Agrifood Research Finland & Univ. Helsinki (MTT)
 |
Location : Jokioinen / Finland |
| Leader : Alan SCHULMAN | |
| Website : www.mtt.fi/english |
Competences:
MTT Agrifood Research competences are in genomics and molecular genetics for marker development and application, high throughput sequencing, and physical and genetic mapping. For anchoring of genetic and physical maps using molecular markers, we have long experience in development and application of SSR, MITE, and transposable element (TE) markers as well as low-throughput SNPs. We have a local Illumina platform (BeadStation) and are genotyping a large collection of barley accessions. We develop and apply TEs as molecular markers. We are also expert in the development of DH barley lines for mapping. We use of molecular markers for gene isolation, mapping, and genetic diversity studies. For sequencing, we have both “454” and Sanger sequencing. Barley transformation is in house and active. We develop and apply tools for annotation of the repetitive fraction of the BACs, which is highly important for both marker development and gene annotation.
Role:
MTT Agrifood Research Finland is involved in WP2 and WP6. For task 2.1, it will collect MITE flanks for barley markers. For task 2.3, it will use markers derived from transposable elements and indels. For task 2.5, it will use markers derived from sequenced Brachypodium for tying the physical/recombinational maps together and trial markers for 1H and 3H e.g. by using degenerate primers and chromosome addition lines. In WP6, we will coordinate outreach and interaction with other Triticeae genomics networks.
Staff members’ profile:
Alan Schulman is Professor of Plant Biotechnology at MTT, Group Leader at the Institute of Biotechnology, University of Helsinki. Directs two labs, one in each institution. Educated at Duke (B.A., Botany, 1979) and Yale Universities (M.S., 1981; M. Phil. 1982; Ph.D., 1986, Cell and Developmental Biology). Coordinates COST Action FA0604; earlier coordinated an ESF Network, and three NKJ and NIF Nordic projects. Research: first to demonstrate active transposable elements in barley, and has since both carried out basic research on the life cycle and genetic consequences of these major genomic components as well as developed and applied methods to use them as molecular markers. The group had a major EST sequencing project that contributed to the international barley microarray project, and now applies microarrays to problems of grain development and quality as well as disease resistance in barley.
References:
- Druka, A., Muehlbauer, G., Druka, I., Caldo, R., Baumann, U., Rostoks, R., Schreiber, A., Wise, R., Close, T., Kleinhofs, A., Graner, A., Schulman, A., Langridge, P., Sato, K., Hayes, P., McNicol, J., Marshall, D. & Waugh, R. 2006. An atlas of gene expression from seed to seed through barley development. Funct. Integr. Genomics DOI: 10.1007/s10142 006 0025 4
- Kalendar, R., Vicient, C.M., Peleg, O., Anamthawat-Jonsson, K., Bolshoy, A. and Schulman, A.H. 2004. LARD retroelements: Novel, non-autonomous components of barley and related genomes. Genetics 166(3): 1437-1450.
- Boyko, E., Kalendar, R., Korzun, V. Korol, A., Schulman, A.H., Bikram, G. 2002. Aegilops tauschii high density genetic map of expressed and repeated fractions of the genome provides unique insights into cereal chromosome structure and function. Plant Mol. Biol. 48: 767 - 790. Cover photo.
- Vicient, C.M., Kalendar, R. and Schulman, A.H. 2001. Envelope-class retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants. Genome Res. 11: 2041-2049.
- Vicient, C.M., Jääskeläinen, M., Kalendar, R. and Schulman, A.H. 2001. Active retrotransposons are a common feature of grass genomes. Plant Physiol. 125: 1283-1292.
- Shirasu, K., Schulman, A.H., Lahaye, T. & Schulze-Lefert, P. 2000. A contiguous 66 kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res. 10: 908-915
- Kalendar, R., Tanskanen, J., Immonen, S., Nevo, E. & Schulman, A.H. 2000. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc. Natl. Acad. Sci. USA 97(12): 6603-6607.
- Jääskeläinen, M., Mykkänen, A.-H., Arna, T., Vicient, C., Suoniemi, A., Kalendar, R., Savilahti, H. & Schulman, A.H. 1999. Retrotransposon BARE-1: Expression of encoded proteins and formation of virus-like particles in barley cells. Plant J 20(4): 413-422.
- Vicient, C.M., Suoniemi, A., Anamthawat Jónsson, K., Tanskanen, J., Beharav, A., Nevo, E. & Schulman, A.H. 1999. Retrotransposon BARE 1 and its role in genome evolution in the genus Hordeum. Plant Cell 11(9): 1769-1784.
- Suoniemi, A., Tanksanen, J. & Schulman, A.H. 1998. Gypsy-like retrotransposons are widespread in the plant kingdom. Plant J. 13: 699-705.
Show all the institutions
This project is supported by the European Commission under the 7th Framework Programme
for Research and Technological Development