Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: 1. NSF sponsored project- A graduate student and postdoc, along with our collaborator Dr. Tom Davis' lab, generated a substantial number of trasnformed strawberry lines harboring overexpression and RNAi suppression constructs. Evaluation of plant phenotypes have initiated. These are the fundamental goals laying the foundation of the project. 2. Photosensors in starwberry- Dr. Mithu Chatterjee has developed plant lines containing modification of expression patterns of major photosensors. These will be studied in 2009. 3. The work by former student Denise Tombolato was expanded toward publication, driven primarily by work done by Folta. 4. A platform for fingerprinting major Florida strawberry cultivars was developed and implemented. The work is being performed with Dr. Natalia Peres and Dr. Craig Chandler. 5. Sequencings of the strawberry genome in conjunction with the consortium led by UF and Virginia Tech has led to capture of 12x coverage. Currently assembly and annotation is being performed, with substantial hinderance from a steep learning curve. The draft sequence will be compelte in 2009. 6. ~35 fosmids were sequenced and deposited to Genbank, representing 1% of the strawberry genome. 7. Visiting scientist Katrina Mouhu developed many lines that will affect the flowering time of strawberry. These will be functionally tested next. 8. Efforts with Dave Clark, Harry Klee and others initiated the basis for the UF Flavor Center, an effort designed to assist breeding for flavor. PARTICIPANTS: Kayla Shea Childers, undergaduate researcher, refined plant illumination techniques and participated in fingerprinting; Sasha Ricaurte, undergraduate researcher, participated in the nematode project and flavor project; Dr. Kaichun Zhang, visiting scientist, participated in plant transformation; Dr. Mithu Chatterjee, postdoc, developed hundreds of transgenic strawberry lines for furher analysis; Kyle Schimitt, undergraduate researcher, defined conditions for transformation of specific strawberry lines; Fadhli Mad Atari, new graduate student, initiated a study of optimizing transformation of new starwberry lines; Dr. Toktam Sadat Taghavi, visiting scientist (U. Tehran) has initiated study of hydroponic system design to accellerate study of nitrogen uptake in wild strawberry; Dr. Ruxandra Gala (Angers, France) visited to learn how to transform strawberry. TARGET AUDIENCES: We are providing functional informaiton to validate findings from bioinformatics efforts. Our efforts in fingerprinting and marker development will impact breeding programs and industry. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
see above.
Publications
- Piquenas A, Albequerue, M., Folta, K.M. (2009) Explant Selection in Plant Transformation. In: Kole C (ed) Development and Deployment of Transgenic Plants. Springer Verlag, New York, p in press
- Pontaroli AC, Rogers, R.L., Zhang, Q., Davis, T.M., Folta, K.M., San Miguel, P., Bennetzen, J.L. (2009) Gene content and distribution in the nuclear genome of Fragaria vesca. Plant Genome
- Shulaev V, Korban S, Sosinski B, Abbott A, Aldwinckle H, Folta K, Iezzoni A, Main D, Arus P, Dandekar A, Lewers K, Brown S, Davis T, Gardiner S, Potter D, Veilleux R (2008) Multiple models for Rosaceae genomics. PLANT PHYSIOLOGY 147:985-1003
- Chandler CK, Folta, K.M., Dale, A., Herrington, M. (2009) Strawberries. In: Badeness DBaM (ed) Fruit Crop Breeding. Springer, New York, p in press
- Slovin JP, Schmitt, K., Folta, K.M. (2009) An inbred line of the diploid strawberry Fragaria vesca f. semperflorens for testing gene function. BMC-Plant Methods:in press
- Folta KM, Susan E.Gardiner (2009a) Genetics and Genomics of Rosaceae. Springer, New York
- Folta KM, Susan E. Gardiner (2009b) Genomics-Based Opportunities in Apricot. In: Folta KM, Gardiner, Susan E. (ed) Genetics and Genomics of Rosaceae. Springer, New York
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Progress 10/01/05 to 09/30/06
Outputs
Over the last year we have made substantial progress in structural and functional genomics in strawberry. Structural genomics efforts through the USDA grant showed that the subgenome of octoploid strawberry mostly resembles that of diploid strawberry F. iinumae, and not the F. vesca that was anticipated. The order of SNPs and SSRs is much more reminiscent of the former than the latter and this is a revolutionary finding that refutes the cytological data. Additionally, with Dr. Tom Davis we have sequenced 1% of the strawberry genome. A series of random and directed fosmids have been sequenced and assembled. This information constitutes the first glimpse into the genome of this organism. Gene order and spacing is about the same as in Arabidopsis and there is evidence of mobile elements. We have used this information to devise primer pairs that flank the interval. From this polymorphisms can be sought between adjacent genes and used in linkage mapping. Seven such markers
have been added to the diploid linkage map. The functional genomics studies traced the expression of genes associated with photoperiodic flowering. We discovered that the photoperiodic regulator CONSTANS maps to linkage group six, is expressed only on short days and can complement the Arabidopsis co mutant. We have also made significant use of octoploid and diploid transformation systems and are generating plants for field analysis.
Impacts
The new markers will be used to assist breeders in identifying day neutral and short day cultivars. The sequence from the genome allows comparative efforts to other rosaceous crops.
Publications
- Folta, K.M. and Davis, T.M. (2007) Transformation Systems to Study Gene Function in Fragaria. Proc. N. Amer. Strawberry Symp.
- Stewart, P.J., Winslow, A.R. and Folta, K.M. (2007) An Initial Characterization of Fragaria CONSTANS mRNA levels in Short-Day and Day-Neutral Cultivars. Proc. N. Amer. Strawberry Symp.
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Progress 10/01/04 to 09/30/05
Outputs
Accomplishments follow: <BR><BR> <B>1. EST sequencing and cataloging.</B> The EST sequencing project performed in conjunction with the Genome Database for Rosaceae was completed, with over 1500 ESTs sequenced and deposited to public databases. Funding was also obtained from the Florida Strawberry Growers to sequence 3000 additional ESTs. EST libraries were generated from developing flowers, ripening fruit and roots of various developmental stages. <BR><BR> <B>2. Development of the LF9 strawberry genetic line.</B> The parameters for efficient transformation and regeneration of the LF9 strawberry transgenic were assessed. Over 20 constructs were obtained from several international sources for integration into our exclusive patent-pending plant line. <BR><BR> <B>3. Idenficiation and characterization of PGIPs in Florida cultivars</B> The sequences from a family of polygalacturonase-inhibiting protein (PGIP) genes was obtained from octoploid strawberry cultivars. These
sequences represent the most likely candidates for meaningful development for transgenic plants with increased capacity to resist common diseases. The work showed important differences between the PGIP genes present in North American vs. European cultivars. <BR><BR> <B>4. Gene Pair Haplotypes.</B> A USDA award was obtained to study structural genomic relationships between gene pairs in strawberry, based on microcolinearity with corresponding sequences in model systems. Using this strategy, the variability present in a number of loci has been resolved and can now be employed as genetic markers in mapping endeavors. <BR><BR> <B>5. Genetic Mapping in the Diploid Strawberry</B> Visiting scientist Dr. Dan Sargent came to Florida to expand our capacity to map genes of interest in his interspecific population. 14 genes were mapped based on EST sequences, more will be done in the near future. These efforts contribute strongly to the growing strawberry linkage map. <BR><BR> <B>6.
Characterization of strawberry cystatins as nematode antifeedants.</B> Work performed in the Atkinson laboratory illustrates that overexpression of cystatins, plant cysteine protease inhibitors, can slow nematode feedling and colonization on many agriculturally-relevant plants. To meet the impending challenges to strawberry in a post-methyl bromide era, the family of strawberry cystatins has been identifed and they are now being studied to identify isoforms that may be useful to combat nematode-associated crop loss. <BR><BR> <B>7. The photoperiodic signaling pathway</B> Work in the laboratory has unveiled the strawberry orthologs of genes that regulate photoperiodic flowering. The expression of these genes was traced in short-day and day-neutral plants and the work is being prepared for publication. <BR><BR> <B>8. The ASAP method </B> A method has been devised to obtain sequence information from the plastid quickly and inexpensively. The method was used to sequence the entire
strawberry inverted repeat region. Patent protection has been obtained. The method has been applied to many other species and represents one of the most highly accessed reports at BMC-Genomics.
Impacts
The EST sequences from this program represent over 50% of those sequenced from strawberry. The new transgenic line offers high-throughput assessment of gene function in the Rosaceae, and has been recieived with great international interest. The pilot studies in cystatins, PGIPs and photoperiod genes will shape physiological studies and trangenic design. The Gene-Pair-Haplotype data and diploid mapping efforts have contributed to mapping studies in corresponding species, helping to place additional markers of known function as well as aid in the understanding of Fragaria structural genomics.
Publications
- Folta, K.M., M. Staton, P.J. Stewart, S. Jung, D.H.Bies, C. Jesudurai, D. Main (2005) Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria x ananassa) BMC Plant Biology, 5:12.
- Dhingra, A, K.M. Folta (2005) ASAP: Amplification, sequencing, and annotation of plastomes. BMC-Genomics, 6:176.
- Folta KM, Howard L, Dhingra A, Stewart PJ, Chandler CK (2006) Characterization of LF9, an octoploid straweberry genotype selected for rapid regeneration and transformation. Plant Cell Reports (in press)
- Bassil, N.H., Dunn, M., Folta, K.M. and Lewers, K (2006) Microsatellite markers for Fragaria from Strawberry Festival ESTs. Mol Ecol Notes. (in press)
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