J. Antoni Rafalski

Business address:

E.I. du Pont de Nemours & Co. (Inc.)

Crop Genetics

DuPont Experimental Station

Building 353 Room 118A

P.O.Box 80353

Wilmington DE19880-0353

Tel. 302-695-2634

Fax 302-695-2726

Email

Academic Affiliation

Adjunct Professor, University of Delaware Dept. of Plant and Soil Sciences and Biotechnology Institute.

Education:

- M.Sc.(Chemistry) Adam Mickiewicz University, Poznan, Poland

- Ph.D. (Chemistry) Adam Mickiewicz University, Poznan, Poland

- Postdoctoral: Yale University, New Haven, CT, USA, w. Prof. Dieter Soll

- Study leave with Prof. Sydney Brenner at Cambridge University (UK), Dept. of Medicine, Molecular Genetics Unit

Employment:

1984 - current, DuPont Crop Genetics / Pioneer HiBred International. Research on molecular and population genetics of maize: genetic association mapping, linkage disequilibrium, analysis of allelic non-homologies in the maize genome, analysis of gene expression using DNA arrays, plant genome mapping, EST sequencing, application of SSR, SNP, RAPD and RFLP genetic markers in plant breeding), Current position: Research Fellow.

1981-1984 - Research Associate at the Department of Molecular Biophysics and Biochemistry, Yale University, Prof. Dieter Soll (research on plant ribosomal RNA genes and wheat endosperm storage protein gene structure)

1978-1981 - Group Leader and Member of the Scientific Council at the Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.

Selected Research Highlights

Identification of multiple allelic non-homologies in maize

Identification of high LD regions in maize elite germplasm (2003)

Analysis of the effects of selection at the maize y1 locus (2002)

Development of maize single nucleotide polymorphism markers (1999)

Implementation of DNA array technology at DuPont (1998-9)

Development of DuPont EST process (1996)

Large scale SSR (microsatellite) isolation in Soybean (1994)

Invention of ISA (Inter-SSR-Amplification (1993)

Invention of RAPD Markers (1989)

First saturated RFLP Map of Soybean (1990)

First DNA sequence of HIV Virus (1984)

First DNA sequence of a wheat storage protein gene (gliadin) 1983

Statement of Research Interests:

Our research is focused on molecular genetics and genomics of maize. We are especially interested in understanding the allelic diversity of the maize genome, and in developing tools for genetic association mapping - that is associating specific alleles at candidate genes or across the whole genome with phenotypes of interest to plant breeders. To this end we analyze single nucleotide polymorphisms (SNPs) in maize genes across wide collections of maize inbred lines. To understand the limitations of association mapping, we study linkage disequilibrium in maize. We also do DNA sequencing of selected segments of the maize genome (100-300 kb range) to understand evolution of allelic differences and the mechanisms which generate non-homologous insertions in some maize alleles. For an example of recent research see Palaisa K. et al. The Plant Cell 15 (2003) 1795-1806, or a review on plant SNPs: Rafalski, A., Current Opinion in Plant Biology 5(2002) 94-100.

Past and Present Visiting Scientists / Postdoctoral Fellows

Chaz Andre, Michele Morgante, Wayne Powell, Renato Tarchini, Jian-Ming Lee, Dinakar Bhattramakki, Stephan Brunner.

Graduate Students

Kelly Palaisa (graduated from University of Delaware 2003)

Teaching activities

Faculty of CSH Molecular Breeding Course

Faculty of Molecular Breeding Course, International Potato Center, Peru

Organized and taught Bioinformatics / EST Data base class at DuPont

Team teaching: Bioinformatics graduate class at University of Delaware (Prof. G. Gao)

Editorial Activities

Associate Editor: Plant Science, Molecular Breeding

Selected Recent publications

• Palaisa, K, Morgante, M., Williams, M. and Rafalski, A.

  Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci.

  The Plant Cell 15 (2003) 1795-1806.

• Ching, A and Rafalski, A.

  Rapid Genetic Mapping of ESTs Using SNP Pyrosequencing and Indel Analysis

  Cellular and Molecular Biology Letters 7 (2002) 803-810

• J.-M. Lee, M.E. Williams, S.V. Tingey and J.A. Rafalski

  DNA Array Profiling of Gene Expression Changes During Maize Embryo Development

  Functional and Integrative Genomics 2 (2002) 13-27

• Ching, A and Rafalski, A

  Rapid EST Mapping and SNP Genotyping of Individuals Using Pyrosequencing

  Maize Genetics Newsletter 76 (2001) paper 29.

  http://www.agron.missouri.edu/mnl/76/29ching.html

• Rafalski, A.

  Applications of Single Nucleotide Polymorphisms in Crop Plant Genetics

  Current Opinion in Plant Biology 5(2002) 94-100.

• Rafalski, A.

  Plant Genomics: Present State and A Perspective on Future Developments

  Briefings in Functional Genomics and Proteomics 1 (2002) 80-94.

• Rafalski, A.

  Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Science 162 (2002) 329-333.

• Ching, A., Caldwell, K., Jung, M., Dolan, M., Smith, H., Tingey, S., Morgante, M. and Rafalski, A.

  SNP frequency and haplotype structure of 18 maize genes. BMC Genetics 2002, 3:19 (7Oct2002)
  

• Bhattramakki, D., Dolan, M., Hanafey, M., Wineland, R., Vaske, D., Register III, J.C., Tingey, S.V. and Rafalski, A.

  Insertion-Deletion Polymorphisms in 3'-Regions of Maize Genes Occur Frequently and Can Be Used as Highly Informative Genetic Markers. Plant Mol.Biol. 48 (2002) 539-547.

• Rafalski, A.

  Book Review: Plant's Fingerprints - Plant Genotyping, The DNA Fingerprinting of Plants. R.J. Henry, Ed. CABI Publishing 2001, Trends in Biotechnology 20 (2002) 133

• Van Dyk, T. K., G. E. Gonye M. J. G. Reeve, E. J. DeRose, M. Dolan, M. K. Hanafey, Y. Wei, J. A. Rafalski, and R. A. LaRossa. 2001. Genome-wide expression profiling with luxCDABE gene fusions, p. 461-464. In J. Case, P. Herring, B. Robison, S. Haddock, L. Kricka, and P. Stanely (ed.), Proceedings of the 11th International Symposium on Bioluminescence and Chemiluminescence. World Scientific, Singapore.

• Bhattramakki, D. and Rafalski, A.

  Discovery and application of single nucleotide polymorphism markers in plants. In: Plant Genotyping: The DNA Fingerprinting of Plants. R. J. Henry, Ed. CABI Publishing, Wallingford Oxon, UK, 2001.

• Van Dyk TK, Wei Y, Hanafey MK, Dolan M, Reeve MJ, Rafalski JA, Rothman-Denes LB, LaRossa RA. A genomic approach to gene fusion technology. Proc Natl Acad Sci U S A. 2001, 98, 2555-60.

• Wei, Y, Lee, J.-M., Richmond, C., Blattner, F.R., Rafalski, J.A. and LaRossa, R.A.

  High Density Microarray-Mediated Gene Expression Profiling of Escherichia coli

  J.Bact. 2001, 183, 545-556.

• Tarchini, R., Biddle, P., Wineland, R., Tingey, S. and Rafalski, A.

  The Complete Sequence of 340 kb of DNA around the Rice Adh1-Adh2 Region Reveals Interrupted Colinearity with Maize Chromosome 4

  The Plant Cell 2000, 12, 381-391.

• Jia MH, Larossa RA, Lee JM, Rafalski A, Derose E, Gonye G, Xue Z.

  Global expression profiling of yeast treated with an inhibitor of amino acid

  biosynthesis, sulfometuron methyl.

  Physiol Genomics. 2000 Aug 9;3(2):83-92.

• deBarros EG,Tingey S,Rafalski JA

  Sequence characterization of hypervariable regions in the soybean genome: leucine-rich repeats and simple sequence repeats.

  Genet. Mol. Biol. 2000; 23, 411-415

Patents Co-inverntorship

U.S. Patent 5,126,239 - RAPD technology

U.S. Patent 6,184,036 - Ornithine biosynthesis enzymes

U.S. Patent 6,168,951 - Plant geranylgeranyl transferases

U.S. Patent 6,248,584 - Transcription co-activators

U.S. Patent 6,255,090 - Plant aminoacyl-tRNA synthetase

U.S. Patent 6,037,127 - Method for Detection of Non-Denatured Nucleic Acid Fragments

U.S. Patent 6,271,031 - Quinolinate metabolism enzymes

U.S. Patent 6,278,042 - Plant arsenic transporters

U.S. Patent 6,297,034 - N-end rule pathway enzymes

U.S. Patent 6,303,332 - Corn cDNA encoding southern leaf blight resistance

U.S. Patent 6,306,632 - Chromatin associated proteins

U.S. Patent 6,329,204 - Plant caffeic acid 3-O-methyltransferase homologs

U.S. Patent 6,338,966 - Genes encoding sulfate assimilation proteins

U.S. Patent 6,348,339 - Enzymes involved in degradation of branched-chain amino acids

U.S. Patent 6,346,403 - Methionine metabolic enzymes

U.S. Patent 6,355,462 - Disease resistance factor

U.S. Patent 6,403,859 - Vitamin B metabolism proteins

U.S. Patent 6,451,581 - plant branched-chain amino acid biosynthetic enzymes

U.S. Patent 6,465,717 - Sterol metabolism enzymes

U.S. Patent 6,465,229 - Plant caffeoyl-CoA-O-methyltransferase

U.S. Patent 6,465,234 - N-end rule pathway enzymes

U.S. Patent 6,552,249 - Plant cinnamyl alcohol dehydrogenase

U.S. Patent 6,545,200 - Sterol biosynthetic enzymes

U.S. Patent 6,573,426 - Genes involved in pyrimidine biosynthesis in plants

U.S. Patent 6,596,926 - Phosphatidyccholine biosynthetic enzymes

U.S. Patent RE 38,252 cDNA Encoding Southern :Leaf Blight Resistance

U.S. Patent 6,624,343 - Hexose Carrier Proteins

U.S. Patent 6.630,617 - Enzymes involved in squalene metabolism

U.S. Patent 6,642,435 - Plant Folate Biosynthetic Genes

U.S. Patent 6,660,850 - Nucleic acid encoding a wheat brittle-1 homolog.

Other patents applied for.