Progress 06/21/13 to 03/25/18
Outputs
Progress Report Objectives (from AD-416): Diverse Solanaceous germplasm resources exist for enhancement of cultivated forms of tomato and pepper. Genes that may be valuable for crop improvement are often not well characterized, they may be associated with undesirable traits, or crossing barriers hinder introgression from distant crop relatives. Changes in pathogen virulence and introduction of new crop pathogens can overcome available host resistance, leaving producers vulnerable to crop loss. Available cultivars may not adequately address producer and consumer needs for new crop uses and high-value alternative crops. This project focuses on determining the underlying genetic bases of important traits of tomato and pepper � including fruit quality attributes and resistance to recurring or emerging diseases - and deploying them as finished cultivars, breeding lines, and genetic stocks. Over the five year project period, the following specific objectives will be addressed. Objective 1: Exploit homology between tomato and pepper to identify and transfer anthracnose-resistance from tomato to pepper, and release new pepper anthracnose resistant germplasm, along with molecular markers for marker-assisted selection. Sub-objective 1A. Identify anthracnose resistance-linked markers and candidate loci in tomato and pepper. Sub-objective 1B. Determine identity of species and relatedness of Colletotrichum isolates responsible for pepper anthracnose and relate these findings to knowledge of host/strain virulence specificity for isolates infecting pepper fruit. Objective 2: Identify and characterize genetic resistance to the emerging diseases Groundnut ringspot virus (GRSV) infecting pepper and Potato spindle tuber viroid (PSTVd) infecting tomato, and deliver/release appropriate materials to researchers and breeders. Sub-objective 2A. Identify and characterize pepper host resistance to GRSV. Sub-objective 2B. Identify and characterize tomato host resistance to PSTVd. Objective 3: Develop and release pepper breeding lines with improved quality attributes for the culinary, culinary/ornamental, and minimally processed fresh-cut market. Sub-objective 3A. Develop and release pepper breeding lines with improved quality attributes for the culinary and culinary/ornamental market. Sub-objective 3B. Develop and release pepper breeding lines with improved quality attributes for the minimally processed fresh-cut market. Approach (from AD-416): Next generation sequencing technology will be used for map-based cloning of anthracnose resistance loci from a recombinant, inbred line tomato population that ARS has developed. To bolster identification of candidate genes for anthracnose resistance, a proteomic survey will also be conducted using resistant and susceptible tomato lines. Markers developed from tomato will henceforth be utilized to identify resistance homologues in the pepper species C. baccatum. Resistance loci will be transferred to C. annuum using bridge lines that ARS has developed. Different Colletotrichum species have been identified as the causative organism responsible for recent outbreaks of green pepper anthracnose fruit rot in Ontario and Midwestern, Southeastern and Mid-Atlantic production areas in the U.S. Isolate species identity and relatedness from these regions will be characterized to ascertain if these isolates share a common lineage. Initial screening surveys for GRSV resistance will focus on C. chinense, the species where resistance to the Tospoviruses TSWV and CaCV has been previously identified. Reported Tospovirus resistance and accession passport data will be assessed and a subset of the available C. chinense accessions will be selected to maximize coverage of the species� native distribution range. C. annuum land races and accessions representative of the distribution range of C. frutescens, C. chacoense and C. baccatum will be evaluated in a similar manner. Accessions that exhibit high levels of resistance will be crossed to susceptible genotypes to characterize the inheritance of resistance. Initial screening for PSTVd will focus on core collections established for wild relatives of the cultivated tomato. Core collections to be screened will include S. chilense, S. habrochaites, S. pennellii, S peruvianum, and S. pimpinellifolium. Initial screening will focus on a PSTVd variant isolated from an outbreak in tomato and a second variant isolated from potato with confirmed infectivity on tomato. Infectivity will be quantified using real-time PCR. Ongoing development of ornamental and dual-purpose ornamental/culinary pepper germplasm is carried out via breeding strategies that include backcross breeding for simple traits and pedigree and inbred backcross breeding for complex traits. Improved germplasm is evaluated in cooperation with collaborators and released by ARS. Initial germplasm screening for fresh-cut pepper will focus on accessions that bear fruit with thick pericarp. Using knowledge of market types and available passport data, C. annuum accessions will be selected from commercial sources and the USDA, ARS, Plant Genetic Resources Conservation Unit. Accessions with varied fresh-cut quality attributes will be selected to assess applicability of hyperspectral imaging for high throughput phenotyping of fresh-cut quality. Accessions with divergent fresh-cut quality will be intercrossed in a diallel mating scheme to evaluate combining ability for fresh-cut attributes. Superior accessions will be hybridized with sweet and hot pepper breeding lines and BC2 generation hybrids advanced for phenotyping and public release. Anthracnose: host and pathogen genetic diversity. Anthracnose fruit rot caused by the fungal species Colletotrichum is one of the most serious diseases affecting the production of tomato and pepper in the United States. Anthracnose has been typified as a disease of ripe fruit. However, Colletotrichum diversity and pathogenicity is rising as evidenced by increased incidence of isolates causing disease on immature pepper fruit. ARS scientists in Beltsville, Maryland, in collaboration with Rutgers University, collected over 160 isolates from infected fruit grown in the Mid-Atlantic and Northeastern U.S. to assess genetic diversity and differential host pathogenicity of prevalent isolates. Multi-gene phylogenetic analysis using DNA nucleotide sequence markers was utilized to determine species identities and determine lineage of isolates from different production regions and hosts. The results revealed extensive diversity among Colletotrichum isolates consisting of 15 clades that separated conventional ripe fruit rotters from emergent immature fruit rotting isolates. Based on the fungal diversity in a production region, growers can now determine whether to implement disease management strategies at immature or mature stages of fruit development. This information on pathogen population diversity also enables breeders to more efficiently develop new cultivars resistant to more aggressive strains of the anthracnose pathogen. Tomato plants susceptible and resistant to Colletotrichum were characterized at the genomic level to identify host genes associated with resistance and/or susceptibility. Genotype-by-sequencing (GBS) analysis was performed using a tomato recombinant inbred line population that we developed from a cross of anthracnose susceptible and resistant tomato genotypes. Data analysis was in progress at the termination of this project and is reported in the new project plan. Two chromosomal regions associated with pathogen susceptibility/resistance were identified and fine mapping of these regions has been initiated. In the new project plan, the results will enable development of selectable DNA markers for breeding anthracnose resistant tomato and identification of resistance genes in pepper where robust levels of resistance have been difficult to identify. Pepper virus resistance. New genes for virus resistance must be identified in pepper to address the emergent viruses that threaten crop production. Methodology for screening diverse pepper germplasm for resistance to the tospovirus Groundnut Ringspot Virus was established after new reports of this virus impacting crop production in various parts of Florida. Prior to conducting screening of germplasm for potential resistance to this virus, the tospovirus Tomato Chlorotic Spot Virus (TCSV) emerged in the U.S. and was deemed a significantly greater threat to both pepper and tomato. In consultation with ARS leadership, resources were shifted to identification of pepper genotypes with resistance to TCSV. TCSV is now established in Florida, a major production area for both tomato and pepper. In cooperation with ARS scientists in Beltsville and Florida, diverse pepper germplasm originally collected across the native distribution range for pepper in the Americas was screened for TCSV resistance. We identified pepper accessions grown under greenhouse conditions that exhibited varying levels of resistance to TCSV. Additional studies are planned to identify the most promising accessions and confirm the heritability of resistance. Genetic diversity and heritability for pepper fresh-cut attributes. Fresh pepper (Capsicum) fruit that are sliced and/or diced are referred to as fresh-cut products. The shelf-life of fresh-cut product from commercial pepper cultivars is insufficient for practical use in fresh- cut applications. Little knowledge has been available describing the genetic diversity of attributes that may contribute to pepper fresh-cut quality and the heritability of these attributes. Utilizing the wealth of available Capsicum genetic resources, ARS scientists at Beltsville, Maryland, in cooperation with Enza Zaden Research USA, characterized genetic diversity in diverse Capsicum germplasm representing four major pepper market classes. Methodology was developed to process and evaluate fresh-cut product electrolyte leakage, water loss, and CO2/O2 evolution in modified atmosphere packaging. Additional criteria were also evaluated. Electrolyte leakage was a reliable measure of fresh-cut tissue integrity and was positively correlated with subjective sensory evaluations of stored product quality. Diversity for attributes that contribute to integrity of fresh-cut product was extensive, indicating that breeding for pepper fresh-cut quality can be undertaken to improve commercial cultivars for use by the fresh-cut produce industry. Moderate to high broad-sense heritability was estimated for fresh-cut product electrolyte leakage. We identified several sweet bell, jalapeno and cherry genotypes, respectively, which retained tissue integrity as fresh-cut product during cold storage. Populations were developed from crosses of advanced pepper breeding lines and commercial cultivars to assess combining ability for fresh-cut quality attributes that contribute to suitability for minimally processed fresh-cut market applications. The results of these first reports of genetic diversity and heritability for fresh-cut attributes in pepper are valuable for public and private pepper breeders to develop superior varieties for use by the fresh-cut vegetable industry. New specialty crop pepper cultivars. Extensive genetic diversity can be found in diverse pepper plant material for plant habit and morphology, immature and mature fruit color, and varying shades of green to purple to black foliage coloration. Although considered a vegetable, this diversity can also be exploited to develop very high value alternative crops for commercial plant propagators and growers. ARS scientists in Beltsville, Maryland, developed four new pepper cultivars that were made available as the Christmas Lights cultivar series. The four cultivars were selected for their distinctive round fruit that are oriented upright, yellow or violet immature and red or orange mature fruit color, and compact growth habit. Commercial trials indicate that these new cultivars are valuable as specialty high-value ornamental vegetables for use as bedding plants and/or potted plants. Trials of related high-value ornamental peppers were conducted and three cultivars were licensed to an industry partner, a commercial grower/ propagator. Commercial growers will benefit from introduction of these new high value specialty pepper cultivars for the wholesale and retail markets. These new cultivars are intended for use by specialty vegetable growers, commercial propagators, and gardeners for use as ornamental vegetable specimen plants, border plants, and in mass plantings. Breeding for specialty peppers with improved flavor, color and related consumer culinary valued attributes continued with multi-location trials of advanced breeding lines for the culinary market. High-value snack peppers with low seed counts and unique fruit shapes ranging from tabasco to bell pod types were selected for stabilization of true breeding lines for release. Populations were constructed to determine the heritability of desirable low seed count in this class of specialty peppers. A manuscript describing those results is in preparation for submission to the publisher. Enhanced eggplant quality and nutritive value. Anthocyanins and phenolic acids are the principal flavonoids that impart nutritive value to eggplant fruit and distinguish it among the top ten vegetables for antioxidant content. Anthocyanins also impart fruit color. Relatively little is known about how growing conditions influence eggplant fruit phenolic acids, compounds that affect fresh fruit quality and distinguish eggplant among the top ten fruits and vegetables for antioxidant content. ARS scientists at Beltsville, Maryland, in cooperation with scientists at the Polytechnic University of Valencia, evaluated cultivated eggplant varieties as well as exotic eggplant relatives in multiple locations under greenhouse and open field conditions to assess the influence of environment on fruit phenolic acid content. We found that different eggplant varieties varied considerably for total content as well as composition of phenolic acids and that varieties were a greater source of variation in comparison to the environment for fruit phenolic acid content. The results are valuable for plant breeders who develop new varieties for different production locations and for vegetable growers and consumers seeking to select varieties with superior fruit quality and nutritive value. In related eggplant research, we characterized the genetic mechanism contributing to altered eggplant fruit color. Anthocyanins are water soluble pigments that impart color and nutritive value to fruits and vegetables. Thorough knowledge of the genetic control of anthocyanin accumulation that would aid breeders in developing improved varieties is lacking in minor crops such as eggplant. In collaboration with the Polytechnic University of Valencia, a spontaneous green-fruited eggplant mutant was identified in a normally purple-fruited eggplant. We characterized the genetic mechanism contributing to altered fruit color. We determined the inheritance of eggplant fruit anthocyanin pigmentation and determined that expression of two transcription factors is critical for anthocyanin biosynthesis. Our new knowledge of genes that are activated and/or suppressed during anthocyanin biosynthesis in the mutant helps scientists better understand how anthocyanin accumulation is regulated, thus assisting breeders in developing improved varieties for the vegetable industry and gardeners. Accomplishments 01 New specialty crop pepper cultivars. Extensive genetic diversity can be found in diverse pepper plant material for plant habit and morphology (form and structure), immature and mature fruit color and varying shades of green to purple to black foliage coloration. Although considered a vegetable, this diversity can also be exploited to develop alternative specialty crops for commercial plant propagators and growers. ARS scientists in Beltsville, Maryland, developed four new ornamental vegetable pepper cultivars that were made available as the Christmas Lights cultivar series. The four cultivars were selected for their distinctive round fruit that are oriented upright, yellow or violet immature and red or orange mature fruit color, and compact growth habit. Commercial trials indicate that these new cultivars are valuable for use as specialty high-value ornamental vegetables for use as bedding plants and/or potted plants whose value far exceeds that of conventional forms of the crop.
Impacts
(N/A)
Publications
- Stommel, J.R., Kozlov, M.A., Griesbach, R.J. 2018. Ornamental pepper (Capsicum annuum L.) cultivars comprising the Christmas Lights cultivar series. HortScience. 53:391-394.
- Park, E., Luo, Y., Marine, S.C., Everts, K.A., Micallef, S.A., Bolten, S.J. , Stommel, J.R. 2018. Consumer preference and physicochemical evaluation of organically grown melon. Postharvest Biology and Technology. 141:77-85.
- Zhou, B., Luo, Y., Bauchan, G.R., Feng, H., Stommel, J.R. 2017. Visualizing pathogen internalization pathways in fresh tomatoes using MicroCT and confocal laser scanning microscopy. Food Control. 85:276-282.
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Progress 10/01/16 to 09/30/17
Outputs
Progress Report Objectives (from AD-416): Diverse Solanaceous germplasm resources exist for enhancement of cultivated forms of tomato and pepper. Genes that may be valuable for crop improvement are often not well characterized, they may be associated with undesirable traits, or crossing barriers hinder introgression from distant crop relatives. Changes in pathogen virulence and introduction of new crop pathogens can overcome available host resistance, leaving producers vulnerable to crop loss. Available cultivars may not adequately address producer and consumer needs for new crop uses and high-value alternative crops. This project focuses on determining the underlying genetic bases of important traits of tomato and pepper � including fruit quality attributes and resistance to recurring or emerging diseases - and deploying them as finished cultivars, breeding lines, and genetic stocks. Over the five year project period, the following specific objectives will be addressed. Objective 1: Exploit homology between tomato and pepper to identify and transfer anthracnose-resistance from tomato to pepper, and release new pepper anthracnose resistant germplasm, along with molecular markers for marker-assisted selection. Sub-objective 1A. Identify anthracnose resistance-linked markers and candidate loci in tomato and pepper. Sub-objective 1B. Determine identity of species and relatedness of Colletotrichum isolates responsible for pepper anthracnose and relate these findings to knowledge of host/strain virulence specificity for isolates infecting pepper fruit. Objective 2: Identify and characterize genetic resistance to the emerging diseases Groundnut ringspot virus (GRSV) infecting pepper and Potato spindle tuber viroid (PSTVd) infecting tomato, and deliver/release appropriate materials to researchers and breeders. Sub-objective 2A. Identify and characterize pepper host resistance to GRSV. Sub-objective 2B. Identify and characterize tomato host resistance to PSTVd. Objective 3: Develop and release pepper breeding lines with improved quality attributes for the culinary, culinary/ornamental, and minimally processed fresh-cut market. Sub-objective 3A. Develop and release pepper breeding lines with improved quality attributes for the culinary and culinary/ornamental market. Sub-objective 3B. Develop and release pepper breeding lines with improved quality attributes for the minimally processed fresh-cut market. Approach (from AD-416): Next generation sequencing technology will be used for map-based cloning of anthracnose resistance loci from a recombinant, inbred line tomato population that ARS has developed. To bolster identification of candidate genes for anthracnose resistance, a proteomic survey will also be conducted using resistant and susceptible tomato lines. Markers developed from tomato will henceforth be utilized to identify resistance homologues in the pepper species C. baccatum. Resistance loci will be transferred to C. annuum using bridge lines that ARS has developed. Different Colletotrichum species have been identified as the causative organism responsible for recent outbreaks of green pepper anthracnose fruit rot in Ontario and Midwestern, Southeastern and Mid-Atlantic production areas in the U.S. Isolate species identity and relatedness from these regions will be characterized to ascertain if these isolates share a common lineage. Initial screening surveys for GRSV resistance will focus on C. chinense, the species where resistance to the Tospoviruses TSWV and CaCV has been previously identified. Reported Tospovirus resistance and accession passport data will be assessed and a subset of the available C. chinense accessions will be selected to maximize coverage of the species� native distribution range. C. annuum land races and accessions representative of the distribution range of C. frutescens, C. chacoense and C. baccatum will be evaluated in a similar manner. Accessions that exhibit high levels of resistance will be crossed to susceptible genotypes to characterize the inheritance of resistance. Initial screening for PSTVd will focus on core collections established for wild relatives of the cultivated tomato. Core collections to be screened will include S. chilense, S. habrochaites, S. pennellii, S peruvianum, and S. pimpinellifolium. Initial screening will focus on a PSTVd variant isolated from an outbreak in tomato and a second variant isolated from potato with confirmed infectivity on tomato. Infectivity will be quantified using real-time PCR. Ongoing development of ornamental and dual-purpose ornamental/culinary pepper germplasm is carried out via breeding strategies that include backcross breeding for simple traits and pedigree and inbred backcross breeding for complex traits. Improved germplasm is evaluated in cooperation with collaborators and released by ARS. Initial germplasm screening for fresh-cut pepper will focus on accessions that bear fruit with thick pericarp. Using knowledge of market types and available passport data, C. annuum accessions will be selected from commercial sources and the USDA, ARS, Plant Genetic Resources Conservation Unit. Accessions with varied fresh-cut quality attributes will be selected to assess applicability of hyperspectral imaging for high throughput phenotyping of fresh-cut quality. Accessions with divergent fresh-cut quality will be intercrossed in a diallel mating scheme to evaluate combining ability for fresh-cut attributes. Superior accessions will be hybridized with sweet and hot pepper breeding lines and BC2 generation hybrids advanced for phenotyping and public release. Objective 1. Colletotrichum fungal isolates as well as tomato plants susceptible and resistant to this pathogen are being characterized at the genomic level to identify genes in the pathogen and host associated with resistance and/or susceptibility. Genotype-by-sequencing (GBS) analysis of tomato recombinant inbred lines susceptible and resistant to the Colletotrichum fungus is in progress via collaboration with West Virginia State University. Data analysis will enable identification of DNA markers linked to pathogen resistance and/or susceptibility. Objective 2. New genes for virus resistance must be identified in pepper to address emergence of viruses classified as tospoviruses that are new to the U.S. or that overcome known host genes for virus resistance. Additional screening of diverse pepper germplasm for emergent tomato chlorotic spot virus (TCSV) resistance is ongoing. Accessions with superior levels of TCSV resistance are being introgressed into adapted pepper breeding lines. Objective 3. Value-added crops can be very profitable in comparison to conventional forms of the commodity. Breeding for specialty peppers with improved flavor, color and related consumer valued attributes continued with multi-location trials of advanced breeding lines for the culinary market. Similar trials of high-value ornamental peppers were conducted and cultivar status material was licensed to an industry partner. Development of pepper populations segregating for fresh-cut quality attributes is ongoing. Breeding lines being developed from these populations will be valuable for development of improved cultivars for minimally processed fresh-cut market applications. Accomplishments 01 Fungal diversity coincides with anthracnose fruit rot. Anthracnose fruit rot is one of the most serious diseases affecting the production of tomato and pepper in the United States. Although anthracnose is generally considered to be a disease of ripe fruit, increased incidence of disease on immature pepper fruit has been observed. ARS scientists in Beltsville, Maryland, in collaboration with Rutgers University, collected fungal samples from infected fruit from the Mid-Atlantic and Northeastern United States to characterize the genetic diversity and virulence of these samples. Extensive diversity among fungal samples was identified. They also identified which samples caused immature fruit to rot, rather than traditional ripe fruit rot. Based on the fungal diversity in a production region, growers can now determine whether to implement disease management strategies at immature or mature stages of fruit development. This information on pathogen population diversity also enables breeders to develop new cultivars resistant to more aggressive strains of the anthracnose pathogen.
Impacts
(N/A)
Publications
- Nimmakayala, P., Aburrie, V.L., Saminathan, T., Alaparthi, S.B., Almeida, A., Hyma, K., Mitchell, S., Davenport, B., Tonapi, K., Yadav, L., Hankins, G., Malkaram, S., Stommel, J.R., Park, M., Choi, D., Rathinasabapathi, B., Reddy, U. 2016. Genome-wide diversity and association mapping for capsaicinoids and fruit weight in Capsicum annuum L. Scientific Reports. 6:38081.
- Nimmakayala, P., Abburi, V.L., Saminathan, T., Alaparthi, S.B., Almeida, A. , Davenport, B., Davidson, J., Vajja, G., Reddy, C., Tomason, Y., Nadimi, M., Hankins, G., Choi, D., Stommel, J.R., Reddy, U. 2016. Genome-wide divergence and linkage disequilibrium analyses for Capsicum baccatum revealed by genome-anchored single nucleotide polymorphisms. Frontiers in Plant Science. 7:1646.
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Progress 10/01/15 to 09/30/16
Outputs
Progress Report Objectives (from AD-416): Diverse Solanaceous germplasm resources exist for enhancement of cultivated forms of tomato and pepper. Genes that may be valuable for crop improvement are often not well characterized, they may be associated with undesirable traits, or crossing barriers hinder introgression from distant crop relatives. Changes in pathogen virulence and introduction of new crop pathogens can overcome available host resistance, leaving producers vulnerable to crop loss. Available cultivars may not adequately address producer and consumer needs for new crop uses and high-value alternative crops. This project focuses on determining the underlying genetic bases of important traits of tomato and pepper � including fruit quality attributes and resistance to recurring or emerging diseases - and deploying them as finished cultivars, breeding lines, and genetic stocks. Over the five year project period, the following specific objectives will be addressed. Objective 1: Exploit homology between tomato and pepper to identify and transfer anthracnose-resistance from tomato to pepper, and release new pepper anthracnose resistant germplasm, along with molecular markers for marker-assisted selection. Sub-objective 1A. Identify anthracnose resistance-linked markers and candidate loci in tomato and pepper. Sub-objective 1B. Determine identity of species and relatedness of Colletotrichum isolates responsible for pepper anthracnose and relate these findings to knowledge of host/strain virulence specificity for isolates infecting pepper fruit. Objective 2: Identify and characterize genetic resistance to the emerging diseases Groundnut ringspot virus (GRSV) infecting pepper and Potato spindle tuber viroid (PSTVd) infecting tomato, and deliver/release appropriate materials to researchers and breeders. Sub-objective 2A. Identify and characterize pepper host resistance to GRSV. Sub-objective 2B. Identify and characterize tomato host resistance to PSTVd. Objective 3: Develop and release pepper breeding lines with improved quality attributes for the culinary, culinary/ornamental, and minimally processed fresh-cut market. Sub-objective 3A. Develop and release pepper breeding lines with improved quality attributes for the culinary and culinary/ornamental market. Sub-objective 3B. Develop and release pepper breeding lines with improved quality attributes for the minimally processed fresh-cut market. Approach (from AD-416): Next generation sequencing technology will be used for map-based cloning of anthracnose resistance loci from a recombinant, inbred line tomato population that ARS has developed. To bolster identification of candidate genes for anthracnose resistance, a proteomic survey will also be conducted using resistant and susceptible tomato lines. Markers developed from tomato will henceforth be utilized to identify resistance homologues in the pepper species C. baccatum. Resistance loci will be transferred to C. annuum using bridge lines that ARS has developed. Different Colletotrichum species have been identified as the causative organism responsible for recent outbreaks of green pepper anthracnose fruit rot in Ontario and Midwestern, Southeastern and Mid-Atlantic production areas in the U.S. Isolate species identity and relatedness from these regions will be characterized to ascertain if these isolates share a common lineage. Initial screening surveys for GRSV resistance will focus on C. chinense, the species where resistance to the Tospoviruses TSWV and CaCV has been previously identified. Reported Tospovirus resistance and accession passport data will be assessed and a subset of the available C. chinense accessions will be selected to maximize coverage of the species� native distribution range. C. annuum land races and accessions representative of the distribution range of C. frutescens, C. chacoense and C. baccatum will be evaluated in a similar manner. Accessions that exhibit high levels of resistance will be crossed to susceptible genotypes to characterize the inheritance of resistance. Initial screening for PSTVd will focus on core collections established for wild relatives of the cultivated tomato. Core collections to be screened will include S. chilense, S. habrochaites, S. pennellii, S peruvianum, and S. pimpinellifolium. Initial screening will focus on a PSTVd variant isolated from an outbreak in tomato and a second variant isolated from potato with confirmed infectivity on tomato. Infectivity will be quantified using real-time PCR. Ongoing development of ornamental and dual-purpose ornamental/culinary pepper germplasm is carried out via breeding strategies that include backcross breeding for simple traits and pedigree and inbred backcross breeding for complex traits. Improved germplasm is evaluated in cooperation with collaborators and released by ARS. Initial germplasm screening for fresh-cut pepper will focus on accessions that bear fruit with thick pericarp. Using knowledge of market types and available passport data, C. annuum accessions will be selected from commercial sources and the USDA, ARS, Plant Genetic Resources Conservation Unit. Accessions with varied fresh-cut quality attributes will be selected to assess applicability of hyperspectral imaging for high throughput phenotyping of fresh-cut quality. Accessions with divergent fresh-cut quality will be intercrossed in a diallel mating scheme to evaluate combining ability for fresh-cut attributes. Superior accessions will be hybridized with sweet and hot pepper breeding lines and BC2 generation hybrids advanced for phenotyping and public release. Objective 1. Colletotrichum fungal isolates as well as tomato plants susceptible and resistant to this pathogen are being characterized at the genomic level to identify genes in the pathogen and host associated with resistance and/or susceptibility. Characterization of fungal isolate virulence on immature and ripe pepper and tomato fruit is ongoing. MiSeq sequencing technology has been completed and data analysis is in progress for determining taxonomic lineage and identification of candidate pathogenicity genes. Next generation sequence analysis of tomato recombinant inbred lines susceptible and resistant to the Colletotrichum fungus has been completed and data analysis is in progress to identify pathogenicity markers during the report period. Objective 2. New genes for virus resistance must be identified in pepper to address emergence of viruses classified as tospoviruses that are new to the U.S. or that overcome known genes for virus resistance. Diverse pepper germplasm originally collected across the native distribution range for pepper in the Americas was screened for tomato chlorotic spot virus (TCSV) resistance. Follow-up screening to validate disease response and a crossing block is in progress to complete population development for inheritance studies during the report period. Cross resistance to GRSV in this material is being evaluated. Objective 3. Value-added crops can be very profitable in comparison to conventional forms of the commodity. Breeding for specialty peppers with improved flavor, color and related consumer valued attributes continued with multi-location trials of advanced breeding lines for the culinary market. Similar trials of high-value ornamental peppers were conducted and cultivar status material was licensed to an industry partner. Populations were developed from crosses of advanced pepper breeding lines and commercial cultivars to assess combining ability for fresh-cut quality attributes that contribute to suitability for minimally processed fresh-cut market applications. Accomplishments 01 Genetic control of anthocyanin accumulation. Anthocyanins are water soluble pigments that impart color and nutritive value to fruits and vegetables. Thorough knowledge of the genetic control of anthocyanin accumulation that would aid breeders in developing improved varieties is lacking in minor crops. ARS scientists at Beltsville, Maryland, identified a spontaneous green-fruited eggplant mutant in a normally purple-fruited eggplant and characterized the genetic mechanism contributing to altered fruit color. This new knowledge of genes that are activated and/or suppressed during anthocyanin biosynthesis in the mutant helps scientists better understand how anthocyanin accumulation is regulated, thus assisting breeders in developing improved varieties for the vegetable industry and gardeners.
Impacts
(N/A)
Publications
- Rivera, Y., Stommel, J.R., Dumm, J.M., Ismaiel, A.A., Wyenandt, A.C., Crouch, J. 2016. First report of Colletotrichum nigrum causing anthracnose disease on tomato fruit in New Jersey. Plant Disease. 100(10): 2162.
- Stommel, J.R., Camp, M.J., Dumm, J.M., Haynes, K.G., Luo, Y., Schoevaars, A. 2016. Inheritance of fresh-cut fruit quality attributes in Capsicum. Journal of the American Society for Horticultural Science. 141(4):308-314.
- Stommel, J.R., Dumm, J.M., Gisbert-Domenech, C., Prohens, J. 2016. A spontaneous eggplant (Solanum melongena L.) color mutant conditions anthocyanin-free fruit pigmentation. HortScience. 51(7):792-798.
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Progress 10/01/14 to 09/30/15
Outputs
Progress Report Objectives (from AD-416): Diverse Solanaceous germplasm resources exist for enhancement of cultivated forms of tomato and pepper. Genes that may be valuable for crop improvement are often not well characterized, they may be associated with undesirable traits, or crossing barriers hinder introgression from distant crop relatives. Changes in pathogen virulence and introduction of new crop pathogens can overcome available host resistance, leaving producers vulnerable to crop loss. Available cultivars may not adequately address producer and consumer needs for new crop uses and high-value alternative crops. This project focuses on determining the underlying genetic bases of important traits of tomato and pepper � including fruit quality attributes and resistance to recurring or emerging diseases - and deploying them as finished cultivars, breeding lines, and genetic stocks. Over the five year project period, the following specific objectives will be addressed. Objective 1: Exploit homology between tomato and pepper to identify and transfer anthracnose-resistance from tomato to pepper, and release new pepper anthracnose resistant germplasm, along with molecular markers for marker-assisted selection. Sub-objective 1A. Identify anthracnose resistance-linked markers and candidate loci in tomato and pepper. Sub-objective 1B. Determine identity of species and relatedness of Colletotrichum isolates responsible for pepper anthracnose and relate these findings to knowledge of host/strain virulence specificity for isolates infecting pepper fruit. Objective 2: Identify and characterize genetic resistance to the emerging diseases Groundnut ringspot virus (GRSV) infecting pepper and Potato spindle tuber viroid (PSTVd) infecting tomato, and deliver/release appropriate materials to researchers and breeders. Sub-objective 2A. Identify and characterize pepper host resistance to GRSV. Sub-objective 2B. Identify and characterize tomato host resistance to PSTVd. Objective 3: Develop and release pepper breeding lines with improved quality attributes for the culinary, culinary/ornamental, and minimally processed fresh-cut market. Sub-objective 3A. Develop and release pepper breeding lines with improved quality attributes for the culinary and culinary/ornamental market. Sub-objective 3B. Develop and release pepper breeding lines with improved quality attributes for the minimally processed fresh-cut market. Approach (from AD-416): Next generation sequencing technology will be used for map-based cloning of anthracnose resistance loci from a recombinant, inbred line tomato population that ARS has developed. To bolster identification of candidate genes for anthracnose resistance, a proteomic survey will also be conducted using resistant and susceptible tomato lines. Markers developed from tomato will henceforth be utilized to identify resistance homologues in the pepper species C. baccatum. Resistance loci will be transferred to C. annuum using bridge lines that ARS has developed. Different Colletotrichum species have been identified as the causative organism responsible for recent outbreaks of green pepper anthracnose fruit rot in Ontario and Midwestern, Southeastern and Mid-Atlantic production areas in the U.S. Isolate species identity and relatedness from these regions will be characterized to ascertain if these isolates share a common lineage. Initial screening surveys for GRSV resistance will focus on C. chinense, the species where resistance to the Tospoviruses TSWV and CaCV has been previously identified. Reported Tospovirus resistance and accession passport data will be assessed and a subset of the available C. chinense accessions will be selected to maximize coverage of the species� native distribution range. C. annuum land races and accessions representative of the distribution range of C. frutescens, C. chacoense and C. baccatum will be evaluated in a similar manner. Accessions that exhibit high levels of resistance will be crossed to susceptible genotypes to characterize the inheritance of resistance. Initial screening for PSTVd will focus on core collections established for wild relatives of the cultivated tomato. Core collections to be screened will include S. chilense, S. habrochaites, S. pennellii, S peruvianum, and S. pimpinellifolium. Initial screening will focus on a PSTVd variant isolated from an outbreak in tomato and a second variant isolated from potato with confirmed infectivity on tomato. Infectivity will be quantified using real-time PCR. Ongoing development of ornamental and dual-purpose ornamental/culinary pepper germplasm is carried out via breeding strategies that include backcross breeding for simple traits and pedigree and inbred backcross breeding for complex traits. Improved germplasm is evaluated in cooperation with collaborators and released by ARS. Initial germplasm screening for fresh-cut pepper will focus on accessions that bear fruit with thick pericarp. Using knowledge of market types and available passport data, C. annuum accessions will be selected from commercial sources and the USDA, ARS, Plant Genetic Resources Conservation Unit. Accessions with varied fresh-cut quality attributes will be selected to assess applicability of hyperspectral imaging for high throughput phenotyping of fresh-cut quality. Accessions with divergent fresh-cut quality will be intercrossed in a diallel mating scheme to evaluate combining ability for fresh-cut attributes. Superior accessions will be hybridized with sweet and hot pepper breeding lines and BC2 generation hybrids advanced for phenotyping and public release. Objective 1. Anthracnose is a fungal disease that may cause yield losses of up to 50% worldwide in tomato and pepper. Whereas anthracnose has been typified as a disease of ripe tomato and pepper fruit, outbreaks are now occurring on immature pepper fruit and anthracnose has emerged as an increasingly serious disease. Additional isolates of Colletotrichum, the causative pathogen, have been collected from infected fruit in Maryland and New Jersey field plots. Characterization of isolate virulence on immature and ripe pepper and tomato fruit is ongoing. Isolates are being characterized at the genomic level to identify genes associated with pathogen virulence and characterize isolate taxonomic diversity. Corresponding research at the plant level is likewise underway. Genomic analysis is in progress to identify genes that distinguish susceptible vs. resistant plants. Objective 2. New genes for virus resistance must be identified in pepper to address emergence of viruses classified as tospoviruses that are new to the U.S. or that overcome known genes for virus resistance. Diverse pepper germplasm originally collected across the native distribution range for pepper in the Americas is being screened for tomato chlorotic spot virus (TCSV) resistance. Objective 3. Value-added crops can be very profitable in comparison to conventional forms of the commodity. Breeding for specialty peppers with improved flavor, color and related consumer valued attributes continued with multi-location trials of advanced breeding lines for the culinary market. Similar trials of high-value ornamental peppers was conducted with a CRADA partner. Studies were completed to more fully assess selected pepper germplasm for attributes that contribute to suitability of the crop for minimally processed fresh-cut market applications. Accomplishments 01 Enhanced vegetable quality and nutritive value: Relatively little is known about how growing conditions influence eggplant fruit phenolic acids, compounds that affect fresh fruit quality and distinguish eggplant among the top ten fruits and vegetables for antioxidant content. ARS scientists at Beltsville, Maryland in cooperation with scientists at the Polytechnic University of Valencia, evaluated commercial eggplant varieties as well as exotic eggplant relatives in multiple locations under greenhouse and open field conditions to assess the influence of environment on fruit phenolic acid content. They found that different eggplant varieties differed considerably for total content as well as composition of phenolic acids and that varieties were a greater source of variation in comparison to the environment for fruit phenolic acid content. The results are valuable for improving the efficiency of plant breeding programs to develop new varieties for diverse production systems and locations as well as for vegetable growers and consumers seeking to select varieties with superior fruit quality and nutritive value.
Impacts
(N/A)
Publications
- Stommel, J.R., Camp, M.J., Luo, Y., Welten, A. 2015. Genetic diversity provides opportunities for improvement of fresh-cut pepper quality. Plant Genetic Resources: Characterization and Utilization. DOI: 10.1017/ S1479262115000131.
- Stommel, J.R., Haynes, K.G., Whitaker, B.D., Prohens, J. 2015. Genotype x environment interactions in eggplant for fruit phenolic acid content. Euphytica. 205:823-836.
- Stommel, J.R., Pushko, M., Haynes, K.G., Whitaker, B.D. 2014. Differential inheritance of pepper (capsicum annum) fruit pigments results in black to violet fruit color. Plant Breeding. DOI:10.1111/PBR.12209.
- Stommel, J.R., Dumm, J.M. 2015. Coordinated regulation of biosynthetic and regulatory genes coincides with anthocyanin accumulation in developing eggplant fruit. Journal of the American Society for Horticultural Science. 140:129-135.
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Progress 10/01/13 to 09/30/14
Outputs
Progress Report Objectives (from AD-416): Diverse Solanaceous germplasm resources exist for enhancement of cultivated forms of tomato and pepper. Genes that may be valuable for crop improvement are often not well characterized, they may be associated with undesirable traits, or crossing barriers hinder introgression from distant crop relatives. Changes in pathogen virulence and introduction of new crop pathogens can overcome available host resistance, leaving producers vulnerable to crop loss. Available cultivars may not adequately address producer and consumer needs for new crop uses and high-value alternative crops. This project focuses on determining the underlying genetic bases of important traits of tomato and pepper � including fruit quality attributes and resistance to recurring or emerging diseases - and deploying them as finished cultivars, breeding lines, and genetic stocks. Over the five year project period, the following specific objectives will be addressed. Objective 1: Exploit homology between tomato and pepper to identify and transfer anthracnose-resistance from tomato to pepper, and release new pepper anthracnose resistant germplasm, along with molecular markers for marker-assisted selection. Sub-objective 1A. Identify anthracnose resistance-linked markers and candidate loci in tomato and pepper. Sub-objective 1B. Determine identity of species and relatedness of Colletotrichum isolates responsible for pepper anthracnose and relate these findings to knowledge of host/strain virulence specificity for isolates infecting pepper fruit. Objective 2: Identify and characterize genetic resistance to the emerging diseases Groundnut ringspot virus (GRSV) infecting pepper and Potato spindle tuber viroid (PSTVd) infecting tomato, and deliver/release appropriate materials to researchers and breeders. Sub-objective 2A. Identify and characterize pepper host resistance to GRSV. Sub-objective 2B. Identify and characterize tomato host resistance to PSTVd. Objective 3: Develop and release pepper breeding lines with improved quality attributes for the culinary, culinary/ornamental, and minimally processed fresh-cut market. Sub-objective 3A. Develop and release pepper breeding lines with improved quality attributes for the culinary and culinary/ornamental market. Sub-objective 3B. Develop and release pepper breeding lines with improved quality attributes for the minimally processed fresh-cut market. Approach (from AD-416): Next generation sequencing technology will be used for map-based cloning of anthracnose resistance loci from a recombinant, inbred line tomato population that ARS has developed. To bolster identification of candidate genes for anthracnose resistance, a proteomic survey will also be conducted using resistant and susceptible tomato lines. Markers developed from tomato will henceforth be utilized to identify resistance homologues in the pepper species C. baccatum. Resistance loci will be transferred to C. annuum using bridge lines that ARS has developed. Different Colletotrichum species have been identified as the causative organism responsible for recent outbreaks of green pepper anthracnose fruit rot in Ontario and Midwestern, Southeastern and Mid-Atlantic production areas in the U.S. Isolate species identity and relatedness from these regions will be characterized to ascertain if these isolates share a common lineage. Initial screening surveys for GRSV resistance will focus on C. chinense, the species where resistance to the Tospoviruses TSWV and CaCV has been previously identified. Reported Tospovirus resistance and accession passport data will be assessed and a subset of the available C. chinense accessions will be selected to maximize coverage of the species� native distribution range. C. annuum land races and accessions representative of the distribution range of C. frutescens, C. chacoense and C. baccatum will be evaluated in a similar manner. Accessions that exhibit high levels of resistance will be crossed to susceptible genotypes to characterize the inheritance of resistance. Initial screening for PSTVd will focus on core collections established for wild relatives of the cultivated tomato. Core collections to be screened will include S. chilense, S. habrochaites, S. pennellii, S peruvianum, and S. pimpinellifolium. Initial screening will focus on a PSTVd variant isolated from an outbreak in tomato and a second variant isolated from potato with confirmed infectivity on tomato. Infectivity will be quantified using real-time PCR. Ongoing development of ornamental and dual-purpose ornamental/culinary pepper germplasm is carried out via breeding strategies that include backcross breeding for simple traits and pedigree and inbred backcross breeding for complex traits. Improved germplasm is evaluated in cooperation with collaborators and released by ARS. Initial germplasm screening for fresh-cut pepper will focus on accessions that bear fruit with thick pericarp. Using knowledge of market types and available passport data, C. annuum accessions will be selected from commercial sources and the USDA, ARS, Plant Genetic Resources Conservation Unit. Accessions with varied fresh-cut quality attributes will be selected to assess applicability of hyperspectral imaging for high throughput phenotyping of fresh-cut quality. Accessions with divergent fresh-cut quality will be intercrossed in a diallel mating scheme to evaluate combining ability for fresh-cut attributes. Superior accessions will be hybridized with sweet and hot pepper breeding lines and BC2 generation hybrids advanced for phenotyping and public release. Objective 1. Colletotrichum fungal isolates as well as tomato plants susceptible and resistant to this pathogen are being characterized at the genomic level to identify genes in the pathogen and host associated with resistance and/or susceptibility. Colletotrichum isolates have been collected from infected fruit in Maryland and New Jersey pepper plots and from the ARS fungal collection in Beltsville. Initial characterization of fungal isolate virulence on immature and ripe pepper and tomato fruit has been completed. Genomic characterization of isolate taxonomic diversity is in progress. Corresponding research at the plant level is likewise underway. Genomic analysis of tomato plants susceptible and resistant to the Colletotrichum fungus is in progress to facilitate identification of genes that distinguish susceptible vs. resistant plants. Objective 2. New genes for virus resistance must be identified in pepper to address emergence of tospoviruses that are new to the U.S. or that overcome known genes for virus resistance. Diverse pepper germplasm originally collected across the native distribution range for pepper in the Americas has been selected to screen for virus resistance. Methodology for screening diverse pepper germplasm for resistance to Groundnut ringspot virus has been established. Emergence of tomato chlorotic spot virus in the U.S. has warranted expansion of the objective to include screening for resistance to this tospovirus as well. Inoculation of plant material will commence with the onset of cooler temperatures in Florida. Objective 3. Value-added crops can be very profitable in comparison to conventional forms of the commodity. Breeding for specialty peppers with improved flavor, color and related consumer valued attributes continued with multi-location trials of advanced breeding lines for the culinary market. Similar trials of high-value ornamental peppers was conducted with cooperators in the U.S. and Netherlands. Studies were completed to assess available pepper crop diversity for attributes that contribute to suitability of the crop for minimally processed fresh-cut market applications. Accomplishments 01 Genetic diversity for pepper fresh-cut attributes. The shelf-life of fresh-cut product from commercial pepper cultivars is insufficient for practical use in fresh-cut applications. Utilizing the wealth of available Capsicum genetic resources, ARS scientists at Beltsville, Maryland in cooperation with Enza Zaden Research USA, characterized genetic diversity in diverse Capsicum germplasm representing four major pepper market classes. Diversity for attributes that contribute to integrity of fresh-cut product was extensive, indicating that breeding for pepper fresh-cut quality can be undertaken to improve commercial cultivars for use by the fresh-cut produce industry. The results of this first report of genetic diversity for fresh-cut applications in pepper are valuable for public and private pepper breeding programs.
Impacts
(N/A)
Publications
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