Project number: |
3329
|
Title of the Project: |
Genome evolution and potato taxonomy studied by in situ hybridization and characterization of the Russian National Collection of Cultivated Potato Species by microsatellites and morphology |
Duration: |
Three years (01 February 2006 - 01 February 2009) +
|
Project coordinators: Drs. Gavrilenko Tatjana, Mironenko Nina, David M. Spooner
The main purposes of the project is to study genome evolution of polyploid potato species, taxonomy of cultivated potatoes and to better document and understand the diversity of Russian National potato collection stored at N.I. Vavilov All-Russian Research Institute of Plant Industry (VIR). To achieve these aims the following four tasks should be solved:
Task 1: Completion of electronic (“passport”) database of the representative subset of cultivated and wild potato species from VIR Collection.
Subtasks Task 1:
-To use GIS tools to conduct a biogeographic analysis of both the 300 living accessions and 150 accession of the original herbarium collections backing up this collection that are deposited at the WIR and LE herbaria.
-To photographically document herbarium (WIR and LE) collections including types of cultivated potato species and to construct a publicly accessible web portal of these data. link
- Transfer about 250 evaluated accessions into in vitro stocks.
- Cryopreservation of ~ 100 accessions of the experimental subset in VIR cryobank.
Task 2: Phenetic analysis of a subset of cultivated species and of accessions of their putative wild species progenitors.
Subtasks Task 2:
- To make a common database of biogeographic, ecological, ploidy, morphological, physiological data for the selected experimental subset.
- Phenetic morphology analysis of a subset of cultivated species and of accessions of their putative wild species progenitors.
- Test the taxonomical predictive utility of the accessions from the experimental subset of cultivated and closely related wild species through assessments of resistance to potato wart and resistance to golden nematode.
- To test the assumed ability of taxonomy to predict the presence of potato wart resistance genes in potato species and association of this resistance with ploidy, morphology, ecology and geography.
Task 3: Studying genetic diversity of a subset of cultivated potatoes and a subset of wild species, which are putative parents of the cultivated species, with microsatellite (SSR) analysis.
Subtasks Task 3:
-Studying genetic diversity of a subset of cultivated potatoes and related wild species with nuclear microsatellite analysis.
-To investigate species diversity and species boundaries of the cultivated potatoes with comparative plastid microsatellite analysis.
-To continue characterize genetic variability in cultivated potatoes and in closely related wild species with other DNA markers with known chromosome localization.
Task 4: Studying genome evolution of natural polyploids in section Petota and genome divergence in close outgroups using in situ hybridization techniques.
Subtasks Task 4:
- GISH and FISH analyses of wild potato polyploidy species from series Longipedicellata, Demissa, Acaulia, Conicibaccata.
-Clarification the relationships between the P, B and A – genomes of potato species and providing new fundamental knowledge about evolution of diploid and polyploid genomes of wild potato species.
-ISH (in situ hybridization) of closely related outgroups Etuberosum and Lycopersicum.
PUBLICATIONS of the project 3329:
1.Gavrilenko T., O. Antonova, A. Shuvalova, E. Krylova, N. Alpatyeva, D. Spooner , L. Novikova. Genetic diversity and origin of cultivated potatoes based on plastid microsatellite polymorphism. Genetic Resources and Crop Evolution (2013) 60:1997-2015.
"Acknowledgement to the original source of publication - Springer. The final publication is available at link.springer.com”.
Supplement 1
Supplement 2
Supplement 3
Supplement 4
Supplement 5
Supplement 6
Supplement 7
Supplement 8
Supplement 9
2. Khiutti A., Afanasenko O., Antonova O., Shuvalov O., Novikova L., Krylova E., Chalaya N., Mironenko N., Spooner D.M., T. Gavrilenko (2012) Characterization of resistance to Synchytrium endobioticum in cultivated potato accessions from the collection of Vavilov Institute of Plant Industry (VIR) collection. Plant Breeding, 131, 744-750.
3. Pendinen G., D. M. Spooner, J. Jiang, and T. Gavrilenko (2012) Genomic in situ hybridization (GISH) reveals both auto- and allopolyploid origins of different North and Central American hexaploid potato (Solanum section Petota) species. Genome. 55: 407–415.
4. Ovchinnikova A., E. Krylova, T. Gavrilenko, T. Smekalova, M. Zhuk, S. Knapp and D. M. Spooner (2011) Taxonomy of cultivated potatoes (Solanum section Petota: Solanaceae), Botanical Journal of the Linnean Society. 2011, 165, 107–155.
5. Gavrilenko T., O. Antonova, A. Ovchinnikova, L. Novikova, E. Krylova, N. Mironenko, G. Pendinen, A. Islamshina, N. Shvachko, S. Kiru, L. Kostina, O. Afanasenko, D. Spooner. A microsatellite and morphological assessment of the Russian National Potato Collection. Genetic Resources and Crop Evolution, 2010, vol.57, N 8: 1151-1164.
"Acknowledgement to the original source of publication - Springer. The final publication is available at link.springer.com”.
Supplement 1
Supplement 2
Supplement 3
Supplement 4
Supplement 5
Supplement 6
Supplement 7
Supplement 8
Supplement 9
6. Spooner D.M., T. Gavrilenko, S.H. Jansky, A. Ovchinnikova, E. Krylova, S. Knapp, R. Simon. Ecogeography of ploidy variation in cultivated potato (Solanum sect. Petota).
American Journal of Botany, 2010.vol. 97, N 12: 2049-2060.
7.Pendinen G., T. Gavrilenko, J. Jiang, D. M. Spooner (2008). Allopolyploid speciation of the tetraploid Mexican potato species revealed by genomic in situ hybridization. Genome, 51, 2008: 714-720.
8.Pendinen G., Gavrilenko T., J. Jiang, D. Spooner. GISH and FISH analyses of tetraploid species of the series Longipedicellata and Conicibaccata. Conference Abstract Book of the 17th Triennial Conference of the EAPR (the European Association for Potato Research), Brasov, Romania, July 06 to 10, 2008, p. 63 – 65.
9. Pendinen G., Gavrilenko T., J.Jiang, D.Spooner. Polyploid nature of Mexican wild potato species of the series Longipedicellata and Demissa. Abstract Book of the Symposium dedicated to memory of Russian cytogeneticist G.A. Levitskiy”. November, 26 – 27. 2008. St.-Petersburg, Russia, p. 80-82.
10. Krylova E.A., Ovchinnikova A.B., T.N. Smekalova, T.A.Gavrilenko, L.Y. Novikova. 2008. Analysis of morphological characters of cultivated and closely related wild potato species from the collection of N.I.Vavilov Institute of Plant Industry. Materials of All-Russian Conference “Fundamental and applied problems of botany in XXIst centaury”. Part 3, Petrozavodsk, September 21-27. 2008, p. 245-247.
11. Ovchinnikova A.B., Krylova E.A., T.N. Smekalova, L.Y. Novikova, S.D. Kiru, L.I. Kostina, T.A.Gavrilenko. 2008. Studying the diversity of cultivated and closely related wild potato species from the collection of VIR based on assessment of their morphological characters. 2nd All-Russian Scientific Conference “Biotechnology for conservation of plant diversity”. August 19-20, 2008, p.315-319
12. Ovchinnikova A.B., E.A. Krylova, V.I. Dorofeev, T.N. Smekalova, I.G. Chukhina, T.A.Gavrilenko. Type herbarium accessions of cultivated species for section Petota Dumort., genus Solanum L., from hebaria of N.I.Vavilov Institute of Plant Industry (WIR) and V.L.Komarov Botanical Institute (LE). 2009, V.94, 4, p.581-587
13. Gavrilenko, T., Antonova, O., Ovchinnikova, A., Novikova, L., Krylova, E., Mironenko, N., Pendinen, G., Smekalova, T., Islamshina, A., Shvachko, N., Kiru, S., Kostina, L., Afanasenko, O., Spooner, D. A Microsatellite and Morphological Assessment of the Russian National Potato Collection. Abstract of the Conference of Botanical Society of America, Snowbird, Utah, USA, 25 - 29 July, 2009.
14. Pendinen, G., Gavrilenko, T., Jiang, J., Spooner, D. Genomic In Situ Hybridization (GISH) Analysis of the Mexican Hexaploid Wild Potato Species. Abstract of the Conference of Botanical Society of America, Snowbird, Utah, USA, 25 - 29 July, 2009.