1a.Objectives (from AD-416)
The underlying genetic bases of key attributes that influence the quality, nutritive value and marketable yield of fresh and/or processed product quality in major Solanaceous crops will be elucidated, and will facilitate the deployment in improved germplasm. Gene expression will be characterized and selectable marker strategies for improving selection efficiency will be developed. The specific goals are:.
1)Development of tomato germplasm with enhanced quality attributes including fruit firmness and carotenoid content and characterization of the genetic control of these attributes. .
2)Identification of quantitative trait loci that influence tomato anthracnose fruit rot resistance. .
3)Development of new pepper germplasm for culinary and ornamental applications; determination of the inheritance of tissue-specific anthocyanin accumulation and characterization of the control of structural and regulatory genes for anthocyanin pigmentation

1b.Approach (from AD-416)
The inheritance of tomato fruit firmness in firm and ultra-firm processing tomato germplasm developed from interspecific Lycopersicon esculentum x L. hirsutum crosses will be determined and genetic variance components estimated. The inheritance of tissue-specific carotenoid content in tomato fruit pericarp, columella and locule tissues will be characterized. Genetic stocks will be developed for use in basic studies on carotenoid accumulation and for use in development of enhanced germplasm. Using RT-PCR, the relationship between variation in lycopene content and tissue-specific expression of carotenoid biosynthetic genes will be assessed. Sequence information of genomic clones of differentially expressed genes will be used to develop selectable markers for enhanced fruit pigmentation. Recombinant L. esculentum inbred tomato lines (RILs) segregating for resistance to anthracnose fruit rot have been developed. AFLP and SSR markers that differentiate parental RIL lines will be utilized for identification of QTL linked to fruit rot resistance. Relative map positions will be determined using introgression line analysis. Pepper germplasm with unique fruit and foliage pigmentation patterns, as well as unique growth habits and fruit characteristics will be developed for culinary, ornamental and dual-purpose applications. The inheritance of growth habit, photoperiod sensitivity, and tissue-specific anthocyanin pigmentation will be studied and genotypes for respective anthocyanin regulatory genes determined via complementation. Utilizing cDNA or partial genomic clones of anthocyanin regulatory and structural genes, the expression of anthocyanin-related genes will be studied with viral-induced color break, related to viral RNA distribution, and the information utilized to develop selectable markers for these genes in pepper.

3.Progress Report
Anthocyanin gene regulation. This research was conducted collaboratively with Virginia Polytechnic Institute and State University. Color attributed to anthocyanins contributes to product sensory quality attributes and potential nutritive value. A Capsicum (pepper) line we have developed, 02C27, accumulates anthocyanin in various tissues and accumulation is markedly sensitive to environmental stress. Real-time PCR analysis of tissues revealed functional but differentially expressed structural and regulatory genes in the anthocyanin biosynthetic pathway coincident with anthocyanin accumulation. Similar results were obtained upon evaluation of gene expression in tissues from genotypes that accumulate anthocyanin in different plant parts. These results enable us to now investigate transcription factor protein interactions to further characterize mechanisms of gene regulation. The results are important for identification of key regulatory elements that influence anthocyanin accumulation and will result in new knowledge to facilitate enhancement of anthocyanin content in pepper and related crops. This research is under National Program 301, Action Plan Component 2, Problem Area 2c and Component 3, Problem Areas 3b and 3c; ARS Strategic Plan Goal 2, Objective 2.2. New Pepper Germplasm. This research was conducted with the Floral and Nursery Plants Research Unit (Genetic Improvement of Floral Crops for Pest, Disease and Stress Tolerance and Ornamental Qualities, 1230-21000-040-00D), and McCorkle Nurseries to determine the genetics of anthocyanin regulatory gene expression. An anthocyanin mutation in Capsicum was selected that results in black foliage color. A comparison was made of anthocyanin regulatory and structural gene expression under inductive and non-inductive conditions. In addition, differences in gene expression between anthocyanin-free and anthocyanin-producing genotypes were made. Because of this research, unique germplasm was created, resulting in the release of four cultivars which are in the process of being patented. This research was one of the FY 2007 milestones (Release pepper germplasm with novel ornamental or dual purpose ornamental/culinary attributes.). This research is under National Program 301, Action Plan Component 2, Problem Area 2c and Component 3, Problem Areas 3b and 3c; ARS Strategic Plan Goal 2, Objective 2.2.

4.Accomplishments
New pepper germplasm. New pepper germplasm is needed to enrich the commercial pepper gene pool which lacks diverse new cultivars to meet market demands for novel culinary, ornamental, and dual-purpose cultivars. Utilizing the rich genetic diversity available in pepper landraces and related species, new pepper cultivars with novel fruit, foliage, and plant growth habit have been developed. Four selections with unique culinary/ornamental characters have been released by ARS and submitted for patent protection. Novel peppers have the highest per unit value of any pepper product and have become a profitable crop for greenhouse pot plant and transplant production and an innovative way for farmers to produce a high value alternative crop. This research is collaborative with the ARS Floral and Nursery Plants Research Unit in Beltsville and two industry partners under a Cooperative Research and Development Agreement (CRADA). This research is under National Program 301, Action Plan Component 2, Problem Area 2c and Component 3, Problem Areas 3b and 3c; ARS Strategic Plan Goal 2, Objective 2.2).

Anthocyanin gene regulation. One of the most important characteristics of ornamental plants and culinary horticultural commodities is color. In breeding for color, conventional approaches rely upon visual selection. These approaches have reached their limit in creating new colors and levels of intensity in many crops. New classical and biotechnological methods are needed to ensure continued progress. Prior research characterized the genetic regulation of pigmentation attributed to anthocyanin compounds in a unique mutant that displayed markedly sensitivity to pigmentation intensity in response to environmental stress. We have expanded this research to evaluate the genetic control of anthocyanin-based pigmentation in pepper plants that differ in fruit, flower and foliar pigmentation due to their genetic makeup. We have identified and characterized the action of key genes that control differentially expressed genes in the anthocyanin biosynthetic pathway. Analysis of three regulatory type genes, termed transcription factors, demonstrated differential expression of these regulatory elements, coincident with anthocyanin accumulation in different plant parts. The results are important for identification of key regulatory elements that influence anthocyanin accumulation and improved pigmentation. This research is cooperative with the ARS Floral and Nursery Products Research Unit in Beltsville and with Virginia Polytechnic Institute and State University, Blacksburg, VA. This research is under National Program 301Action Plan Component 2, Problem Area 2c and Component 3, Problem Areas 3b and 3c; ARS Strategic Plan Goal 2, Objective 2.2.

Tomato fruit firmness. Tomato fruit firmness is an important quality attribute in cultivars used for fresh (intact and fresh-cut) and processed product. New sources of firmness are needed to improve product quality. Prior research determined that fruit firmness can be measured by different methods and that different genes are responsible for firmness as measured by the respective methods. We have developed a breeding population that consists of a series of commercially adapted lines that differ in firmness attributes as determined by different measurement methods. These lines contain distinct genes that control these attributes. This breeding population can be used to identify new genes responsible for tomato fruit firmness. Identification of genes responsible for different components of firmness will afford new opportunities for continued progress in genetic improvement of fruit quality. This research is under National Program 301Action Plan Component 2, Problem Area 2c and Component 3, Problem Areas 3b and 3c; ARS Strategic Plan Goal 2, Objective 2.2.

5.Significant Activities that Support Special Target Populations
Cooperator on USDA/1890 grant proposal with West Virginia State University to increase and promote biotechnology-based genetics in the undergraduate curriculum.

6.Technology Transfer

Number of new CRADAs and MTAs	1
Number of active CRADAs and MTAs	1
Number of patent applications filed	4
Number of new commercial licenses granted	1
Number of non-peer reviewed presentations and proceedings	2
Number of newspaper articles and other presentations for non-science audiences	6

Review Publications
Smith, D.L., Stommel, J.R., Fung, R.W., Wang, C.Y., Whitaker, B.D. 2006. Influence of cultivar and harvest method on postharvest storage quality of pepper (capsicum annuum l.) fruit. Postharvest Biology and Technology. 42:243-247.