Genotyping of hexaploid wheat varieties from different Russian regions

We used molecular-genetic and molecular-cytology approaches to characterize the genomes of 20 varieties of wheat created in different regions of Russia. A molecular-genetic analysis was performed using 29 SSR-markers covering the entire genome, and 41 ISBP-markers localized on chromosome 5B. Analysis of genetic similarity based on the results of molecular genotyping showed that the winter wheat varieties form a common cluster, regardless of the origin or area of cultivation. This is primarily due to the fact that the varieties originating from the European part of Russia were used to establish winter wheat varieties for West Siberia. Comparative analysis of individual dendrograms constructed using 1–2 markers per chromosome, and with the involvement of a larger number of 5B-chromosome markers allowed us to identify varieties with rearrangements of this chromosome and to assess genetic diversity. We found that winter wheat Vassa and spring wheat Chelyaba 75 were clustered closely together. This is an indirect confirmation of the use of winter wheat varieties in the breeding to improve the productive potential of spring wheat. Molecular-cytology analysis by C-banding and fluorescence in situ hybridization (FISH) revealed various chromosomal rearrangements in 8 of 20 cultivars studied, including translocations from S. cereale, Ae. speltoides and Th. intermedium. Thus, a combination of the two approaches allowed us to better characterize genomes of wheat varieties of various origin.

1. Badaeva E.D., Badaev N.S., Gill B.S., Filatenko A. Intraspecific karyotype divergence in Triticum araraticum (Poaceae). Plant Syst. Evol. 1994;192:117-145. DOI 10.1007/BF00985912

2. Badaeva E.D., Dedkova O.S., Gay G., Pukhalskyi V.A., Zelenin A.V., Bernard S., Bernard M. Chromosomal rearrangements in wheat: their types and distribution. Genome. 2007;50:907-926. DOI 10.1139/G07-072

3. Badaeva E.D., Zoshchuk S.A., Paux E., Gay G., Zoshchuk N.V., Röger D., Zelenin A.V., Bernard M., Feuillet C. Fat element – a new marker for chromosome and genome analysis in the Triticeae. Chromosome Res. 2010;18:697-709. DOI 10.1007/s10577-010-9151-x

4. Bedbrook J.R., Jones J., O’Dell M., Thompson R.D., Flavell R.B. A molecular description of telomeric heterochromatin in Secale species. Cell. 1980;19:545-560. DOI 10.1016/0092-8674(80)90529-2

5. Bonman J.M., Babiker E.M., Cuesta-Marcos A., Esvelt-Klos K., Brown-Guedira G., Chao S., See D., Chen J., Akhunov E., Zhang J., Bockelman H.E., Gordon T.S. Genetic diversity among wheat accessions from the USDA National Smal Grains Collection. Crop Sci. 2015;55(3):1243-1253. DOI 10.2135/cropsci2014.09.0621

6. Davoyan R.O., Bebyakina I.V., Davoyan E.R., Bespalova L.A., Puzirnaya O.Y. Use of the synthetic form Triticum miguschovae for common wheat improvement. Proc. of the 3rd Intern. Conf. «Plant Genetics, Genomics, Bioinformatics and Biotechnology». PlantGen 2015. Novosibirsk, 17-21 June. 2015.

7. Devos K.M., Bryan G.J., Collins A.J., Gale M.D. Application of two microsatellite sequences in wheat storage proteins as molecular markers. Theor. Appl. Genet. 1995;90:247-252.

8. Felsenstein J. PHYLIP – Phylogeny Inference Package (Version 3.66). 2006. Available from: http://evolution.genetics.washington.edu/phylip.html.

9. Friebe B., Gill B.S. Chromosome banding and genome analysis in diploid and cultivated polyploid wheats. Methods in Genome analysis in Plants. Boca Raton: CRC Press, 1996:39–60.

10. Friebe B., Yiang J., Raupp W.J., McIntosh A., Gill B.S. Characterization of wheat- alien translocations conferring resistance to diseases and pests: current status. Euphytica. 1996;91:59-87. DOI 10.1007/BF00035277

11. Gill B.S., Friebe B., Endo T.R. Standard karyotype and nomenclature system for description of chromosome bands and structural aberrations in wheat (Triticum aestivum). Genome. 1991;34,:830-839. DOI 10.1139/g91-128

12. Huang X.Q., Börner A., Röder M.S., Ganal M.W. Assessing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers. Theor. Appl. Genet. 2002;105:699-707. DOI 10.1007/s00122-002-0959-4

13. Katalog rayonirovannykh sortov selskokhozyaystvennykh kultur v Rossiyskoy Federatsii. T. 1. [Catalog of zoned varieties agricultural crops in the Russian Federation. V.1. Moscow, Russian State Commission for variety testing of agricultural crops under the Ministry of Agriculture of the Russian Federation, 1992.

14. Khlestkina E.K., Röder M.S., Efremova T.T., Börner A., Shumny V.K. The genetic diversity of old and modern Siberian varieties of common spring wheat as determined by microsatellite markers. Plant Breed. 2004;123:122-127. DOI 10.1046/j.1439- 0523.2003.00934.x

15. Komuro S., Endo R., Shikata K., Kato A. Genomic and chromosomal distribution patterns of various repeated DNA sequences in wheat revealed by a fluorescence in situ hybridization procedure. Genome. 2013;56:131-137. DOI 10.1139/gen-2013-0003

16. Lukaszewski A.J. Frequency of 1RS.1AL and 1RS.1BL translocations in United States wheats. Crop Sci. 1990;30:1151-1153. DOI 10.2135/cropsci1990.0011183X003000050041x

17. Nei M., Li W.H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl Acad. Sci. USA. 1979; 76:5269-5273.

18. Odintsova I.G., Agafonova N.A., Boguslavskiy R.L. Introgressivnye linii myagkoy pshenitsy s ustoychivostyu k buroy rzhavchine, peredannoy ot Aegilops speltoides. Trudy po prikladnoy botanike, genetike i selektsii [Introgression lines of wheat with resistance to leaf rust transferred from Aegilops speltoides. Bulletin of Applied Botany, of Genetics and Plant Breeding]. Leningrad, VIR, 1991;142:106-110.

19. Paux E., Faure S., Choulet F., Röger D., Gauthier V., Martinant J.P., Sourdille P., Balfourier F., Le Paslier M-C., Chauveau A., Cakir M., Gandon B., Feuillet C. Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat. Plant Biotechnol. 2010;8:196-210. DOI 10.1111/j.1467-7652.2009.00477.x

20. Paux E., Röger D., Badaeva E., Gay G., Bernard M., Sourdille P., Feuillet C. Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J. 2006;48:463-474. DOI 10.1111/j.1365-313X.2006.02891.x

21. Paux E., Sourdille P., Mackay I., Feuillet C. Sequence-based marker development in wheat: Advances and applications to breeding. Biotechnol. Adv. 2012;30:1071-1088. DOI 10.1016/j.biotechadv. 2011.09.015

22. Plaschke J., Ganal M.W., Röder M.S. Detection of genetic diversity in closely related bread wheat using microsatellite markers. Theor. Appl. Genet. 1995;91:1001-1007. DOI 10.1007/BF00223912

23. Rayburn A.L., Gill B.S. Isolation of a D-genome specific repeated DNA sequence from Aegilops squarrosa. Plant. Mol. Biol. Rep. 1986;4:102-109. DOI 10.1007/BF02732107

24. Röder M.S., Korzun V., Wendehake K., Plaschke J., Tixier M.H., Leroy P., Ganal M.W. A microsatellite map of wheat. Genetics. 1998; 149:2007-2023.

25. Rutc R.I. Istoriya razvitiya selektsionnoy raboty i sorta selskokhozyaystvennykh kultur Sibirskogo nauchno-issledovatelskogo instituta selskogo khozyaystva [The history of breeding and crop varieties of the Siberian Research Institute of Agriculture]. Novosibirsk, Jupiter, 2004.

26. Salem Kh.F.M., Mattar M.Z. Genetic diversity in old and modern Egyptian bread wheat (Triticum aestivum L.) varieties revealed by simple sequence repeats Egypt. J. Genet. Cytol. 2014;43:143-156.

27. Salina E.A., Adonina I.G.,·Badaeva E.D., Kroupin P.Yu., Stasyuk A.I., Leonova I.N., Shishkina A.A., Divashuk M.G.,·Starikova E.V., Khuat T.M.L., Syukov V.V., Karlov G.I. A Thinopyrum intermedium chromosome in bread wheat cultivars as a source of genes conferring resistance to fungal diseases. Euphytica. 2015;204(1):91-101. DOI 10.1007/s10681-014-1344-5

28. Salina E., Adonina I., Vatolina T., Kurata N. A comparative analysis of the composition and organization of two subtelomeric repeat families in Aegilops speltoides Tausch and related species. Genetica. 2004;122:227-237. DOI 10.1007/s10709-004-5602-7

29. Salina E.A., Leonova I.N., Efremova T.T., Röder M.S. Wheat genome structure: translocations during the course of polyploidization. Funct. Integr. Genomics. 2006b;6:71-80. DOI 10.1007/s10142-005-0001-4

30. Salina E.A., Lim Y.K., Badaeva E.D., Shcherban A.B., Adonina I.G., Amosova A.V., Samatadze T.E., Vatolina T.Yu., Zoshchuk S.A., Leitch A.A. Phylogenetic reconstruction of Aegilops section Sitopsis and the evolution of tandem repeats in the diploids and derived wheat polyploids. Genome. 2006a;49:1023-1035. DOI 10.1139/G06-050

31. Schneider A., Linc G., Molnar-Lang M. Fluorescence in situ hybridization polymorphism using two repetitive DNA clones in different cultivars of wheat. Plant Breeding. 2003;122:396-400. DOI 10.1046/j.1439-0523.2003.00891.x

32. Schneider A., Molnar I., Molnar-Lang M. Utilisation of Aegilops (goatgrass) species to widen the genetic diversity of cultivated wheat. Euphytica. 2008;163:1-19. DOI 10.1007/s10681-007-9624-y

33. Sergeeva E.M., Afonnikov D.A., Koltunova M.K., Gusev V.D., Miroshnichenko L.A., Vrána J., Kubaláková M., Poncet C., Sourdille P., Feuillet C., Doležel J., Salina E.A. Common wheat chromosome 5B composition analysis using low-coverage 454 sequencing the plant genome. Plant Genome. 2014;7(2):1-16. DOI 10.3835/ 10.0031

34. Shamanin V.P. Obshchaya selektsiya i sortovedenie polevykh kul’tur: uchebnoe posobie [General selection and creation of varieties of field crops: a manual]. Omsk: Omsk State Agrarian University Publ., 2006.

35. Sibikeev S.N., Voronina S.A., Krupnov V.A. Genetic control for resistance to leaf rust in wheat-Agropyron lines: Agro 139 and Agro 58. Theor. Appl. Genet. 1995;90(5):618-620. DOI 10.1007/BF00222124

36. Sinigovec M.E. Transfer of resistance to rust from wheat grass to the wheat by the addition and replacement of chromosomes. Genetika = Genetics (Moscow). 1976;12(9):13-20.

37. Sokal R.R., Rholf F.J. Biometry. Ed. W.H. Freeman. N.Y., 1995.

38. Würschum T., Langer S.M., Longin C.F.H., Korzun V., Akhunov E., Ebmeyer E., Schachschneider R., Schacht J., Kazman E., Reif J.C. Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers. Theor. Appl. Genet. 2013;126:1477-1486. DOI 10.1007/s00122-013-2065-1

39. Zikin V.A. Gibridizatsiya – osnova rekombinatsionnoy selektsii rasteniy: metod. rekomendatsii [Hybridization – the Basis of Recombination Breeding of Plants: Method. Recommendations]. Ufa, BNIISKh Publ., 2001.