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United States Department of Agriculture

Agricultural Research Service

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Location: Genetic Improvement for Fruits & Vegetables Laboratory

2009 Annual Report

1a. Objectives (from AD-416)
The objectives of this project focus on determining the underlying genetic bases of quality attributes and nutritive value of Solanaceous vegetables in order to facilitate their deployment in improved germplasm. Diverse Solanaceous germplasm resources exist for enhancement of cultivated forms of tomato, pepper and eggplant. Genes that may be valuable for crop improvement are often not well characterized or they may be associated with undesirable traits. Over the next 5 years we will focus on the following objectives: 1) Develop tomato germplasm with enhanced fresh- and processing-market quality. Research will focus on identification of QTL and candidate genes that contribute to fruit quality, principally fruit firmness attributes. Breeding lines and genetic stocks will be released by ARS for development of germplasm with improved firmness attributes. 2) Develop new Capsicum germplasm with improved culinary and/or ornamental quality. Genetic mechanisms underlying tissue-specific anthocyanin accumulation and fruit flavor will be characterized. Germplasm with unique tissue specificity for anthocyanin/carotenoid pigmentation in foliage, flowers and fruit will be introgressed into genotypes with novel plant habits and fruit shape, size, configuration and flavor. The inheritance of morphological characters will be determined. New novel germplasm will be released. 3) Determine the inheritance of eggplant antioxidant content, principally phenolic acids that influence postharvest quality, in populations developed from crosses of diverse accessions in the eggplant core subset.

1b. Approach (from AD-416)
(Objective 1) QTL and candidate genes that contribute to fruit quality, principally fruit firmness attributes, will be identified in an inbred backcross line population developed from parental lines originating from interspecific Solanum lycopersicum x S. galapagense crosses. These lines exhibit divergent combining ability for fruit compression, puncture resistance and fruit fresh weight. A growing database of mapped SNP markers is available and will be utilized to identify and map firmness QTL. (Objective 2; Sub-objective 2.A) Utilizing divergent genotypes and environmental treatments, we have previously demonstrated differential expression of Capsicum anthocyanin-related structural and regulatory genes in tissues that vary in anthocyanin pigmentation. A dual approach using environmental and genetic mediated modification of anthocyanin pigmentation, combined with TEV-induced silencing will provide multiple avenues to characterize regulation of tissue-specific pigmentation in Capsicum. The effect of light treatment and silencing induced by TEV infection on anthocyanin structural and regulatory gene expression will be characterized. The siRNA/miRNA populations of anthocyanin pigmented and non-pigmented tissue will be compared to evaluate the contribution of small RNAs to regulatory gene expression. Gene expression and small RNA populations will be similarly assessed in a small series of recombinant inbred lines that we have developed which vary in tissue specific anthocyanin pigmentation. (Sub-objective 2.B) Germplasm with unique specificity for anthocyanin/carotenoid pigmentation in foliage, flowers and fruit will be introgressed into genotypes with novel plant habits and fruit shape, size, configuration and flavor. Novel flavor attributes identified in exotic Capsicum germplasm will be characterized and introgressed into C. annuum. Backcross, pedigree and inbred backcross breeding will be utilized. Inheritance of morphological traits will be determined. Analyses will be performed using segregating F2, F3 and backcross populations that we have developed. QTL for flavor attributes will be identified using the principles described in Objective 1 for tomato fruit firmness. (Objective 3) Eggplant accessions with divergent fruit phenolic acid constituents and total phenolic acid content have been selected to determine the inheritance of individual classes of phenolic acid compounds and total phenolic acid content. Segregating F2 backcross populations to respective high and low phenolic acid parents will be developed and utilized to determine the inheritance of total phenolic acid content and individual classes of phenolic acids. Gene action, genetic factors and heritability estimates will be derived.

3. Progress Report
Tomato Fruit Quality. Tomato fruit color and firmness are important product quality determinants. Utilizing tomato mapping populations we developed to identify new genes responsible for tomato fruit firmness and color, additional phenotypic data were collected and SSR and SNP molecular markers identified that distinguish parent lines used to develop mapping populations. Additional markers are required prior to commencing mapping studies. Gene identification will afford new opportunities for fruit quality improvement. Pepper Genetics. Within the genus Capsicum there is abundant genetic diversity for plant habit and fruit and leaf characteristics for creating new plant types to meet today’s consumer needs. Building upon our previous award-winning and patented varieties, new breeding lines with novel character attributes and plant horticultural improvements were advanced to commercial trials for evaluation in culinary and ornamental applications. This germplasm afford growers with innovative opportunities to produce a high value alternative crop. Related research utilizes exotic germplasm (see Accomplishments) for pepper fruit quality improvement. We identified Capsicum baccatum accessions with superior fruit quality attributes. Selected lines were genotyped and are being utilized to develop mapping populations for identification of genes associated with fruit flavor and related quality attributes and introgression into cultivated germplasm. Anthocyanin Genetics. Our evidence for differential tissue-specific expression of anthocyanin structural and regulatory genes in pepper (see Accomplishments) suggests that additional regulatory elements influence pigment accumulation. We have developed protocols for isolation of miRNA from pepper and are sequencing the small RNAs to identify regulatory elements that interact with anthocyanin structural and regulatory gene products. In complimentary studies on eggplant, we are characterizing anthocyanin structural and regulatory gene expression and sequence diversity. Available results reveal commonalities as well as differences in the genetic control of anthocyanin pigmentation across Solanaceous species. The results are relevant to the evolution of anthocyanin color genetics and enhanced pigmentation. Phytonutrients. An abundance of phytochemicals with putative human health benefits have been described. Additional information on their inheritance and efficacy is needed to develop new plants with superior nutritive value. Eggplant fruit phenolic acids contribute to fruit nutritive value and culinary quality. Building upon our previous research on phenolic acids, we characterized eggplant fruit phenolic acid composition in a mapping population developed by cooperators to identify genes important for product quality. The results will facilitate development of superior eggplant germplasm.

4. Accomplishments
1. Pepper Genetic Diversity. The exotic pepper species Capsicum baccatum is recognized as a potentially valuable source of genes for pepper quality improvement. However, this germplasm is poorly characterized and genes that may be valuable for crop improvement have not been identified. Utilizing morphological and chemical analyses and molecular markers, we characterized the genetic diversity present in the USDA, ARS Capsicum baccatum germplasm collection. Extensive diversity for fruit and plant chemical and morphological attributes was identified. Whereas genetic marker-based analysis revealed that wild forms of this species formed distinct relatedness groups consistent with geographic origin, cultivated forms of the species exhibited intensive mixture of accessions from across the distribution range. The results are important for 1) preservation and management of crop germplasm resources, and 2) in pepper crop improvement programs for selection of genetically informative accessions with genes for improved product quality.

2. Anthocyanin gene regulation. Considerable diversity exists in plant tissues for the presence and intensity of water soluble anthocyanin pigments. Whereas the genes responsible for the biosynthesis of these compounds are well characterized, a major gap in our knowledge exists concerning regulatory mechanisms which control differential accumulation of anthocyanins in different plant tissues. We evaluated expression of regulatory and structural genes in genetic stocks of pepper (Capsicum) with contrasting anthocyanin pigmentation in fruits, flowers and leaves and determined that anthocyanin structural and regulatory gene expression was required for pigment accumulation in fruits and flowers. In contrast, elevated expression of regulatory genes was not required for structural gene expression and anthocyanin accumulation in foliar tissue. The results demonstrated that different genetic mechanisms account for pigmentation in reproductive and vegetative tissues and is important for elucidating the genetic control of pigment biosynthesis and development of new plants with enhanced pigmentation.

5. Significant Activities that Support Special Target Populations
ARS scientists cooperated with the ARS Information Staff in support of the ARS Science for Kids education program. A web based presentation was produced highlighting the research programs pepper related research. The target audience is elementary/middle school children.

Review Publications
Lightbourn, G., Winkel, B., Griesbach, R.J., Stommel, J.R. 2009. Transcription Factor Families Regulate the Anthocyanin Biosynthetic Pathway in Capsicum. Journal of the American Society for Horticultural Science. 134:244-251.

Last Modified: 10/18/2017
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