Project Number: 5320-21000-011-00
Project Type: Appropriated

Start Date: May 16, 2006
End Date: May 15, 2011

Objective:
To develop new knowledge about the genetics, genomics, and transgenics of selected tropical crops by completely sequencing and characterizing the non-recombinant region of the papaya sex chromosome, producing a draft genomic sequence of the entire papaya genome, characterizing a set of papaya's flower organ and disease resistance genes, developing an improved ability to regulate gene expression, and producing and evaluating new transgenic approaches for resistance to papaya ringspot virus disease. Results will include the development of a papaya genomics database, a high-density genetic map combining AFLPs and microsatellites with markers flanking major genes controlling fruit size and disease reaction. Markers developed for genetic and physical mapping and marker assisted selection in papaya will be shared with researchers worldwide. The genetic maps generated from different mapping populations will be linked together by a common set of microsatellite markers. Results of the proposed research will significantly advance the development of genomic tools and knowledge for papaya improvement. The genetic resources generated from this project will enhance the capacity for positional cloning of important novel traits from this little-studied tropical fruit crop.

Approach:
(1) Fingerprint and end-sequence approximately 40,000 clones from our existing bacteria artificial chromosome (BAC) library for anchoring the whole genome shotgun (WGS) sequence data that will be produced from two WGS libraries of the papaya genome, (2) mine the papaya BAC end and genomic sequences to develop 4,000 microsatellite markers (simple sequence repeats or SSRs) for constructing a high density genetic map of the papaya genome of at least 1,000 SSRs for combining with our amplified fragment length polymorphism (AFLP) map, (3) assemble and annotate the papaya genome sequences, (4) select a core set of evenly distributed SSRs to map major genes controlling fruit size and disease reactions, (5) develop a transient gene silencing system for functional genomic analysis in papaya, (6) characterize novel papaya disease resistance genes with the functional genomic tool, (7) determine the relationship between transgene copy number and gene silencing, (8) characterize the activity of SCYLV P0 and other viral suppressors of post-transcriptional gene silencing (PTGS) in Nicotiana benthamiana as a model system for application to sugarcane, (9) identify papaya genes with tissue-specific expression patterns for developing tissue-specific promoters, (10) use segmented and synthetic gene technology to develop and subsequently characterize transgenic papaya with resistance to wide range of papaya ringspot virus (PRSV) strains, (11) measure the extent, if any, of gene flow from commercial transgenic papaya to adjacent nontransgenic papaya fields, (12) develop and commercialize a transgenic Kapoho with segmented coat protein genes for the Hawaiian papaya industry, (13) develop data that are necessary to have the Rainbow transgenic papaya deregulated in Japan, and (14) develop, transfer, and commercialize transgenic papaya for developing countries with focus on Bangladesh.