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Completion of the Peach Genome Database: A Reference Genome for Rosaceae

NRI Award # 2005-35300-15452

PI: Albert G. Abbott, Co-PIs: W. Vance Baird, Doreen Main, Jeff Tomkins, Gregory Reighard, Bryon Sosinski, and Pere Arus
Clemson University, Clemson, SC 29634
E-mail: aalbert@clemson.edu
Telephone: 864-656-3060 


Accomplishments:

Aim 1: Complete construction of the physical/genetic map of peach using HICF (High information content fingerprinting) of the existing physical map framework contig clones and those of larger insert libraries of the haploid cultivar 'Lovell'.

Progress: We have substantially completed this project aim. We have fingerprinted 20,000 BAC clones using HICF technologies. These fingerprints include the original physical map of peach and additional fingerprints from larger insert BAC libraries constructed from the haploid and dihaploid "Lovell". Current estimates of genome coverage are at approximately 303 Mb which in excess of the complete peach genome (270 Mb). The map consists of 2,138 high confidence contigs only those questionable contigs supported by hybridization data have been included. 83% of the contigs are composed of between 3 and 25 clones. 252 contigs are anchored on the Prunus general genetic map through hybridization to mapped markers. We are currently BAC end sequencing specific contigs to look for merges using overgo probes. We are targeting regions of important genetically mapped characters initially as we are interested in several important characters (eg. Plum pox virus resistance/susceptibility). Initial results show that overgo probes to BAC ends can successfully merge contigs.

Aim 2: Incorporate the physical map data into the Genome Database for Rosaceae (GDR) to provide a reference genome for identification and cloning of genes important to Rosaceous crop development and sustainability.

Progress: All our data is submitted regularly to the database and the current peach genome physical map is up to date and is being utilized by numerous laboratories in the search for candidate genes or markers.

Aim 3: Complete development of a high density genetic marker set anchored on the physical map to provide the tools necessary for marker assisted selection, comparative mapping and molecular map development in the less well characterized Rosaceae species.

Progress: We have completed physical mapping of 120 of 400 genetically anchored SSR's developed in the Prunus genomics community. We will complete the remaining 220 in spring 2008 and finalize the merging of the physical and genetic maps of peach. These SSR sequences are strengthening the integration of the general Prunus genetics map and the physical map/EST database and positioning orphan contigs on the current merged genetic/physical map. We are already using the physical map in several comparative mapping projects to study genome evolution and to identify candidate genes for important characters in Rosaceae species.

Broad Impacts:

Although most of the outcomes we have anticipated, we are impressed with the overall utility of the data to work across species boundaries. In summer of 2007, we have hosted three researchers (Dr. Veronique Decrooq, and graduate students (G. Marandel, P. Pilarova) from two countries (France, Czech Republic) working collaboratively to comparatively map the regions of the apricot genome that confer resistance to Plum Pox Virus. These scientists are specifically interested in utilizing the physical/genetic map for peach as the starting point in development of probes to assist identification of the PPV resistance gene/s through assembly of the genomic interval region that confers resistance to PPV in apricot. Work recently completed in our lab in cooperation with Dr. Marisa Badenes (IVIA, Spain) and her student Elsa Maria Vera Ruiz have implemented these probes to identify and assemble the apricot genomic interval. The results suggest that the genomes are highly collinear and that the peach genome can be used very effectively for this purpose. These results will be presented at PAG 2008.

We are also using the data of the physical map to comparatively map regions in species outside of the family, in particular chestnut (Fagaceae). Marked regions of the chestnut genome, having resistance genes for chestnut blight, are being comparatively examined with peach and significant preservation of the genomes suggests that peach could provide gene information in the critical regions under study (Georgi unpublished results). These results will be presented at PAG 2008. In our initial sequence comparative work with other species, we find high preservation of genome structure in the Prunus species and a highly significant preservation of the genome with member outside of Rosaceae, in particular Poplar. Microsynteny studies in sequenced regions of the peach genome and poplar demonstrate almost complete preservation of gene repertoire and order. Additionally, the peach genome represents a more ancestral state thus allowing the evolution of duplicated regions in poplar to be examined. These results will be presented at PAG 2008.

Deliverables:

  • Publications:
  • Zhebentyayeva, T. N., R. Horn, J. Mook, A. Lecouls, L. Georgi, A.G. Abbott, G. L. Reighard, G. Swire-Clark, and W.V. Baird. 2006. A physical framework for the peach genome. Acta Hort. 713: 83-88
  • Horn R., Lecouls A.-C., Callahan A., Dandekar A., Garay L., McCord P., Howad W., Chan H.,Verde I., Ramaswamy K., Main D., Jung S., Georgi L., Forrest S., Mook J., Zhebentyayeva T.N., Yu Y., Kim H.R., Jesudurai C., Sosinski B.A., Arus P., Baird V., Parfitt D., Reighard G., Scorza R., Tomkins J., Wing R., Abbott A.G. 2005. Candidate gene database and transcript map for peach, a model species for fruit trees. Theor.Appl. Genet. 110: 1419-1428
  • Sook Jung, Christopher Jesudurai, Margaret Staton, Zhidian Du, Stephen Ficklin, Ilhyung Cho, Albert Abbott, Jeffrey Tomkins and Dorrie Main, Sept. 9, 2004. GDR Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research BMC Bioinformatics 2004, 5:130
  • Sook Jung, Albert Abbott, Christopher Jesudurai, Jeff Tomkins and Dorrie Main. 2005. Fequency, Type, Localization and Annotation of SSRs in Rosaceae ESTs, Functional and Integrated Genomics, 5(3):136-43.
  • Jung,S., Main, D., Staton, M., Cho, I., Zhebentyayeva, T., Arús, P.and A. Abbott 2006. Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes. BMC Genomics 2006, 7:81
  • Bielenberg, D.G., Y. Wang, G.L. Reighard and A.G. Abbott. 2006. Sequencing and analysis of the peach EVG locus. Acta Hort. 713: 73-82.
  • Lalli, D. A., Decroocq, V., Blenda, A.V. , Schurdi-levraud, V., Garay, L., Le Gall, O., Damsteegt, V., Reighard, G.L., and A. G. Abbott, 2005. Identification and mapping of resistance gene analogs (RGAs) in Prunus: A resistance map for Prunus. Theor. Appl.Genet. Theor. Appl. Genet. 111:1504-1513
  • Lalli, D.A., Krška, B. ,Abbott, A.G., Badenes, M.L., Damsteegt, V., Polák, J. , Salava, J. A Genetic Linkage Map for an Apricot (Prunus armeniaca L.) BC1 Population Mapping Plum Pox Virus Resistance, in press, Tree Genetics and Genomes.
  • Sook Jung, Margaret Staton, Taein Lee, Anna Blenda, Randall Svancara, Albert Abbott and Dorrie Main GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. 2007. Nucleic Acids Res. Oct. 11 advance access published on line: pg, 1-7
  • TN Zhebentyayeva, G.Swire-Clark, LL Georgi, L Garay, S Jung, S Forrest, AV Blenda, B Blackmon, J Mook, R Horn, W Howad, D Main, JP Tomkins, WV Baird, P. Arus, B. Sosinski, GL Reighard2, AG Abbott, A framework physical map for peach, a model Rosaceae species. Accepted, Tree Genetics and Genomes
  • Sook Jung, Derick Jiwan, Ilhyung Cho, Taein Lee, Albert Abbott, Bryon Sosinski and Dorrie Main, Extensive conservation of gene order and content between Prunus and Populus but not between Prunus and Arabidopsis. Submitted: Genome Biology.
  • Presentations:
  • Zhebentyayea, T. N. 2006, The peach physical/genetic map database: a tool for Rosaceae genomics. Rosaceae Genome Conference 3, Napier, New Zealand
  • Lalli, D. A., Decroocq, V., Blenda, A.V., Schurdi-Levraud, V., . Garay ,L, , Le Gall, O., Damsteegt, V., Reighard, G. L., and Abbott, A. G. (2006) A Resistance map for Prunus. 3rd International Rosaceae Genomics Conference. Napier, New Zealand, March 19-22, 2006.
  • Albert Abbott, Tatyana Zhebentyayeva, Ginger Swire-Clark, Laura Georgi, Samuel Forrest, Barbara Blackmon , Jeff Tomkins , Vance Baird, Gregory Reighard, Physical map for peach, a genomic foundation for fruit tree genetics and breeding, Eucarpia, Sept. 16-20, 2007, Zaragoza Spain
  • Meeting Abstracts:
  • Those cited in presentations above and PAG 2007:
  • PAG 2007:
    • Tatyana Zhebentyayeva1, Ji Hae Jun1, Bryon Sosinski,4 Sriyani, Rajapakse1, W. Vance Baird2, Robert Ballard1, , Ralph Scorza3, and Albert Abbott1 . A second generation linkage genetic map for f2 peach suncrest x bailey population P 470 Albert Abbott, Tatyana Zhebentyayeva1 , Renate Horn1 , Ginger Swire-Clark2, Jennifer Mook1 , 1 Laura Georgi1 , Samuel Forrest1, Barbara Blackmon 3, Jeff Tomkins 3, Vance Baird2 , Gregory Reighard2 . An enchanced physical framework for peach. P 471 Osama Sajer, Ralph Scorza, Albert Abbott, and Renate Horn, Identification of Markers Closely Linked to the Peach "Pillar" Gene, P 472 Sook Jung, Margaret Staton, Taein Lee, Anna Blenda, Albert Abbott and Dorrie Main, Genome Database for Rosaceae P 938
  • PAG 2008:
    • Albert Abbott, Tatyana Zhebentyayeva, Ginger Swire-Clark, Laura Georgi, Samuel Forrest, Barbara Blackmon , Jeff Tomkins , Vance Baird, Gregory Reighard, Physical map for peach, a genomic foundation for fruit tree genetics and breeding, Fruit and Nuts Workshop, Oral presentation.
  • Web sites: Genome Database for Rosaceae (GDR)
  • Community resources generated (sequences, populations, plant materials) All of our current work is directed at providing a community resource for Rosaceae researchers. We have generated in this project, a physical/genetic map resource for peach to serve as a model for Rosaceae genomics and gene discovery. We have provided a physical map for peach anchored on the general Prunus genetic map, provided extensive peach EST resources (~30,000 EST sequences from fruit, shoot and root) with several thousand unigenes mapped on the physical map/genetic map resource. We have provided a resistance gene map for Prunus that is already being used to identify potential candidate resistance genes for nematodes, Plum Pox Virus, powdery mildew and others. In addition we have provided targeted genomic sequences for comparative genome evolutionary studies among the species.
  • Patents: Evergrowing Gene Patent filed 2006
  • Training:
  • Under this current project and the former original project the following personnel have been associated.
  • Undergraduates:
  • 2005-06 Jonathan Duncan: Molecular mapping of fruit quality characters in peach 2006-07
  • W. Thompson: comparative genomics of peach and apricot
  • Graduate Students:
  • D. Lalli, Ph.D. Genetics 2006 : Resistance gene map and comparative genomics of peach and apricot
  • S. Forrest, Ph,D. Genetic 2007: BAC library construction and EST mapping.
  • Fan Shenghua Ph.D. Genetics 2007: Mapping of chilling requirement genes.
  • Bode Olukulu Ph.D. Genetics 2009: Comparative genomics of peach and other important Rosaceae species
  • Visiting Graduate Students:
  • Gregoire Marandel, May 2007- Sept. 2007, INRA, Bordeaux France, Comparative physical mapping of PPV resistance in apricot and peach
  • Petra Pilarova, May 2007- Nov. 2007, Czech Republic, Mapping of PPV resistance in the apricot variety Harlayne.
  • Elsa Maria Vera Ruiz, IVIA, Valencia Spain, Oct. 2007, Comparative physical mapping of PPV resistance region in apricot and peach.
  • Postdoctoral Associates:
  • Anne-Claire Lecouls 2000-2002, Peach Physical mapping, and EST databases.
  • Tetyana Zhebentenyayeva 2003-present, Peach Physical mapping, EST databases, identification and characterization of important genes in Rosaceae biology.
  • Technicians:
  • Lilibeth Garay 2000-2004: EST mapping
  • Jennifer Mook 2001-2006: peach physical mapping, accounts manager
  • Visiting Scientists:
  • Dr. Ignazio Verde, Rome Italy, 2002, peach physical map
  • Dr. Jaroslav Salava Czech Republic, 2001-, Comparative mapping of peach and apricot disease resistance loci.
  • Dr. Marisa Badenes IVIA Valencia Spain 2003,2006 Comparative mapping of peach and apricot.
  • Dr. Claudia Ricciolini CNR Perugia 2004, RGA mapping in Prunus
  • Dr. Donato Giannino ( Rome, Italy) May 05, Physical mapping in peach
  • Dr. Jahn Davik ( Trondheim, Norway) Sept. 2006-Aug 2007, Comparative mapping in peach and strawberry.
  • Dr. Renate Horn (Rostock Germany) 2005- one month/year, identification of genes critical to tree architecture in peach.
  • Dr. Veronique Decroocq (INRA, Bordeaux France, May 2007-Oct. 2007, Physical mapping of PPV. Resistance gene regions in apricot and peach
  • Dr. Jahn Davik (Norweigan institute of Agriculture and Environment Res.) Sept. 2006-Nov. 2007, Comparative mapping and sequencing of the evg region in strawberry and peach.

Collaborations:

All or many of the above listed visiting scientists have worked in collaborations that this project has made possible. In addition, we have begun to collaborate with the strawberry community to develop a physical map of strawberry (prepared a BAC library to diploid strawberry), we are working collaboratively with the Scottish Crops Institute to comparatively sequence regions of the genome of peach and raspberry carrying genes that control winter dormancy. We have initiated a project to understand nitrogen fixation in Rosaceae with several investigators at Clemson and at other institutions in the US. We are collaborating with several groups on biomass production in peaches and other trees and finally, we are cooperating with JGI to get the genome of peach completely sequenced as a reference genome for Rosaceae. In a new parallel project, we are providing physical map information, peach Genomic DNA and physical map tiling paths to Dr. Richard McCombie for some preliminary Solexa sequencing studies.