Agritec Plant Research Ltd.,Plant Biotechnology Department,Zemědělská 2520/16,CZ-787 01 Šumperk,Czech Republic
Mini-biography
I have gained MSc. Degree in Plant Biotechnology and PhD. in Plant Molecular Biology at Charles University in Prague. Initially working on androgenesis and related stress biology namely heat-shock proteins. As post-doc at ETH Zurich I have switched subject to genetic of photoperiodism. Second post-doc position I spent on meristem patterning, studying function of ARGO genes and miRNAs. Last three years I have finally settled in Agritec Plant Research Ltd., doing applied research mainly on genetic resources and genetic transformation of pea and flax. Current activities deal with usage of repetetive elements, such as retrotransposons and microsatellites, for genetic diversity and population structure studies. Another research in the group deals with genetic modification of pea for virus and pest resistance and as tool for production of biopharmaceuticals, development of markers for breeders linked to disease resistance, as well as tissue culture such as somatic embryogenesis of other legumes.
Activities of GL-TTP are fully in frame of our running, publicly founded research project and enables us to be in touch with experts in field of legume research and exchange of scientific information.
Characterisation of genetic diversity and structure analysis within pea (Pisum sativum L.) germplasm at AGRITEC Ltd. collection
Smýkal P.
1, Jarkovský J.
2, Corander J.
3 and Hýbl M.
11. Agritec Plant Research Ltd., Plant Biotechnology Department, Zemědělská 2520/16, CZ-787 01 Šumperk, Czech Republic.
2. Department of Mathematics and Statistics P.O. Box 68, FIN-00014, University of Helsinki, Finland.
3. Institute of Biostatistics and Analysis, Masaryk University, Kamenice 3, CZ625 00 Brno, Czech Republic
smykal@agritec.czA large collection, 1 244 accessions, of the Pisum genus is conserved and maintained at AGRITEC Ltd. Šumperk. To facilitate the management and increase efficiency of the use, a core collection is being currently developed. Also for breeding it is important to know the genetic basis of cultivars, especially to see if it has not become too narrow to render crops more vulnerable to diseases or pests.
To begin with, the 164 accessions representing Czech and Slovak varieties bred over last 50 years were selected for evaluation of genetic diversity in this study. They were characterised by 42 morphological descriptors in two growth seasons (2004 and 2005), and DNA of bulk made from 10 plants per accession was investigated by microsatellite SSR and retrotransposon-based markers. The emphasis was put on easily scorable co-dominant RBIP (Retrotransposon-Based Insertion Polymorphism) markers based on the PDR-1 Ty1-copia element and microsatellite SSR loci. Additionally, high copy Ty3-gypsy type elements, Ogre and Cyclop, were successfully applied in multiplex IRAP (Inter-Retrotransposon Amplified Polymorphism) format (Smýkal 2006).
In total, 12 selected SSRs, 25 RBIP and 2 IRAP markers produced altogether 56 scorable polymorphic data points for each accession. Cluster analysis of genetic distance by Ward method has yielded 6 to 7 clusters both for SSR and RBIP data. Euclidean distance clustering of morphological characters structured set into 5 to 7 clusters respectively. To enable integration and evaluation of all data, Bayesian method using BAPS software was applied. The most informative showed the consecutive calculation, first by morphological followed by molecular data. Based on morphology the best clustering by log of marginal likelihood was achieved for 3 or 6 clusters, with clear separation of fodder, dry seed and afila types of pea. The correspondence with Principle Component Analysis was performed. Clusters were further refined by DNA data into 12,17 a 4 sub-clusters demonstrating structuring of the investigated set. The most informative ordination method for molecular data was Multidimensional Scaling. Division into 3 distinct breeding periods (prior to 1960, 1960-75, 1975 till recent) has revealed decrease in genetic diversity over time. Analysis of 10 individual plants for given accessions demonstrated heterogeneity/ composed nature rather than residual heterozygosity. The possibility of genetic drift over the period of germplasm maintenance was found in several cases. All these results are used in further work aiming at core collection development.
Acknowledgements: This work was financially supported by the Ministry of Education of Czech Republic research project MSM 2678424601.
Smykal P. 2006. Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification. J Appl Genet. 47(3):221-30.
