and fruit data from the 2010 field experiments; Ms. Johnson is assaying resistance of sub-NILs to P. infestans isolates in growth chamber experiments. Undergraduate assistants help with field, lab and greenhouse tasks, and were trained in plant genetics and breeding research methods, including PCR-marker analysis, greenhouse plant care, propagation via seed and cuttings, and data collection. Two undergraduate students did internships in the St.Clair lab. One student used the tomato genome sequence to identify annotated genes located within stm9 and their putative or known functions. The other student conducted pot experiments to evaluate rooting medias and methods to measure differences in root and shoot growth. Dr. St.Clair teaches an annual undergraduate class in plant breeding (PLS154) at UC-Davis. This research project was used to illustrate marker-assisted breeding and use of wild germplasm for crop improvement. A class laboratory exercise was developed on PCR-based primer design for marker-assisted selection. The students used information from a tomato genetics database (SGN) to determine if the markers were polymorphic among parent lines and thus potentially useful for selecting desired genotypes. TARGET AUDIENCES: Fresh water for agricultural production is a limited resource in many parts of the US, particularly the arid west. Water stress decreases crop productivity and yield. Cultivated tomato (Solanum lycopersicum) is sensitive to stress caused by limited water availability, and fruit yields are reduced. Breeding cultivated tomato for productivity under limited water would enhance agricultural sustainability. Wild tomato species have the ability to grow with limited water and withstand drought episodes. Genes in wild tomato species that confer water stress tolerance can be identified and used to breed tolerance in cultivated tomato. Previously, we identified a region on chromosome 9 in wild tomato (Solanum habrochaites) that confers resistance to rapid onset water stress caused by root chilling. The basis of this response is the ability to rapidly respond to water stress via root signaling to the leaves to close their pores (stomata), thereby preventing wilting (water loss). In this project, we are using genetics and genomic techniques to identify the gene(s) from wild tomato that confer tolerance to rapid-onset water stress. We will create tomato breeding lines containing the water stress tolerance gene(s) from wild tomato using marker-assisted selection. The breeding lines with the wild tomato gene(s) will be tested in field and greenhouse experiments to determine the role of these gene(s) in providing tolerance to limited water availability. Breeding lines with wild tomato gene(s) will also serve as a resource for breeding water stress tolerant cultivars that will enhance agricultural productivity and conserve valuable fresh water supplies. We are determining the DNA markers tightly linked to late blight resistance QTLs from wild tomato (S. habrochaites), creating advanced generation tomato breeding lines containing the P. infestans resistance QTLs, and determining DNA markers linked to horticultural trait loci. The linked markers and advanced breeding lines will enable plant breeders to perform marker-assisted transfer of the valuable resistance QTL alleles from wild S. habrochaites into their elite inbred breeding lines used as parents in commercial F1 hybrid cultivars. From the mapping of horticultural trait loci, we may also discover favorable alleles from wild tomato that could prove beneficial to breeding. Our project will bridge the gap between discovery of valuable QTL alleles in wild relatives of crop species and the effective deployment of the wild species QTL alleles in breeding programs to enhance development of improved cultivars. Target audiences include seed company tomato breeders, tomato growers, consumers, and tomato industry members. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
For our rapid onset water stress research, we identified recombinant progeny for the QTL stm9 region to use for high resolution mapping. We used 17 single nucleotide polymorphisms (SNPs) markers to genotype 1,926 progeny and identified 35 heterozygous recombinant sub-near-isogenic lines (sub-NILs). The self-pollinated progeny were genotyped with SNPs to select homozygotes for 18 unique recombinant genotype classes. Sub-NILs are undergoing self-pollination to generate ample seed for experiments. A hydroponic tank experiment with replicated vegetative cuttings from a subset of 9 heterozygous sub-NILs was conducted. Significant differences were detected for shoot turgor maintenance under rapid-onset water stress. An 8X genomic S. habrochaites bacterial artificial chromosome (BAC) library was constructed by AGI from our leaf tissue. The BAC library filters will be used to identify BAC clones for the stm9 region. Preliminary greenhouse pot experiments were initiated with a NIL for stm9 from S. habrochaites and S. lycopersicum cv. T5 to assess responses to normal versus water-restriction treatments. Traits being measured include fresh and dry weights of shoots and roots assessed at the 3-, 5- and 7- true leaf stages. The results will be used to design experiments to evaluate recombinant sub-NILs for their responses to water restriction. For our late blight resistance research, we marker-selected sub-NILs for resistance QTLs lb5 and lb11 from S. habrochaites and generated ample seed for replicated field experiments. In 2009, 120 recombinant sub-NILs for the two QTLs plus control lines were evaluated in replicated field experiments (three replications per line at each of four locations in Davis and Salinas) for resistance to late blight and horticultural traits. Data analyses indicated that additional replications were needed to refine the chromosomal intervals for trait QTLs and assess potential linkage drag. In 2010, 83 sub-NILs (a subset of the 120 sub-NILs) were evaluated in replicated field experiments with four to five replications per line at each of four locations in Davis and Salinas. Field data collection on P. infestans resistance, plant and fruit horticultural traits was completed in October. All trait data and marker genotype data for the sub-NILs is being analyzed to high-resolution map the QTLs for each trait, and identify tightly linked markers. Sub-NILs with resistance to P. infestans and acceptable horticultural traits have been identified. The set of 120 sub-NILs are also being evaluated for resistance to several different P. infestans isolates from California in replicated experiments in growth chambers. Experiments for one isolate have been completed, and testing of two other isolates is underway. Testing the sub-NILs against several isolates will permit assessment of QTL x isolate interactions, if present. The results from data analyses for P. infestans resistance from field and growth chamber experiments will be compared to determine if the same chromosome intervals confer resistance to this pathogen.
Publications
- St.Clair, D.A. (2010) Quantitative disease resistance and quantitative resistance loci (QRLs) in breeding. Annual Review Phytopathology 48: 247-268.
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Progress 01/01/09 to 12/31/09
Outputs
OUTPUTS: Our research program on tomato breeding and genetics focuses on discovery and use of genes governing agriculturally important traits in wild tomato species for genetic improvement of cultivated tomato (SOLANUM LYCOPERSICUM, formerly LYCOPERSICON ESCULENTUM). Currently we are investigating quantitative resistance to late blight disease (RLB), tolerance to chilling temperatures (CT) and water stress (WS). The pathogen PHYTOPHTHORA INFESTANS (late blight), chilling temperatures, and water stress can cause significant losses in fruit yield and quality. Wild tomato (S. HABROCHAITES, formerly L. HIRSUTUM) is resistant to LB, and tolerant to chilling and water stress. Our research approach includes using interspecific populations (cultivated tomato x wild) to map quantitative trait loci (QTL) and marker-assisted selection (MAS) of target QTLs to transfer favorable wild species alleles into cultivated tomato. DNA markers linked to target QTLs are used for MAS to select backcross progeny containing desired wild species alleles at QTLs. RLB QTLs from S. HABROCHAITES were fine mapped previously, but linkage drag for undesirable horticultural traits was evident. We are in the process of high-resolution mapping two RLB QTLs on chromosomes 5 (lb5b) and 11 (lb11b). High resolution mapping will further narrow the MAS target RLB QTL regions, reduce linkage drag for undesirable traits, and enhance use of wild species QTL alleles in MAS breeding. Recombinants for each QTL (lb5b and lb11b) were marker-selected and phenotyped in 2009 replicated field experiments at multiple locations for disease resistance and horticultural traits. Multiple QTLs for the traits were detected within the two chromosome regions, and QTL x location interactions were evident for most traits. Field experiments will be repeated in 2010 to better resolve the QTL intervals. Previously, we determined that CT from S. HABROCHAITES was strongly associated with a major QTL on chromosome 9 (designated stm9) for shoot turgor maintenance (stm) under root chilling, and we fine-mapped stm9 to a 2.7 cM interval. Physiological experiments indicate that root-shoot signaling is involved in stomatal control and stm, and tolerance to rapid-onset water stress (WS) is associated with CT. Marker-selected paired near-isogenic lines for the stm9 region are undergoing physiological characterization to obtain additional data on the phenotypic effects of stm9. Concurrently, recombinants for stm9 are being marker-selected and will be used for high-resolution mapping to narrow the region(s) responsible for the CT and WS phenotype. A BAC library for S. HABROCHAITES is under construction at AGI and will be used for physical mapping of stm9 and determination of the genes located in this region. The ultimate target for MAS breeding is the causal gene or genes for the desirable trait phenotype. PARTICIPANTS: PI/PD Dina St.Clair leads the project, sets priorities, organizes tasks, and supervises project personnel. Personnel include UCD graduate students Emily Johnson, Erron Haggard, and Erin Arms, technician Rochelle Ng (formerly an undergraduate assistant), and undergraduate assistant Rebecca Pelton. Project activities in 2009 included: growing tomato seedlings and plants in the greenhouse; PCR-based marker genotyping of recombinant progeny for QTL regions; greenhouse plant care; harvesting and de-seeding fruit; seeding out and transplanting recombinant lines to replicated 2009 field plot experiments in Davis and Salinas; collecting phenotype data on late blight disease and horticultural traits from field experiments; data analyses. Ms. Johnson and Ms. Ng performed marker genotyping and selection, Mr. Haggard and Ms. Johnson focused on field experiments and data collection, Ms. Ng assisted with collecting field experiment data, and undergraduates assisted with both lab and greenhouse tasks (i.e., seeding out flats, transplanting, plant care, and fruit harvest). Undergraduate assistants were trained to perform tasks required for plant genetics and breeding research, such as DNA extractions, PCR-marker reactions, PCR-primer design, gel electrophoresis of PCR products, genotype data collection, phenotype data collection, data recording, tomato seed extractions, and greenhouse plant care methods. TARGET AUDIENCES: PI/PD Dina St.Clair communicates research progress and results to tomato growers, seed company breeders, and tomato industry representatives via presentations, meetings, and informal interactions. St.Clair teaches an annual undergraduate class in plant breeding at UC-Davis. In the class, results from this project was used as a real-life example of marker-assisted breeding and use of wild germplasm for crop improvement. A class laboratory exercise was developed on PCR-based primer design for marker-assisted selection in tomato. The students used information on a web-based tomato database to determine if the markers were polymorphic and thus potentially useful for selecting desired genotypes. In addition, one undergraduate student participated in an internship on aspects of DNA genotyping (e.g., primer design for PCR-based markers, primer testing, PCR reaction optimization) as part of this project. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
A combination of genetics, breeding, and genomics approaches are being used to understand the genetic basis of agriculturally important quantitative traits, transfer valuable wild species genes to cultivated tomato, and create improved tomato germplasm. Genetic variation for most traits is quite limited in cultivated tomato, hampering breeding improvement efforts. Wild tomato species are an invaluable source of genes for genetic improvement of cultivated tomato, contributing to increases in agricultural productivity and sustainability. Wild species genes that control traits such as resistance to pathogens and tolerance to abiotic stresses are being transferred to cultivated tomato using marker-assisted selection (MAS) for the desired wild genes in progeny plants from crosses of cultivated and wild tomatoes. MAS breeding is a non-transgenic, consumer-acceptable, and efficient method of genetic improvement. We have created improved cultivated tomato germplasm containing valuable wild species genes using MAS breeding. Advanced germplasm provides a foundation for breeding modern cultivars that require fewer agricultural inputs. A reduction of agricultural inputs such as pesticides, fungicides, and fertilizers, and efficient use of irrigation water, lessens environmental impacts and production costs, enhancing agricultural productivity and sustainability.
Publications
- No publications reported this period
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Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: Our tomato breeding and genetics research program focuses on the discovery and use of genes governing agriculturally important traits in wild tomato species for genetic improvement of cultivated tomato (LYCOPERSICON ESCULENTUM, or SOLANUM LYCOPERSICUM). The traits chilling tolerance (CT), resistance to late blight disease (RLB) and resistance to aphids are being investigated. The pathogen PHYTOPHTHORA INFESTANS (late blight), chilling temperatures, and aphid infestations can cause significant losses in fruit yield and quality. Our research approach includes using interspecific populations (cultivated tomato x wild) to map quantitative trait loci (QTL) for traits such as RLB and CT, and marker-assisted selection (MAS) of target QTLs to transfer favorable wild species alleles into cultivated tomato. DNA markers linked to target QTLs were used for MAS to select backcross progeny containing desired wild species alleles at QTLs for RLB and CT. RLB QTLs from L. HIRSUTUM were fine mapped previously using recombinant sub-near-isogenic lines (sub-NILs) obtained via MAS, but linkage drag for undesirable traits was evident. We are in the process of high-resolution mapping two RLB QTLs on chromosomes 5 (lb5b) and 11 (lb11b). Recombinants for each QTL have been identified, and these will be phenotyped in the field in 2009. High resolution mapping will further narrow the MAS target RLB QTL regions, reduce linkage drag for undesirable wild species traits, and enhance use of wild species QTL alleles in MAS breeding. CT from L. HIRSUTUM was strongly associated with a major QTL on chromosome 9 (designated stm9) for shoot turgor maintenance (stm) under root chilling; stm9 was fine-mapped previously to a 2.7 cM interval. Physiological experiments indicate that root-shoot signaling is involved in stomatal control and stm. We have marker-selected paired near-isogenic homozygous lines for the stm9 region to continue physiological characterization of this QTL. Interspecific inbred backcross lines (IBLs) from susceptible L. ESCULENTUM and aphid-resistant L. HIRSUTUM were obtained previously. Two aphid-resistant IBLs in hybrid combination with commercial inbred lines expressed resistance in most hybrid combinations, suggesting resistance is dominant. Over 100 markers across the genome were screened on the IBLs. Additional markers will be required to find those linked to aphid resistance genes; new high-throughput genotyping platforms would help this effort. Identification of markers linked to aphid-resistance genes would be useful for MAS breeding. PARTICIPANTS: PI/PD Dina St.Clair leads the project, sets priorities, organizes tasks, and supervises project personnel, including senior researcher Dr. Marilyn West, graduate student Emily Johnson, and undergraduate assistants Stacey Fong, Rochelle Ng, and Ari Vlahakis. Project activities in 2008 included: growing thousands of seedlings in the greenhouse; extracting DNA from leaf samples; PCR-based marker genotyping of segregating recombinant progeny; marker selection; transplanting recombinant plants into pots; caring for plants in the greenhouse; harvesting and de-seeding of thousands of fruit; and growing the next generation of plants to obtain sufficient seed for 2009 field experiments. Dr. West and Ms. Johnson focused on performing marker genotyping and selection, Dr. St.Clair focused on greenhouse-based tasks (i.e., seeding out flats, transplanting, plant care, and fruit harvest), and the undergraduates assisted with both lab and greenhouse tasks. Undergraduate assistants were trained to perform tasks required for plant genetics and breeding research, including DNA extractions, PCR-marker reactions, PCR primer design, gel electrophoresis of PCR products, genotype data collection, data recording on spreadsheets, tomato seed extractions, and greenhouse plant care methods. TARGET AUDIENCES: PI/PD Dina St.Clair communicates research progress and results to tomato growers, seed company breeders, and tomato industry representatives via presentations, meetings, and informal interactions. St.Clair teaches an annual undergraduate class in plant breeding at UC-Davis. In the class, this project was used as a real-life example of marker-assisted breeding and use of wild germplasm for crop improvement. A class laboratory exercise was developed on PCR-based primer design for marker-assisted selection in tomato. The students used information on a web-based tomato database to determine if the markers were polymorphic and thus potentially useful for selecting desired genotypes. In addition, two undergraduate students participated in internships that focused on aspects of DNA genotyping (e.g., primer design for PCR-based markers, primer testing, PCR reaction condition optimization) as part of this project. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
We are using a combination of genetics, breeding, and genomics approaches to understand the genetic basis of agriculturally important traits, transfer valuable wild species genes to cultivated tomato, and create improved tomato germplasm. Genetic variation for most traits is quite limited in cultivated tomato, hampering breeding improvement efforts. Fortunately, wild tomato species are a valuable source of genes for genetic improvement of cultivated tomato, leading to increases in agricultural productivity and sustainability. Wild species' genes that control traits such as resistance to pathogens, pests, and tolerance to abiotic stress are being transferred to cultivated tomato using marker-assisted selection (MAS) for the desired wild genes in progeny plants from crosses of cultivated and wild tomatoes. MAS breeding is a non-transgenic, consumer-acceptable, and efficient method of genetic improvement. We have created improved cultivated tomato germplasm containing valuable wild species' genes using MAS breeding. Advanced germplasm provides a foundation for breeding modern cultivars that require fewer agricultural inputs. A reduction of agricultural inputs such as pesticides, fungicides, and fertilizers, and efficient use of irrigation water, lessens environmental impacts and production costs, enhancing agricultural productivity and sustainability.
Publications
- TAN, X., MEYERS, B.C., KOZIK, A., WEST, M.A.L., MORGANTE, M., ST.CLAIR, D.A., BENT, A.F. AND MICHELMORE, R.W. 2007. Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis. BMC Plant Biology 7:56. (www.biomedcentral.com/1471-2229/7/56).
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Progress 01/01/07 to 12/31/07
Outputs
A primary focus of our tomato breeding and genetics research is the discovery and utilization of genes controlling agriculturally important traits in wild tomato species for genetic improvement of cultivated tomato (LYCOPERSICON ESCULENTUM, or SOLANUM LYCOPERSICUM). Traits currently under study include chilling tolerance (CT), resistance to late blight disease (RLB) and resistance to aphids. The pathogen PHYTOPHTHORA INFESTANS (late blight) and chilling temperatures can cause significant yield and fruit quality losses, while aphid infestations reduce yields. Our approach includes using interspecific populations to map quantitative trait loci (QTL) for traits such as RLB and CT, and marker-assisted selection (MAS) of target QTLs for introgression of favorable wild species alleles into cultivated tomato. DNA markers linked to target QTLs were used for MAS to select progeny containing desired wild species alleles at QTLs for RLB and CT. Previously, we fine-mapped three RLB
QTLs from L. HIRSUTUM using recombinant sub-near-isogenic lines (sub-NILs) obtained via MAS. RLB QTL on chromosomes 4, 5 and 11 (designated as QTLs lb4, lb5b, lb11b) were mapped to intervals of 6.9, 8.8 and 15.1 cM, respectively. We are currently performing high-resolution mapping of two RLB QTLs (lb5b, lb11b) to further narrow the MAS target regions, reduce linkage drag for undesirable wild species traits, and enhance the use of wild species QTL alleles in MAS breeding. CT from L. HIRSUTUM was strongly associated with a major QTL on chromosome 9 (designated stm9) for shoot turgor maintenance (stm) under root chilling; sub-NILs were used to fine-map stm9 to a 2.7 cM interval. Physiological experiments indicate that root-shoot signaling is involved stomatal control and stm under root chilling conditions. Field experiments to evaluate the effect of stm9 on CT of growth of plants under field conditions are planned. Aphid resistance was assessed previously in interspecific inbred
backcross lines (IBLs) derived from crossing susceptible L. ESCULENTUM and aphid-resistant L. HIRSUTUM. Six IBLs were identified as most consistently resistant over two years of field trial, and are a source of genetic resistance for further breeding efforts. We evaluated the combining ability of two of the resistant IBLs in hybrid combination with commercial inbred lines; resistance was expressed in most hybrid combinations. We are currently identifying markers potentially linked to aphid-resistance genes in the IBLs that may prove useful for MAS breeding.
Impacts
A combination of genetics, breeding, and genomics approaches is being used to understand the genetic basis of agriculturally important traits, transfer valuable wild species genes to cultivated tomato, and create improved tomato germplasm. Genetic variation is limited in cultivated tomato for most traits, hampering breeding improvement efforts. Fortunately, wild tomato (LYCOPERSICON) species are a valuable source of genes for genetic improvement of cultivated tomato, leading to increases in agricultural productivity and sustainability. Wild species genes that control traits such as resistance to pathogens, pests, and tolerance to abiotic stress are being transferred to cultivated tomato using marker-assisted selection (MAS) for the desired wild genes in progeny plants from crosses of cultivated and wild tomatoes. MAS breeding is a non-transgenic and efficient method of genetic improvement. Improved cultivated tomato germplasm containing valuable wild species genes has
been created. Advanced germplasm provides a foundation for breeding modern cultivars that require fewer agricultural inputs. A reduction of agricultural inputs such as pesticides, fungicides, and fertilizers, and efficient use of irrigation water, lessens environmental impacts and production costs, enhancing agricultural productivity and sustainability.
Publications
- WEST, M.A.L., KIM, K., KLIEBENSTEIN, D.J., VAN LEEUWEN, H., MICHELMORE, R.W., DOERGE R.W., AND ST.CLAIR, D.A. 2007. Global eQTL mapping reveals the complex genetic architecture of transcript level variation in Arabidopsis. Genetics 175:1441-1450.
- VAN LEEUWEN, H., KLIEBENSTEIN, D.J., WEST, M.A.L., KIM, K., R. VAN POECKE, KATAGIRI, F., MICHELMORE, R.W., DOERGE, R.W., AND ST.CLAIR, D.A. 2007. Natural variation among Arabidopsis thaliana accessions for transcriptome response to exogenous salicylic acid. Plant Cell 19: 2099-2110.
- CHEN, J., AGRAWAL, V., RATTRAY, M., WEST, M., ST.CLAIR, D.A., MICHELMORE, R.W., COUGHLAN, S.J., AND MEYERS, B.C. 2007. A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis. BMC Genomics 8: 414. (www.biomedcentral.com/bmcgenomics/).
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Progress 01/01/06 to 12/31/06
Outputs
The identification of genes controlling agriculturally important traits in wild tomato species and the transfer of these genes from wild to cultivated tomato (LYCOPERSICON ESCULENTUM; new name SOLANUM LYCOPERSICUM) for genetic improvement is the focus of our tomato breeding and genetics research. Traits currently under study include chilling tolerance (CT), resistance to late blight (RLB) and resistance to aphids. The pathogen PHYTOPHTHORA INFESTANS (late blight) and chilling temperatures can cause significant yield and fruit quality losses, while aphid infestations reduce yields. Previously, quantitative trait loci (QTL) for RLB and CT were mapped in interspecific populations and QTLs identified for introgression. Marker-assisted selection (MAS) with DNA markers linked to the QTL regions were used to select interspecific progeny containing the desired wild species alleles at these QTLs. Several RLB QTLs were fine-mapped previously using recombinant sub-near-isogenic
lines (sub-NILs) obtained via MAS. RLB QTL on chromosomes 4, 5 and 11 (designated as QTLs lb4, lb5b, lb11b) were mapped to intervals of 6.9, 8.8 and 15.1 cM, respectively. Future efforts would focus on high-resolution mapping of the RLB QTLs to further narrow the target regions for MAS, reduce linkage drag and facilitate the practical use of these wild species QTLs in MAS breeding efforts. QTLs from L. HIRSUTUM associated with shoot turgor maintenance under root chilling temperatures were mapped previously and CT was most strongly associated with a QTL on chromosome 9 (designated as stm9). Sub-NILs were used to fine map stm9 to a 2.7 cM interval which can serve as a target for future MAS breeding for CT. Physiological experiments with plants containing stm9 suggest that a root-shoot signal is involved in shoot turgor maintenance under root chilling temperatures. Future efforts would include field experiments to evaluate the effect of stm9 on CT of plants under field conditions and
high-resolution mapping of stm9. Aphid resistance was assessed previously in two interspecific inbred backcross line (IBL) populations derived from crossing aphid-resistant L. HIRSUTUM and L. PENNELLII with susceptible L. ESCULENTUM. The most consistently resistant IBLs over two years of field trials were from the HIRSUTUM-derived population. These six highly aphid-resistant IBLs are a source of genetic resistance for further breeding efforts. A new project is in progress to identify markers linked to the aphid resistance genes from HIRSUTUM in the resistant IBLs and to evaluate the combining ability of several of the resistant IBLs with commercial inbred lines.
Impacts
Cultivated tomato frequently lacks the needed genetic diversity for breeding improvement of many agriculturally important traits. In contrast, wild tomato species contain a wealth of genetic variation. Genes that control agricultural traits in wild tomato species can be used in breeding cultivated tomato for improvement of agricultural productivity and sustainability. Transfer of wild species' genes for resistance to pathogens, pests and chilling tolerance to cultivated tomato germplasm can be accomplished using DNA marker-assisted selection (MAS) on progeny plants obtained from sexual crosses of cultivated x wild tomatoes for the desired genes. MAS is a non-transgenic method of genetic improvement. Improved cultivated germplasm containing valuable wild species' genes serves as a foundation for development of cultivars requiring fewer agricultural production inputs. Reduction of agricultural inputs such as pesticides and fungicides lessen environmental impacts and
production costs for growers, enhancing agricultural production and sustainability.
Publications
- KLIEBENSTEIN, D.J., WEST, M.A.L., VAN LEEUWEN, H., LOUDET, O., DOERGE, R.W., AND ST.CLAIR, D.A. 2006. Identification of QTLs controlling gene expression networks defined a priori. BMC Bioinformatics 7:308 (doi10.1186/1471-2105-7-308).
- KLIEBENSTEIN, D.J., WEST, M.A.L., VAN LEEUWEN, H., KIM, K., DOERGE, R.W., MICHELMORE, R.W., AND ST.CLAIR, D.A. 2006. Genomic survey of gene expression diversity in Arabidopsis thaliana. Genetics 172:1179-1189.
- GOODSTAL, F.J., KOHLER, G.R., RANDALL, L.B., BLOOM, A.J., AND ST.CLAIR, D.A. 2005. A major QTL introgressed from wild Lycopersicon hirsutum confers chilling tolerance to cultivated tomato (Lycopersicon esculentum). Theoretical and Applied Genetics 111:898-905.
- WEST, M.A.L., VAN LEEUWEN, H., KOZIK, A., KLIEBENSTEIN, D.J., DOERGE R.W., ST.CLAIR, D.A., AND MICHELMORE, R.W. 2006. High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis. Genome Research 16:787-795.
- KOHLER, G.R. AND ST.CLAIR, D.A. 2005. Variation for resistance to aphids (Homoptera: Aphididae) among tomato inbred backcross lines derived from wild Lycopersicon species. Journal of Economic Entomology 98:988-995.
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Progress 01/01/05 to 12/31/05
Outputs
The identification and transfer of genes from wild to cultivated tomato (LYCOPERSICON ESCULENTUM) for improved chilling tolerance (CT), resistance to late blight (RLB) and aphids is the current focus of our tomato breeding and genetics research. The pathogen PHYTOPHTHORA INFESTANS (late blight) and chilling temperatures can cause significant yield and fruit quality losses, while aphids reduce yields. Previously, quantitative trait loci (QTL) for RLB and CT were mapped in interspecific populations and QTLs identified for introgression. DNA markers linked to the QTL regions were used to select interspecific progeny lines containing the desired wild species alleles at these QTLs (i.e., marker-assisted selection, MAS). RLB QTLs on chromosomes 3, 4, 5 and 11 were transferred into cultivated tomato using backcrossing and MAS. Selected QTLs were fine-mapped using recombinant sub-near-isogenic lines (sub-NILs) obtained via MAS for RLB QTL on chromosomes 3, 4, 5 and 11
(designated as QTLs lb3, lb4, lb5b, lb11b). Sub-NILs were tested in replicated field trials, and disease data was used to fine map each of these resistance QTLs to smaller chromosomal segments. QTLs lb4, lb5b and lb11b mapped to smaller intervals of 6.9, 8.8 and 15.1 cM, respectively, resulting in more suitable targets for MAS breeding efforts. The presence of severe fertility problems in the lb3 sub-NILs prevented fine-mapping of resistance loci, but a fertility locus was identified. Two CT QTLs from L. HIRSUTUM on chromosomes 5 and 9 associated with turgor maintenance under root chilling temperatures were individually introgressed into L. ESCULENTUM using MAS and NILs were developed. The NILs were tested in replicated experiments and CT was measured as shoot turgor maintenance under root chilling temperatures. CT was most strongly and consistently associated with the QTL on chromosome 9 (designated as stm9). Sub-NILs were obtained for fine mapping, and stm9 was localized to a 2.7 cM
interval. This defined 2.7 cM stm9 region can serve as a target for future MAS breeding for CT and high-resolution mapping. Physiological experiments with plants consisting of reciprocal grafts of roots and shoots of parental lines and marker-selected backcross plants with stm9 strongly suggest that a root-shoot signal is involved in shoot turgor maintenance under root chilling temperatures. Sub-NILs for stm9 are being used for further physiological studies to characterize the basis of CT. Aphid resistance was assessed in two interspecific inbred backcross line (IBL) populations derived from crossing aphid-resistant L. HIRSUTUM and L. PENNELLII with susceptible L. ESCULENTUM. The most consistently resistant IBLs over two years of field trials were from the HIRSUTUM-derived population. These six highly aphid-resistant IBLs are a source of genetic resistance for further breeding efforts.
Impacts
Genes in wild tomato species that control agriculturally important traits can be used in breeding to improve cultivated tomato for agricultural productivity and sustainability. Transfer of wild species genes for resistance to pathogens, pests and chilling tolerance to cultivated tomato germplasm can be accomplished using molecular marker-assisted selection as a non-transgenic tool for effective gene transfer. Improved cultivated germplasm containing valuable wild species genes serves as a foundation for development of cultivars requiring fewer agricultural production inputs. Reduction of agricultural inputs such as pesticides and fungicides lessen environmental impacts and production costs for growers, enhancing agricultural production and sustainability.
Publications
- GOODSTAL, F.J., KOHLER, G.R., RANDALL, L.B., BLOOM, A.J., AND ST.CLAIR, D.A. 2005. A major QTL introgressed from wild Lycopersicon hirsutum confers chilling tolerance to cultivated tomato (Lycopersicon esculentum). Theoretical and Applied Genetics (published online DOI 10.1007/s00122-005-0015-2).
- BROUWER, D.J. AND ST.CLAIR, D.A. 2004. Fine mapping of three quantitative trait loci for late blight resistance in tomato using near isogenic lines (NILs) and sub-NILs. Theoretical and Applied Genetics 108:628-638.
- BROUWER, D.J., JONES, E.S., AND ST.CLAIR, D.A. 2004. QTL analysis of quantitative resistance to Phytophthora infestans (late blight) in tomato, and comparisons to potato. Genome 47:475-492.
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Progress 01/01/04 to 12/31/04
Outputs
Our tomato breeding and genetics research has focused on the identification and transfer of genes from wild to cultivated tomato (LYCOPERSICON ESCULENTUM) for chilling tolerance (CT), resistance to blackmold (RBM), late blight (RLB) and aphids. The pathogens PHYTOPHTHORA INFESTANS (late blight) and ALTERNARIA ALTERNATA (blackmold) and chilling temperatures can all cause significant yield and fruit quality losses, while aphids reduce yields. Previously, quantitative trait loci (QTL) for RBM, RLB, and CT were mapped in interspecific populations and QTLs identified for introgression. DNA markers linked to the QTL regions were used to select progeny lines containing the desired wild species alleles at these QTLs (i.e., marker-assisted selection, MAS). RLB QTLs on chromosomes 3, 4, 5 and 11 and RBM QTLs on chromosomes 2, 3, 9 and 12 were transferred into cultivated tomato using backcrossing and MAS. L. CHEESMANII alleles at RBM QTL conferred resistance in an L. ESCULENTUM
background, and the QTL on chromosome 2 had the largest positive effect on resistance. Selected QTLs were fine-mapped using sub-near-isogenic lines (sub-NILs) obtained via MAS for RBM QTL on chromosome 2 and RLB QTL on chromosomes 3, 4, 5 and 11 (lb3, lb4, lb5b, lb11b). Sub-NILs were tested in replicated field trials, and disease data was used to fine map each of these resistance QTLs to smaller chromosomal segments. QTLs lb4, lb5b and lb11b mapped to intervals of 6.9, 8.8 and 15.1 cM, respectively, resulting in more suitable targets for MAS breeding efforts. Fine mapping of lb3 was not possible due to severe fertility problems in the sub-NILs, but a fertility locus was mapped. RBM QTL on chromosome 2 was located to a 20 cM region. Two CT QTLs from L. HIRSUTUM on chromosomes 5 and 9 were individually introgressed into L. ESCULENTUM using MAS and NILs were developed. The NILs were tested in replicated experiments and CT (measured as shoot turgor maintenance under chilling temperatures)
was most strongly associated with the QTL on chromosome 9 (stm9). Sub-NILs were derived from NILs for fine mapping, and stm9 was localized to a 3 cM interval. Sub-NILs are being used for further physiological studies to characterize the basis of CT. Aphid resistance was assessed in two interspecific inbred backcross line (IBL) populations derived from L. HIRSUTUM and L. PENNELLII, and the most consistently resistant IBLs over two years of field trials were from the HIRSUTUM-derived population. These highly resistant IBLs are a source of aphid resistance for further breeding efforts. An assessment of cultivated tomato germplasm mainly from California indicated that a minimum of 7 AFLP primer pairs revealed unique banding patterns for all 74 cultivars even though some cultivars were genetically related, indicating the value of the AFLP markers for cultivar fingerprinting.
Impacts
Genes controlling agriculturally important traits that are present in wild tomato species can be used to improve cultivated tomato for agricultural productivity and sustainability. Transfer of wild species' genes for resistance to pathogens, pests and chilling to cultivated tomato germplasm using molecular markers as tools for gene transfer can facilitate development of cultivars requiring fewer agricultural inputs. Reduced chemical inputs lessen environmental impacts and production costs for growers, enhancing agricultural production.
Publications
- KOHLER, G.R. AND ST.CLAIR, D.A. 2005. Variation for resistance to aphids (Homoptera: Aphididae) among tomato inbred backcross lines derived from wild Lycopersicon species. Journal of Economic Entomology (In Press).
- BLOOM, A.J., ZWIENIECKI, M.A., PASSIOURA, J.B., RANDALL, L.B., HOLBROOK, N.M., AND ST.CLAIR, D.A. 2004. Water relations under root chilling in a sensitive and tolerant tomato species. Plant, Cell and Environment 27:971-979.
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Progress 01/01/03 to 12/31/03
Outputs
Tomato germplasm enhancement research has emphasized the identification and transfer of genes from wild to cultivated tomato (LYCOPERSICON ESCULENTUM) for chilling tolerance (CT), resistance to blackmold (RBM) and late blight (RLB). The pathogens PHYTOPHTHORA INFESTANS (late blight) and ALTERNARIA ALTERNATA (blackmold) and chilling temperatures can all cause significant yield and fruit quality losses. Previously, quantitative trait loci (QTL) for RBM, RLB, and CT were mapped in interspecific populations and QTLs identified for introgression. DNA markers linked to the QTL regions were used to select progeny lines containing the desired wild species alleles at these QTLs (i.e., marker-assisted selection, MAS). RLB QTLs on chromosomes 3, 4, 5 and 11 and RBM QTLs on chromosomes 2, 3, 9 and 12 were transferred into cultivated tomato using backcrossing and MAS. BC3S1 lines containing different combinations of one to four RLB QTLs from L. HIRSUTUM were identified using MAS,
then field-tested in 2001 and assayed in replicated disease screens during 2002. Lines containing RLB QTLs on chromosomes 5 and 11 were most consistently resistant in all three types of disease assays, while RLB QTL on chromosome 4 was most associated with stem resistance. L. CHEESMANII alleles at RBM QTL on chromosomes 2, 3 and 9 in BC1S2 progeny conferred resistance in an L. ESCULENTUM background; the QTL on chromosome 2 had the largest positive effect on resistance. Sub-near-isogenic lines (sub-NILs) for RBM QTL on chromosome 2 and RLB QTL on chromosomes 3, 4, 5 and 11 (lb3, lb4, lb5b, lb11b) were developed from NILs using MAS. Sub-NILs were tested in replicated field trials in 2002, and disease data was used to fine map each of these resistance QTLs to smaller chromosomal segments, resulting in more suitable targets for MAS breeding efforts. QTLs lb4, lb5b and lb11b mapped to intervals of 6.9, 8.8 and 15.1 cM, respectively. Fine mapping of lb3 was not possible due to severe
fertility problems in the sub-NILs, but a fertility locus was mapped. RBM QTL on chromosome 2 was located to a 20 cM region. Two CT QTLs from L. HIRSUTUM on chromosomes 5 and 9 were individually introgressed into L. ESCULENTUM using MAS and NILs were developed. The NILs were tested in replicated experiments and CT (measured as shoot turgor maintenance under chilling temperatures) was most strongly associated with the QTL on chromosome 9. Sub-NILs are being derived from the NILs for fine mapping. NILs and sub-NILs will also be used for further physiological studies to characterize the basis of CT. Reciprocal grafts between shoots and roots of plants containing either ESCULENUM or HIRSUTUM alleles at these CT QTLs suggest that both shoot and root signaling is involved in CT. An assessment of cultivated tomato germplasm primarily from California with AFLP markers was conducted. Of the 26 AFLP primer pairs used to genotype 74 cultivars, 102 (9.3%) of 1092 bands scored were polymorphic. A
minimum of 7 primer pairs revealed unique banding patterns for all 74 cultivars even though many cultivars were genetically related, indicating the value of AFLPs for cultivar fingerprinting.
Impacts
Genes controlling agriculturally important traits that are present in wild species can be used to improve cultivated tomato for agricultural sustainability. Wild species' alleles at genes for resistance to pathogens and chilling can facilitate development of cultivars requiring fewer agricultural inputs, thus reducing environmental impacts and production costs.
Publications
- BROUWER, D.J. AND ST.CLAIR, D.A. 2004. Fine mapping of three quantitative trait loci for late blight resistance in tomato using near isogenic lines (NILs) and sub-NILs. Theoretical and Applied Genetics (In Press).
- BROUWER, D.J., JONES, E.S., AND ST.CLAIR, D.A. 2004. QTL analysis of quantitative resistance to Phytophthora infestans (late blight) in tomato, and comparisons to potato. Genome (In Press).
- PARK, Y.H., WEST, M.A.L., AND ST.CLAIR, D.A. 2004. Evaluation of AFLPs for germplasm fingerprinting and assessment of genetic diversity in cultivars of tomato (Lycopersicon esculentum L.). Genome (In Press).
- ROBERT, V.JM., WEST, M.A.L., INAI, S., CAINES, A., ARTZEN, L., SMITH, J.K. and AND ST.CLAIR, D.A. 2001. Marker-assisted introgression of blackmold resistance QTL alleles from wild Lycopersicon cheesmanii to cultivated tomato (L. esculentum) and evaluation of QTL phenotypic effects. Molecular Breeding 8:217-233.
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Progress 01/01/02 to 12/31/02
Outputs
Research on tomato germplasm enhancement is focused on the identification and transfer of genes from wild to cultivated tomato (LYCOPERSICON ESCULENTUM) for chilling tolerance (CT), resistance to blackmold (RBM) and late blight (RLB). Chilling temperatures during tomato production and the pathogens ALTERNARIA ALTERNATA (blackmold) and PHYTOPHTHORA INFESTANS (late blight) can all cause significant yield and fruit quality losses. Previously, quantitative trait loci (QTL) for RBM, RLB, and CT were mapped in interspecific populations and QTLs identified for introgression. RLB QTLs on chromosomes 3, 4, 5 and 11 and RBM QTLs on chromosomes 2, 3, 9 and 12 were introgressed into cultivated tomato using backcrossing and marker-assisted selection (MAS). DNA markers linked to the QTLs were used to select progeny lines containing the desired alleles at these QTLs. BC3S1 lines containing different combinations of one to four RLB QTLs from L. HIRSUTUM were identified using MAS,
then field-tested in 2001 and assayed in disease screens during 2001-02. Lines containing RLB QTLs on chromosomes 5 and 11 were most consistently resistant in all types of assays, while RLB QTL on chromosome 4 was most associated with stem resistance in the field. L. CHEESMANII alleles at RBM QTL on chromosomes 2, 3 and 9 in BC1S2 progeny selected using MAS conferred resistance in an L. ESCULENTUM background; the QTL on chromosome 2 had the largest positive effect. Sub-near-isogenic lines (sub-NILs) for RBM QTL on chromosome 2 and RLB QTL on chromosomes 3, 4, 5 and 11 were developed from NILs and field-tested in 2002. Data on the sub-NILs was used to fine map each of these resistance QTLs to smaller chromosomal segments, resulting in more suitable targets for future MAS breeding efforts. Three CT QTLs from L. HIRSUTUM are being individually introgressed into L. ESCULENTUM using MAS during backcrossing to develop NILs. Sub-NILs will be derived from the NILs for QTL fine mapping. NILs
and sub-NILs will also be used for further physiological studies to characterize the basis of CT (measured as turgor maintenance under chilling temperatures). Reciprocal grafts between shoots and roots of plants containing either ESCULENUM or HIRSUTUM alleles at these CT QTLs suggest that both shoot and root signaling is involved in CT.
Impacts
Genes controlling agriculturally important traits that are present in wild species can be used to improve cultivated tomato for agricultural sustainability. Wild species' genes for resistance to pathogens and chilling can permit the development of cultivars that require fewer chemical inputs, reducing environmental impacts and enhancing economics of production.
Publications
- TRUCO, M.J., RANDALL, L.B., BLOOM, A.J., AND ST.CLAIR, D.A. 2000. Detection of QTLs associated with shoot wilting and root ammonium uptake under chilling temperatures in an interspecific backcross population from Lycopersicon esculentum x L. hirsutum. Theoretical and Applied Genetics 101:1082-1092.
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Progress 01/01/01 to 12/31/01
Outputs
Tomato germplasm enhancement research is focused on introgression of genes for various agriculturally important traits, including resistance to blackmold (RBM), late blight (RLB), and chilling tolerance (CT), from wild to cultivated tomato (LYCOPERSICON ESCULENTUM). Quantitative trait loci (QTL) for RBM, RLB, and CT were mapped previously in interspecific populations. Selected RLB QTL on chromosomes 3, 4, 5 and 11, and RBM QTL on chromosomes 2, 3, 9 and 12, were introgressed into cultivated tomato using backcrossing and marker-assisted selection (MAS) with DNA markers linked to the QTL to select progeny lines containing different combinations of the desired QTL. BC3S1 lines containing different combinations of 1 to 4 RLB QTL from L. HIRSUTUM were identified using MAS, then field-tested and assayed in disease screens in 2001. Lines containing RLB QTLs on chromosomes 5 and 11 tended to be most resistant, and further testing is in progress. BC1S2 progeny with 1-3 RBM QTL
from L. CHEESMANII were identified with MAS and field tested in 1999; L. CHEESMANII alleles at RBM QTL on chromosomes 2, 3 and 9 conferred resistance in an L. ESCULENTUM background. Near-isogenic lines (NILs) for RBM QTL on chromosome 2 and RLB QTL on chromosomes 3, 4, 5 and 11 have been developed. These NILs were used to derive sub-NILs that will be field-tested in 2002 to fine map the resistance loci to smaller chromosomal segments and determine the location of loci involved in linkage drag. Three QTLs for CT (as measured by turgor maintenance) from L. HIRSUTUM are being individually introgressed into L. ESCULENTUM using MAS during backcrossing to develop NILs. Sub-NILs will be derived from the NILs and used for fine mapping of the 3 CT QTLs, as well as for further phyiological studies to characterize turgor maintenance under chilling. A subset of breeding lines derived from L. PENNELLII and L. HIRSUTUM that were field tested in 2000-2001 exhibited significant resistance to aphids
during both years; these lines are suitable as donor parents for further breeding efforts.
Impacts
Genes controlling agriculturally important traits that are present in wild species can be used to improve cultivated tomato for agricultural sustainability. For example, wild species' genes for resistance to diseases, pests, and chilling can permit the development of cultivars that require fewer chemical inputs, reducing environmental impacts and enhancing economic returns to the grower.
Publications
- ROBERT, V.JM., WEST, M.A.L., INAI, S., CAINES, A., ARTZEN, L., SMITH, J.K. and AND ST.CLAIR, D.A. 2001. Marker-assisted introgression of blackmold resistance QTL alleles from wild Lycopersicon cheesmanii to cultivated tomato (L. esculentum) and evaluation of QTL phenotypic effects. Molecular Breeding (In Press).
- FRANCIS, D.M., KABELKA, E., BELL, J., FRANCHINO, B., AND ST.CLAIR, D.A. 2001. Resistance to bacterial canker in tomato (Lycopersicon hirsutum LA 407) and its progeny derived from crosses to L. esculentum. Plant Disease 85:1171-1176.
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Progress 01/01/00 to 12/31/00
Outputs
Tomato germplasm enhancement efforts are focusing on introgression of genes for various agriculturally important traits, including resistance to blackmold (RBM) and late blight (RLB) from wild to cultivated tomato. Quantitative trait loci (QTL) for RBM and RLB were identified. Selected RLB QTL on chromosomes 3, 4, 5 and 11 and RBM QTL on chromosomes 2, 3, 9 and 12 were introgressed into cultivated tomato using marker-assisted selection (MAS) with DNA markers linked to the QTL to select progeny containing different combinations of the desired QTL. A MAS program was used to introgress 4 RLB QTL from L. HIRSUTUM, and the BC3S1 generation will be field-tested in 2001. BC1S2 progeny with 0-3 RBM QTL from L. CHEESMANII were identified with MAS and phenotypically evaluated in field trials during 1998-99. Certain lines were significantly more resistant than L. ESCULENTUM checks. L. CHEESMANII alleles at RBM QTL on chromosomes 2, 3 and 9 confer resistance in an L. ESCULENTUM
background. QTL for chilling tolerant ammonium uptake and turgor maintenance were mapped in a BC1 interspecific population from L. HIRSUTUM; growth chamber experiments verified that the HIRSUTUM allele at the QTL on chromosome 9 maintains growth under chilling. Breeding lines derived from L. PENNELLII exhibited significant resistance to certain insect species.
Impacts
Genes controlling agriculturally important traits present in wild species can be used to improve cultivated tomato and enhance the sustainability of agriculture. For example, wild species' genes for disease and pest resistances will permit the development of cultivars that can produce a crop requiring less or no chemical inputs, reducing environmental impacts of agriculture and enhancing economic returns to the grower.
Publications
- HARTMAN, J.B. AND ST.CLAIR, D.A. 1999. Variation for aphid resistance and acylsugar expression among and within Lycopersicon pennellii-derived inbred backcross lines of tomato and their F1 progeny. Plant Breeding 118:531-536. CHEN, F.Q., FOOLAD, M.R., HYMAN, J., ST.CLAIR, D.A., BEELAMAN, R.B. 1999. Mapping of QTLs for lycopene and other fruit traits in a Lycopersicon esculentum x L. pimpinellifolium cross and comparison of QTLs across tomato species. Molecular Breeding 5:283-299.
- TRUCO, M.J., RANDALL, L.B., BLOOM, A.J., AND ST.CLAIR, D.A. 2000. Detection of QTLs associated with shoot wilting and root ammonium uptake under chilling temperatures in an interspecific backcross population from Lycopersicon esculentum x L. hirsutum. Theoretical and Applied Genetics 101:1082-1092.
- JOHNSON, W.C., JACKSON, L.E., OCHOA, O., VAN WIJK, R., PELEMAN, J., ST.CLAIR, D.A., MICHELMORE, R.W. 2000. Lettuce, a shallow-rooted crop, and Lactuca serriola, its wild progenitor, differ at QTL determining root architecture and deep soil water exploitation. Theoretical and Applied Genetics 101:1066-1073.
- MORRIS, P.F., CONNOLLY, M.S. AND ST.CLAIR, D.A. 2000. Genetic diversity of Alternaria alternata isolated from tomato in California assessed using RAPDs. Mycological Research 104:286-292.
- HARTMAN, J.B. AND ST.CLAIR, D.A. 1999. Combining ability for beet armyworm (Spodoptera exigua) resistance and horticultural traits of selected Lycopersicon pennellii-derived inbred backcross lines of tomato. Plant Breeding 118:523-530.
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Progress 01/01/99 to 12/31/99
Outputs
Tomato germplasm enhancement efforts are focussing on introgression of genes for resistance to blackmold (RBM) and late blight (RLB) from wild to cultivated tomato. Quantitative trait loci (QTL) for RBM and RLB were identified, and selected RLB QTL on chromosomes 3, 4, 5 and 11 are being (and RBM QTL on chromosomes 2, 3, 9 and 12 were) introgressed into cultivars using marker-assisted selection (MAS). DNA markers linked to QTL were used in MAS to select progeny containing desired QTL. MAS identified backcross self (BC1S1) progeny containing different combinations of QTL for RBM. A MAS program is in progress for introgressing 4 RLB QTL, and is currently at the BC3S1 generation. BC1S2 progeny with 0-3 QTL for RBM were phenotypically evaluated in field trials during 1998-99. Single QTL homozygous lines were significantly more resistant than L. ESCULENTUM checks, indicating CHEESMANII alleles at certain RBM QTL confer resistance in an L. ESCULENTUM background. QTL for
chilling tolerant ammonium uptake and turgor maintenance were mapped in a BC1 interspecific population from L. HIRSUTUM LA 1778; growth chamber experiments verified that the HIRSUTUM allele at the QTL on chromosome 9 maintains growth under chilling. Breeding lines with increased insect resistance were developed using L. PENNELLII.
Impacts
Genes controlling agriculturally important traits present in wild species can be used to improve cultivated tomato and enhance the sustainability of agriculture. For example, wild species' genes for disease and pest resistances will permit the development of cultivars that can produce a crop requiring less or no chemical inputs, reducing environmental impacts of agriculture and enhancing economic returns to the grower.
Publications
- HARTMAN, J.B. AND ST.CLAIR, D.A. 2000. Combining ability for beet armyworm (Spodoptera exigua) resistance and horticultural traits of selected Lycopersicon pennellii-derived inbred backcross lines of tomato. Plant Breeding (In press).
- HARTMAN, J.B. AND ST.CLAIR, D.A. 2000. Variation for aphid resistance and acylsugar expression among and within Lycopersicon pennellii-derived inbred backcross lines of tomato and their F1 progeny. Plant Breeding (In press).
- MORRIS, P.F., CONNOLLY, M.S. AND ST.CLAIR, D.A. 2000. Genetic diversity of Alternaria alternata isolated from tomato in California assessed using RAPDs. Mycological Research (In press).
- CHEN, F.Q., FOOLAD, M.R., HYMAN, J., ST.CLAIR, D.A., BEELAMAN, R.B. 1999. Mapping of QTLs for lycopene and other fruit traits in a Lycopersicon esculentum x L. pimpinellifolium cross and comparison of QTLs across tomato species. Molecular Breeding 5:283-299.
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Progress 01/01/98 to 12/31/98
Outputs
Tomato germplasm enhancement is focussing on introgression of genes for resistance to blackmold (RBM) and late blight (RLB) from wild to cultivated tomato. RFLP mapping was used to detect quantitative trait loci (QTL) for RBM and RLB. Selected RLB QTL on chromosomes 3, 4, 5 and 11 and RBM QTL on chromosomes 2, 3, 9 and 12 are being introgressed into cultivars using marker-assisted selection (MAS). RFLP markers linked to QTL were converted to PCR-based markers and used in MAS of progeny with desired QTL regions. MAS identified backcross self (BC1S1) progeny containing different combinations of QTL for RBM. A MAS program is in progress for introgressing RLB QTL, and is currently at the BC3 generation. BC1S2 progeny with 0-3 QTL for RBM were phenotypically evaluated in field trials during 1998. Single QTL homozygous lines were significantly more resistant than L. ESCULENTUM checks, indicating CHEESMANII alleles at RBM QTL confer resistance. Additional BC1S2 lines will be
field-tested in 1999. Cultivars vary for ability to cross with accessions of L. HIRSUTUM, and can be selected to facilitate interspecific introgression. QTL for chilling tolerant ammonium uptake and turgor maintenance were mapped in a BC1 interspecific population from L. HIRSUTUM LA 1778. Inbred backcross lines derived from L. PENNELLII varied for resistance to insects.
Impacts
(N/A)
Publications
- HARTMAN, J.B. and ST.CLAIR, D.A. 1998. Variation for insect resistance and horticultural traits in tomato inbred backcross populations derived from LYCOPERSICON PENNELLII. Crop Science
- BLOOM, A.J., RANDALL, L.B., MEYERHOFF, P.A. and ST.CLAIR, D.A. 1998. The chilling sensitivity of root ammonium influx in a cultivated and wild tomato. Plant, Cell and Environment 21:191-199.
- SACKS, E.J. and ST.CLAIR, D.A. 1998. Variation among seven genotypes of LYCOPERSICON ESCULENTUM and 36 accessions of L. HIRSUTUM for interspecific crossability. Euphytica 101:185-191.
- ST.CLAIR, D.A. 1998. Breeding for blackmold resistance in processing tomatoes. Annual Report to the California Tomato Research Institute.
- ST.CLAIR, D.A. 1998. Breeding tomatoes for pathotype non-specific resistance to late blight. Annual Report to the California Tomato
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Progress 01/01/97 to 12/01/97
Outputs
Tomato germplasm enhancement research has focused on introgression of genes for resistance to blackmold (RBM) and late blight (RLB) from wild to cultivated tomato. RFLP mapping to detect quantitative trait loci (QTL) has been completed for RBM and RLB. RLB QTL were detected on chromosomes 1, 2, 3, 4, 5, 11 and RBM QTL on chromosomes 2 (two total), 3 (two total), 6, 8, 9, 12. Selected QTL (RLB QTL 3, 4, 5 and 11; RBM QTL 2 (two), 3, 9 and 12) are being introgressed into cultivated tomato using marker-assisted selection (MAS). RFLP markers linked to RBM and RLB QTL are being converted to PCR-based markers for use in MAS. The first backcross generation to L. ESCULENTUM has been obtained and PCR markers linked to QTL for RBM have been used to identify progeny containing desired QTL; these have been self-pollinated and the backcross self (BC1S1) progeny are being subjected to MAS to select plants containing different combinations of resistance QTL. A similar program is in
progress for introgressing RLB QTL. Progeny containing different combinations of QTL for RBM will be phenotypically evaluated in the field during 1998; superior fines will be selected. Genetic differences for crossability of L. ESCULENTUM cultivars with accessions of L. HIRSUTUM and L. PERUVIANUM has been established; cultivars can be selected to facilitate interspecific introgression efforts.
Impacts
(N/A)
Publications
- SACKS, E.J. 1996. Improving the efficiency of introgressing genes from LYCOPERSICON HIRSUTUM and L. PERUVIANUM to L. ESCULENTUM. Ph.D.
- ST.CLAIR, D.A. 1997. Breeding and genetics of processing tomatoes. Annual Report to the California Tomato Research Institute and the California League of Food Processors.
- SACKS, E.J. and ST.CLAIR, D.A. 1998. Variation among seven genotypes of LYCOPERSICON ESCULENTUM and 36 accessions of L. HIRSUTUM for interspecific crossability. Euphytica (in press).
- SACKS, E.J., GERHARDT, L.M., GRAHAM, E.B., JACOBS, J., THORRUP, T.A. and ST.CLAIR, D.A. 1997. Variation among 41 genotypes of tomato (LYCOPERSICON ESCULENTUM) for crossability to L. PERUVIANUM. Annals
- ST.CLAIR, D.A. 1997. Breeding tomatoes for pathotype non-specific resistance to late blight. Annual Report to the California Tomato
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Progress 01/01/96 to 12/30/96
Outputs
Tomato germplasm enhancement research has focused on introgression of genes for fruit soluble solids (FSS), resistance to blackmold (RBM) and late blight (RLB) from wild to cultivated tomato. RFLP mapping to detect quantitative trait loci (QTL) has been completed for FSS and RBM, and is in progress for RLB. FSS QTL were detected on chromosomes 2, 3, 6, 7, 9, 10, 11, 12 and RBM QTL on chromosomes 2a, 2b, 3a, 3b, 6, 8, 9, 12. Selected QTL (FSS QTL 2, 3 and 12; RBM QTL 2a, 2b, 3b, 9, 12) will be introgressed into cultivated tomato using marker-assisted selection (MAS). RFLP markers linked to RBM and FSS QTL are being converted to PCR-based markers for use in MAS. The first backcross generation to L. ESCULENTUM has been obtained and PCR markers linked to QTL for RBM and FSS will be used to identify progeny containing desired QTL to use in additional backcrossing. Progeny containing different combinations of QTL for RBM and FSS will be phenotypically evaluated and compared
in the field during 1998. Genetic differences for crossability of L. ESCULENTUM cultivars with accessions of L. HIRSUTUM and L. PERUVIANUM has been verified with a series of replicated experiments. Tomato pollen can be stored cryogenically for at least a year without loss of viability.
Impacts
(N/A)
Publications
- TRIANO, S. R. 1996. Inbred backcross breeding for the introgression of quantitative traits and the identification of trait-correlated RFLP markers in tomato. Ph.D. Thesis.
- SACKS, E.J. and ST.CLAIR D. A. 1996. Cryogenic storage of tomato pollen: effect on fecundity. HortScience 31:477-478.
- SACKS, E.J. 1996. Improving the efficiency of introgressing genes from LYCOPERSICON HIRSUTUM and L. PERUVIANUM to L. ESCULENTUM. Ph.D. Thesis. ST.
- CLAIR, D. A. 1996. Breeding and genetics of processing tomatoes. Annual Reports to the California Tomato Research Institute and the California League ofFood Processors. ST.
- CLAIR, D. A. 1996. Breeding and genetics of fresh market tomatoes. Annual Report to the California Tomato Commission.
- TRIANO, S. R. and ST. CLAIR, D. A. 1995. Processing tomato germplasm with improved fruit soluble solids. HortScience 30:1477-1478.
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