High-Resolution Physical Mapping of the Apple Genome by BAC Fingerprinting


NRI Award #2005-35300-15538
PI: Schuyler S. Korban, Co-PI: Jonathan E. Beever
University of Illinois, Urbana, IL 61801
E-mail: korban@uiuc.edu
Telephone: 217-333-8298
Website: http://korban.nres.uiuc.edu/


Accomplishments:
  • Constructed a genome-wide framework for a physical map of the apple genome by restriction fingerprinting of 74,281 BAC clones.
  • The map consists of 2,702 contigs, and it is estimated to span ~927 Mb in physical length.
  • New genetic markers such as EST-derived and BAC-end sequence-based SSR markers, SNPs and indel markers, and sequence characterized amplified region (SCAR) markers have been developed.
  • These newly developed markers together with previously reported SSR markers are being used to anchor physical BAC contigs to the apple genetic map that is under construction.
  • Previously published SSR markers were selected to anchor the BAC contigs onto the genetic map using PCR-based screening procedure of the BAC library. To date, a total of 280 SSR markers (257 single-locus and 15 multiple-locus) have been used to screen the BAC library.
  • Approximately 2,000 BAC clones selected from different BAC contigs were sequenced at both ends. New genetic markers, including 51 SNPs, 6 indels, and 4 SCARs have been developed based on BAC-end sequences, and used to directly anchor their corresponding BAC contigs onto the genetic map.
  • Approximately 180 candidate SSR markers have also been identified from BAC- end sequences. In addition, a total of 51 sequence-tagged connectors (STCs) have been developed as well. These STCs have been used to screen the BAC library, and these results will be used to merge overlapping contigs.
  • Screened publicly available apple SSR markers (272 SSRs) for polymorphisms in the parents ‘Golden Delicious’ and ‘Coop17’ of our mapping population.
  • Screened over 300 apple EST-SSRs for size and polymorphism in ‘Golden Delicious’ and ‘Coop17’.
  • Screened 180 SSRs derived from BAC-end sequences for polymorphism in ‘Golden Delicious’ and ‘Coop17’.
  • Data generated from testing 117 individuals of the ‘Golden Delicious’ x ‘Coop17’ progeny with polymorphic SSRs are being used to prepare a data file for linkage mapping using the program JoinMap version 4.0.
Broad Impacts:

The apple is highly self-incompatible thus contributing to its high level of heterozygosity. In our project, we have assembled apple BAC clones into contigs, with an average estimated size of ~340 kb in physical length, thus generating a physical map of ~927 Mb in length. At this time, we are anchoring this physical map onto the genetic map with the help of molecular markers, previously published and newly discovered, in order to establish an integrated genome-wide map for the apple. We are now able to modify our BAC contig assembly based on our screening with the large numbers of diverse molecular markers that we are employing. We are making excellent progress in anchoring the physical map onto the genetic map.

Deliverables:
  • Publications
    • Han, Y., K. Gasic, B. Marron, J.E. Beever, and S.S. Korban. 2007. A BAC-based physical map of the apple genome. Genomics 89: 630-637.
    • Han, Y. and S.S. Korban. 2007. Spring: A novel family of miniature inverted-repeat transposable elements in the apple genome. Genomics 90:195-200.
    • Han, Y., E. Bendik, F. Sun, K. Gasic, and S.S. Korban. 2007. Genomic isolation of genes encoding starch branching enzyme II (SBEII) in apple: Towards characterization of evolutionary disparity in SbeII genes between monocots and eudicots. Planta 226:1265- 1276.
    • Han, Y., K. Gasic, and S.S. Korban. 2007. Multiple-copy cluster-type organization and evolution of genes encoding O-methyltransferases in apple. Genetics 176: 2625-2635.
    • Naik, S., C. Hampson, K. Gasic, G. Bakkeren, and S.S. Korban. 2006. Development and linkage mapping of E-STS and RGAs for functional gene homologues in apple. Genome 49:959-968.
  • Presentations
    • A presentation entitled “Insights and thoughts on preparing a successful USDA-NRI proposal”, ASHS Workshop on CSREES, USDA Integrated Competitive Programs Grantsmanship, Annual Meetings of the American Society for Horticultural Science, Scottsdale, AZ, July 18, 2007.
    • A presentation entitled “Apple genomics research”, University of Illinois, Urbana, IL, Oct. 5, 2006.
    • A seminar on “New resources for apple genomics” at the Katholike University of Leuven, Leuven, Belgium, July 3, 2006.
    • A seminar on “Advances in apple genomics resources” at the Universidade Federal de Santa Catarina, Santa Catarina, Brazil, April 12, 2006.
    • A presentation on “Developing a physical map for the apple genome” - 3rd International Rosaceae Genomics Conference, Napier, Hawkes Bay, New Zealand, March 21, 2006.
  • Meeting Abstracts
    • Han, Y., K. Gasic, J.E. Beever, and S.S. Korban. 2008. Towards integrating a genetic map with a physical map of the apple genome. Plant & Animal Genome Conf. XVI (in press).
    • Korban, S.S. 2008. A genome-wide physical map for the apple genome. Plant & Animal Genome Conf. XVI (in press).
    • Gasic, K., Y. Han, S. Kertbundit, V. Shulaev, A.F. Iezzoni, E.W. Stover, R.L. Bell, M.E. Wisniewski , and S.S. Korban. 2008. Transferability of apple EST-derived SSRs to other Rosaceae species. Plant & Animal Genome Conf. XVI (in press).
    • Wisniewski, M.E., C.L. Bassett, T.S. Artlip, J. Norelli, Y. Han, and S.S. Korban. 2008. Sequence and expression analysis of three CBF-like genes from apple (Malus x domestica). Plant & Animal Genome Conf. XVI (in press).
    • Han, Y., S. Vimolmangkang, S. Rosales-Mendoza, K. Gasic, and S.S. Korban. 2008. A gene family encoding flavonoid 3’-hydroxylase in the apple (Malus × domestica Borkh.). Plant & Animal Genome Conf. XVI (in press).
    • Norelli, J.L., S.E. Gardiner, C.L. Bassett, R.E. Farrell, A. Baldo, H.S. Aldwinckle, M. Malnoy, E. Borejsza-Wysocka, D.A. Lalli, M.E. Wisniewski, J-M. Celton, and S.S. Korban. 2008. Functional genomics to develop tools to breed fire blight resistant apples. Plant & Animal Genome Conf. XVI (in press).
    • Han, Y., K. Gasic, and S.S. Korban. 2007. Structure, expression, and duplication of genes encoding O-methyltransferases in apple (Malus × domestica Borkh.). Plant Biology & Botany Abstracts, P20045, p. 133.
    • Han, Y. and S.S. Korban. 2007. A novel family of miniature inverted-repeat transposable elements is associated with genes in apple. Plant Biology & Botany Abstracts, P27014, p. 165.
    • Han, Y., E. Bendik, F. Sun, K. Gasic, and S.S. Korban. 2007. Genomic isolation and characterization of genes encoding starch branching enzyme II (SBEII) in apple. HortScience 42:975-976.
    • Han, Y., K. Gasic, S. Kertbundit, B. Marron, J.E. Beever, and S.S. Korban. 2007. A first draft of a genome-wide physical map for the apple. Plant & Animal Genome Conf. XV P- 455, p.215.
    • Han, Y. and S.S. Korban. 2007. Two sets of transposons within members of a gene family encoding caffeic acid O-methyltransferases in apple. Plant & Animal Genome Conference XV P- 460, p.216.
    • Han, Y., K. Gasic, S. Kertbundit, B. Marron, J.E. Beever, and S.S. Korban. 2006. Development of a genome-wide physical map for the apple. 3rd International Rosaceae Genomics Conference Abstracts, p. 52.
    • Han, Y., K. Gasic, S. Kertbundit, B. Marron, J.E. Beever, and S.S. Korban. 2006. Developing a genome-wide physical map of the apple genome. Plant & Animal Genome Conf. XIV Abstracts –P-496, p. 225.
  • Web sites
  • http://korban.nres.uiuc.edu/
  • Community resources generated (sequences, populations, plant materials)
  • EST-SSRs, BAC-end SSRs, BAC-SNPs, EST-SNPs, scaffold of a physical map, a genetic map, mapping population
  • Training:
  • Yuepeng Han - Postdoctoral - he has been involved in BAC fingerprinting and assembly of BAC clones into contigs, BAC-end sequencing, BAC-end SSRs, BAC SNPs, screening of BAC library, anchoring BAC contigs.
  • Kesenija Gasic - Postdoctoral - she has been involved in developing EST-SSRs, screening parent of mapping population, and progeny with various molecular markers, developing genetic map.
  • Brandy Marron - Research Specialist - she has been involved in BAC fingerprinting
  • Sunee Kertbundit – Fulbright scholar- she was involved in developing SSR markers.
  • Mark Danielson - undergraduate student - he worked as a student helper in preparing media for BAC DNA extractions.
  • Suresh Naik - Postdoctoral (in a collaborative effort with Dr. Cheryl Hampson) - developing EST-SSRs and assessing their utility in mapping.
Collaborations:
  • Collaborations with HortResearch scientists (Dr. Sue Gardiner, Dr. David Chagné, Dr. Gavin Ross, among others) on developing molecular markers
  • Collaborations with various US scientists, including Drs. Michael Wisniewski, Vladimir Shulaev, Amy Iezzoni, Ed Stover, and Richard Bell on transferability of EST-SSRs across Rosaceae.
  • Interactions and collaborations with Dr. John Norelli and his team on the fireblight project.
  • Collaborations with Prof. Wannes Keulemans and his team (Belgium) on linkage mapping.
  • Interactions with Dr. Cheryl Hampson (Agri-Canada) on EST-SSRs and mapping.
  • Interactions with various US, European, and New Zealand scientists about apple mapping efforts in the family Rosaceae.