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Agronomy Science Baner text

Vol. 72 No. 4 (2017)

Articles

Modern genotyping technologies used to analyze the variability of collections at the Polish National Center for Plant Genetic Resources at Radzikow (PBAI – NRI)

DOI: https://doi.org/10.24326/as.2017.4.7
Submitted: December 30, 2018
Published: 2017-12-19

Abstract

Plant biodiversity protection is the main objective of the Polish National Center for Plant Genetic Resources (NCPGR), Plant Breeding and Acclimatization Institute – National Research Institute. Over 83,000 accessions are deposited in the long-term repository, acquired during domestic and foreign expeditions and exchanges. Their proper description is important from the point of view of conservation and breeding. Molecular researches are carried out to determinate the species, inter-population diversity, and genetic background of economic traits. This aim is achieved with various methods, and the newest are based on sequencing (NGS). Examples of objects that have been included in molecular research are oats (species identification within the 2,500 collection), a collection of 4,000 barley landraces from all over the world (genetic determinants of useful traits), wild wheat collections and wild relatives (source of disease resistance).

References

  1. Boczkowska M., Tarczyk E., 2013. Genetic diversity among Polish landraces of common oat (Avena sativa L.). Genet. Resour. Crop. Ev. 60 (7), 2157–2169.
  2. Boczkowska M., Nowosielski J., Nowosielska D., Podyma W., 2014. Assessing genetic diversity in 23 early Polish oat cultivars based on molecular and morphological studies. Genet. Resour. Crop. Ev. 61(5), 927–941.
  3. Boczkowska M., Harasimiuk M., Onyśk A., 2015. Studies on genetic variation within old Polish cultivars of common oat. Cereal Res. Commun. 43 (1), 12–21.
  4. Boczkowska M., Łapiński B., Kordulasińska I., Fu-Dostatny D., Czembor J.H., 2016. Promoting the Use of Common Oat Genetic Resources through Diversity Analysis and Core Collection Con-struction. PLoS ONE 11(12): e0167855.
  5. Boczkowska M., Onyśk A., 2016. Unused genetic resources: a case study of Polish common oat germplasm. Ann. Appl. Biol. 169, 155–165.
  6. Boczkowska M., Żebrowski J., Nowosielski J., Kordulasińska I., Nowosielska D., 2017. Environ-mentally-related genotypic, phenotypic and metabolic diversity of oat (Avena sativa L.) landraces based on 67 Polish accessions. Genet. Resour. Crop. Ev. 246 (64), https://doi.org/10.1007/s10722-017-0555-8.
  7. Budak H., Shearman R.C., Parmaksiz I., Gaussoin R.E., Riordan T.P., Dweikat I., 2004. Molecular characterization of Buffalograss germplasm using sequence-related amplified polymorphism markers. Theor. Appl. Genet .108 (2), 328–334.
  8. Buermans H.P.J., den Dunnen J.T., 2014. Next generation sequencing technology: Advances and applications. BBA Mol. Basis Dis. 1842, 1932–1941.
  9. Chen S.S., Chen G.Y., Chen H., Wei Y.M., Li W., Liu Y.X., Liu D.C., Lan X.J., Zheng Y.L., 2012. Mapping stripe rust resistance gene YrSph derived from Tritium sphaerococcum Perc. with SSR, SRAP, and TRAP markers. Euphytica 185 (1), 19–26.
  10. Courtois B., Audebert A., Dardou A., Roques S., Ghneim-Herrera T., Droc G., Frouin J., Rouan L., Gozé E., Kilian A, Ahmadi N., Dingkuhn M., 2013. Genome- wide association mapping of root traits in a Japonica rice panel. PLoS ONE 8 (11), 1–18.
  11. Dai X.J., Yang Y.Z., Zhou L., Ou L.J., Liang M.Z., Li W.J., Kang G.P., Chen L.B., 2012. Analysis of indica- and japonica-specific markers of Oryza sativa and their applications. Plant Syst. Evol. 298 (2), 287–296.
  12. Dean R.E., Dahlberg J.A., Hopkins M.S., Mitchell S.E., Kresovich S., 1998. Genetic Redundancy and Diversity among ‘Orange’ Accessions in the U.S. National Sorghum Collection as Assessed with Simple Sequence Repeat (SSR) Markers. Crop Sci. 4 (39), 1215–1221.
  13. Dumlupinar Z., Brown R., Campbell R., Jellen E.N., Anderson J., Bonman J.M., Carson M., Chao S., Obert D., Jackson E., 2016. The art of attrition: development of robust oat microsatellites. Plant Breed. 135 (3), 323–334.
  14. Fazekas A.J., Kuzmina M.L., Newmaster S.G., Hollingsworth P.M., 2012. DNA Barcoding Methods for Land Plants. DNA Barcodes: Methods and Protocols. Kress W. J., Erikson D. L. edt, Methods Mol Biol 858 Springer Science + Business Media 858, 223–252.
  15. Food and Agriculture Organization of the United Nations, 2010. The Second Report on the State of the World’s plant genetic resources for food and agriculture Commission on Genetic Resources for Food and Agriculture. FAO, Rome.
  16. Hollingsworth P. M., Graham S. W., Little D. P., 2011. Choosing and Using a Plant DNA Barcode. PLoS ONE 6(5): e19254.
  17. Hou Y.C., Yan Z.H., Wei Y.M., Zheng Y.L., 2005. Genetic diversity in barley from west China based on RAPD and ISSR analysis. Barley Genet. Newsletter 35, 9–22.
  18. Jaccoud D., Peng K., Feinstein D., Kilian A., 2001. Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res. 29(4), E25.
  19. Joshi S.P., Gupta V.S., Aggarwal R.K., Ranjekar P.K., Brar D.S., 2000. Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor. Appl. Genet. 100 (8), 1311–1320.
  20. Li G., Quiros C. F., 2001. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor. Appl. Genet. 103, 455–461.
  21. López-Sesé A.I., Staub J., Katzir N., Gómez-Guillamón M.L., 2002. Estimation of between and within accession variation in selected Spanish melon germplasm using RAPD and SSR markers to assess strategies for large collection evaluation. Euphytica 127 (1), 41–51.
  22. Malepszy, S. red., 2001. Biotechnologia Roślin. Wydawnictwo Naukowe PAN, Warszawa.
  23. McCouch S.R., McNally K.L., Wang W., Hamilton R.S., 2012. Genomics of gene banks: a case study in rice. Am. J. Bot. 99(2), 407–423.
  24. Michelmore R.W., Paran I., Kesseli R.V., 1991. Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc. Natl. Acad. Sci. USA 88 (21), 9828–9832.
  25. Onyśk A., Boczkowska M., 2017. M13-tailed simple sequence repeat (SSR) markers in studies of genetic diversity and population structure of common oat germplasm. In: S. Gasparis (ed.), Oat Methods in Molecular Biology 1536. Humana Press, New York, 159–168.
  26. Pachota K., Niedziela A., Orłowska R., Bednarek P., 2016. Nowoczesne metody genotypowania DArT i GBS w hodowli gatunków roślin użytkowych. Biul. IHAR 279, 3–18.
  27. Pietrusińska A., 2010. Wykorzystanie markerów molekularnych do wprowadzania genów odporno-ści na rdzę brunatną (Puccinia recondita f. sp. tritici) i mączniaka prawdziwego (Blumeria graminis f. sp. tritici) do pszenicy ozimej. Biul. IHAR 256, 31–54.
  28. Pietrusińska A., Czembor J.H., 2015. Piramidyzacja genów – powszechne narzędzie używane w programach hodowlanych. Gene pyramiding – a tool commonly used in breeding programs breeding programs. Biul. IHAR 278, 3–16.
  29. Pietrusińska A., Czembor J.H., Czembor P.Cz., 2011. Pyramiding of two resistance genes for leaf rust and powdery mildew resistance in common wheat. Cereal Res. Commun. 39 (4), 577–588.
  30. Pietrusińska A., Czembor P. Cz., 2007. Ocena wybranych metod izolacji DNA pod względem ich przydatności w hodowli pszenicy. Biul. IHAR 236, 41–48.
  31. Pietrusińska A., Czembor P.Cz., Czembor J.H., 2013. Lr39 + Pm21, as a new effective combination of resistance genes for leaf rust and powdery mildew. Czech J. Genet. Plant 49, 109–115.
  32. Poczai P., Varga I., Laos M., Cseh A., Bell N., Valkonen J.P.T., Hyvönen J., 2013. Advances in plant gene-targeted and functional markers: a review. Plant Methods 9(6). DOI: 10.1186/1746-4811-9-6.
  33. Podyma W., Boczkowska M., Wolko B., Fu-Dostatny D., 2016. Morphological, isoenzymatic and ISSRs-based description of diversity of eight sand oat (Avena strigosa Schreb.) landraces. Genet. Resour. Crop. Ev. 64 (7), 1661–1674.
  34. Powell W., Machray G.C., Provan J., 1996. Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1(7), 215–222.
  35. Quail M.A., Smith M., Coupland P., Otto T.D., Harris S.R., Connor T.R., Bertoni A., Swerdlow H.P., Gu Y., 2012. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 341(13).
  36. Ribaut J.M., Hoisington D., 1998. Marker-assisted selection: new tools and strategies. Trends Plant Sci. 3 (6), 236–239.
  37. Roldan-Ruiz I., Dendauw J., Van Bockstaele E., Depicker A., De Loose M., 2000. AFLP markers reveal high polymirphic rates in ryegrasses (Lolium spp.). Mol. Breed. 6, 125–134.
  38. Sanger F., Nicklen S., Coulson A.R., 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74(12), 5463–5467.
  39. Sansaloni C., Petroli C., Jaccoud D., Carling J., Detering F., Grattapaglia D., Kilian A., 2011. Diversity Arrays Technology (DArT) and next-generation sequencing combined: genome- wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus. BMC Proceedings 5 (Suppl. 7): P54.
  40. Tanhuanpää P., Kalendar R., Schulman A.H., Kiviharju E., 2008. The first doubled haploid linkage map for cultivated oat. Genome 51(8), 560–569.
  41. Tanksley S.D., McCouch S.R., 1997. Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277(5329), 1063–1066.
  42. Uysal H., Fu Y.B., Kurt O., Peterson G.W., Diederichsen A., Kusters P., 2010. Genetic diversity of cultivated flax (Linum usitatissimum L.) and its wild progenitor pale flax (Linum bienne Mill.) as revealed by ISSR markers. Genet. Resour. Crop. Ev. 57 (7), 1109–1119.
  43. Von Cruz M., Kilian A., Dierig D.A., 2013. Development of DArT marker platforms and genetic diversity assessment of the U.S. Collection of the new oilseed crop lesquerella and related species. PLoS ONE 8 (5), e64062.
  44. Westman A.L., Kresovich S., 1999. Simple sequence repeat (SSR)-based marker variation in Brassica nigra genebank accessions and weed populations. Euphytica 109(2), 85–92.
  45. Wolko B., Bartkowiak-Broda I., 1997. Metody diagnostyki molekularnej w hodowli roślin. Materiały z I Krajowej Konferencji „Hodowla Roślin”, Poznań, 19–20 listopada 1997, 389–402.
  46. Xie X.M., Zhou F., Zhang X.Q., Zhang J.M., 2009. Genetic variability and relationship between MT-1 elephant grass and closely related cultivars assessed by SRAP markers. J. Genet. 88(3), 281–290.

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