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MTT/BI Plant Genomics Laboratory

  • Retrotransposons as drivers of genomic change
  • Identification of disease resistance and quality trait genes through functional genomics

T he MTT/BI Plant Genomics Laboratory is a joint laboratory of the Institute of Biotechnology and of MTT Agrifood Research. At MTT, the lab belongs to the Genomics Research programme, which includes plants, animals, and microbes, di­rected by Prof. Alan H. Schulman within the Department of Biotechnology and Food Research. Plant Genomics has two laboratories, the MTT/BI joint lab at Viikki and a laboratory at Jokioinen, which work together and comprise 25 members. The MTT/BI group studies retrotransposons as drivers of genomic change and as markers for this change, uses these and other marker systems for map-based cloning of genes for disease resistance and quality traits, and analyses the role of candidate genes through the application of functional genomics tools such as microarrays. To sup­port these goals, the Jokioinen lab develops and applies doubled-haploid populations for mapping in barley, rye, oat, and Brassica and maps traits in these crops. We also have implemented barley transformation using Agrobacterium . Potato di-haploids and fusions have been produced and are being used to develop novel glycoalkaloids as pharmaceutical lead compounds.

The Plant Genomics group has a long-term programme to understand the role of retrotransposons in genome dynamics. These mobile elements replicate in a way similar to retroviruses and create daughter copies that integrate throughout the genome. We are working to establish the details of their lifecycle, the role of cel­lular regulation of their capacity for enormous copy number increase and mutagenic genome disruption, and their effect on genomic and cellular function. Members of the group are currently studying transcriptional regulation of the barley BARE ret­rotransposons of barley and the translation, processing and the assembly of virus-like particles. We are also investigating how successful non-autonomous retrotrans­posons, especially Cassandra , parasitize other retrotransposons for needed proteins and evade cellular regulation by using novel pol III transcription.

Selected publications

Vogel JP, Garvin DF, Rokshar D, Bevan MW et al. Genome sequence analysis of the model grass Brachypodium distachyon. Nature. 2010; 463: 763-768.

Schulte D, Close TJ, Graner A, Langridge P, Matsumoto T, Muehlbauer G, Sato K, Schulman AH, Waugh R, Wise RP, Stein N. The International Barley Sequencing Consortium (IBSC) - at the threshold of efficient access to the barley genome. Plant Physiology. 2009; 49: 142-147

Chang W, Schulman AH. The BARE retrotransposon produces multiple groups of rarely polya­denylated transcripts from two differentially regulated promoters. Plant Journal. 2008; 56: 40-50.

Kalendar R, Tanskanen J, Chang W, Antonius K, Sela H, Peleg O, Schulman AH. Cassandra ret­rotransposons carry independently transcribed 5S RNA. Proc Natl Acad Sci USA. 2008; 105: 5833-5838.

Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell AJ, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH. A unified classification system for eukaryo­tic transposable elements. Nature Rev Genet. 2007; 8: 973-982.

Photo by Veikko Somerpuro

 

Group leader Schulman

Principal Investigator

Alan Schulman