Molecular karyotyping of Siberian wild rye (Elymus sibiricus L.) with oligonucleotide fluorescence in situ hybridization (FISH) probes

Autoři: Jihong Xie aff001;  Yan Zhao aff002;  Linqing Yu aff001;  Ruijuan Liu aff003;  Quanwen Dou aff003
Působiště autorů: Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China aff001;  College of Grassland, Resource and Environmental Science, Inner Mongolia Agricultural University, Hohhot, China aff002;  Key Laboratory of Crop Molecular Breeding, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China aff003;  Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, China aff004
Vyšlo v časopise: PLoS ONE 15(1)
Kategorie: Research Article


Siberian wild rye (Elymus sibiricus L.), an allotetraploid species, is a potentially high-quality perennial forage crop native to temperate regions. We used fluorescently conjugated oligonucleotides, representing ten repetitive sequences, including 6 microsatellite repeats, two satellite repeats, and two ribosomal DNAs, to characterize E. sibiricus chromosomes, using sequential fluorescence in situ hybridization and genomic in situ hybridization assays. Our results showed that microsatellite repeats (AAG)10 or (AGG)10, satellite repeats pAs1 and pSc119.2, and ribosomal 5S rDNA and 45S rDNA are specific markers for unique chromosomes. A referable karyotype ideogram was suggested, by further polymorphism screening, across different E. sibiricus cultivars with a probe mixture of (AAG)10, Oligo-pAs1, and Oligo-pSc119.2. Chromosomal polymorphisms vary between different genomes and between different individual chromosomes. In particular, two distinct forms of chromosome E in H genome were identified in intra- and inter-populations. Here, the significance of these results, for E. sibiricus genome research and breeding, and novel approaches to improve fluorescence in situ hybridization-based karyotyping are discussed.

Klíčová slova:

Fluorescent in situ hybridization – Genome complexity – Chromosome pairs – Karyotypes – Oligonucleotides – Population genetics – Karyotyping – DNA probes


1. Baum BR, Edwards T, Ponomareva E, Johnson DA. Are the Great Plains wildrye (Elymus canadensis) and the Siberian wildrye (Elymus sibiricus) conspecific? A study based on the nuclear 5S rDNA sequences. Botany-Botanique. 2012;90(6): 407–21. doi: 10.1139/b2012-013

2. Klebesadel LJ. Siberian Wildrye (Elymus sibiricus L.): Agronomic characteristics of a potentially valuable forage and conservation grass for the north. Agron J. 1969;61(6): 855–859. doi: 10.2134/agronj1969.00021962006100060008x

3. Mao P, Han J, Wu X. Effects of harvest time on seed yield of Siberian wildrye. Acta Agrestia Sinica. 2003;11: 33–37.

4. Lei YT, Zhao YY, Yu F, Li Y, Dou QW. Development and characterization of 53 polymorphic genomic-SSR markers in Siberian wildrye (Elymus sibiricus L.). Conserv Genet Resour. 2014;6(4): 861–864. doi: 10.1007/s12686-014-0225-5

5. Zhou Q, Luo D, Ma L, Xie W, Wang Y, Wang Y, et al. Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing. Sci Rep. 2016;6: 20549. doi: 10.1038/srep20549 26853106; PubMed Central PMCID: PMC4744933.

6. Ma X, Chen SY, Zhang XQ, Bai SQ, Zhang CB. Assessment of worldwide genetic diversity of Siberian Wild Rye (Elymus sibiricus L.) germplasm based on gliadin analysis. Molecules. 2012;17(4): 4424–4434. doi: 10.3390/molecules17044424 22499189; PubMed Central PMCID: PMC6268020.

7. Xie W, Zhang J, Zhao X, Zhang Z, Wang Y. Transcriptome profiling of Elymus sibiricus, an important forage grass in Qinghai-Tibet plateau, reveals novel insights into candidate genes that potentially connected to seed shattering. BMC Plant Biol. 2017;17(1): 78. doi: 10.1186/s12870-017-1026-2 28431567; PubMed Central PMCID: PMC5399857.

8. Xie WG, Zhao XH, Zhang JQ, Wang YR, Liu WX. Assessment of genetic diversity of Siberian wild rye (Elymus sibiricus L.) germplasms with variation of seed shattering and implication for future genetic improvement. Biochem Syst Ecol. 2015;58: 211–218. doi: 10.1016/j.bse.2014.12.006

9. Zhao X, Zhang J, Zhang Z, Wang Y, Xie W. Hybrid identification and genetic variation of Elymus sibiricus hybrid populations using EST-SSR markers. Hereditas. 2017;154(1): 15. doi: 10.1186/s41065-017-0053-1 29255380; PubMed Central PMCID: PMC5727920.

10. Danilova TV, Friebe B, Gill BS. Development of a wheat single gene FISH map for analyzing homoeologous relationship and chromosomal rearrangements within the Triticeae. Theor Appl Genet. 2014;127(3): 715–730. doi: 10.1007/s00122-013-2253-z 24408375

11. Said M, Hřibová E, Danilova TV, Karafiátová M, Čížková J, Friebe B, e tal. The Agropyron cristatum karyotype, chromosome structure and cross-genome homoeology as revealed by fluorescence in situ hybridization with tandem repeats and wheat single-gene probes. Theor Appl Genet. 2018;131: 2213–2227. doi: 10.1007/s00122-018-3148-9 30069594

12. Said M, Kubaláková M, Karafiátová M, Molnár I, Doležel J, Vrána J. Dissecting the complex genome of crested wheatgrass by chromosome flow sorting. Plant Genome. 2019;12:180096. doi: 10.3835/plantgenome2018.12.0096 31290923

13. Dewey DR. The genomic system of classification as a guide to intergeneric hybridization in the perennial Triticeae. Stadler Gen. 1984;35(1): 202. doi: 10.2307/1221077

14. Dou QW, Zhang TL, Tsujimoto H. Physical mapping of repetitive sequences and genome analysis in six Elymus species by in situ hybridization. J Syst Evol. 2011;49(4): 347–352. doi: 10.1111/j.1759-6831.2011.00138.x

15. Cuadrado A, Carmona A, Jouve N. Chromosomal characterization of the three subgenomes in the polyploids of Hordeum murinum L.: New insight into the evolution of this complex. PLoS ONE. 2013;8(12). doi: 10.1371/journal.pone.0081385 24349062; PubMed Central PMCID: PMC3862567.

16. Dou Q, Liu R, Yu F. Chromosomal organization of repetitive DNAs in Hordeum bogdanii and H. brevisubulatum (Poaceae). Comp Cytogenet. 2016;10(4): 465–81. doi: 10.3897/CompCytogen.v10i4.9666 28123672; PubMed Central PMCID: PMC5240503.

17. Danilova TV, Friebe B, Gill BS. Single-copy gene fluorescence in situ hybridization and genome analysis: Acc-2 loci mark evolutionary chromosomal rearrangements in wheat. Chromosoma. 2012;121(6): 597–611. doi: 10.1007/s00412-012-0384-7 23052335.

18. Tang Z, Yang Z, Fu S. Oligonucleotides replacing the roles of repetitive sequences pAs1, pSc119.2, pTa-535, pTa71, CCS1, and pAWRC.1 for FISH analysis. J Appl Genet. 2014;55(3): 313–8. doi: 10.1007/s13353-014-0215-z 24782110.

19. Rayburn AL, Gill BS. Isolation of a D-genome specific repeated DNA sequence from Aegilops squarrosa. Plant Mol Biol Rep. 1986;4(2): 102–109. doi: 10.1007/BF02732107

20. Bedbrook JR, Jones J, O’Dell M, Thompson RD, Flavell RB. A molecular description of telomeric heterochromatin in Secale species. Cell. 1980;19(2): 545–560. doi: 10.1016/0092-8674(80)90529-2 6244112

21. Kato A. Air drying method using nitrous oxide for chromosome counting in maize. Biotech Histochem. 1999;74(3): 160–166. doi: 10.3109/10520299909047968 10416789

22. Giorgi D, Farina A, Grosso V, Gennaro A, Ceoloni C, Lucretti S. 2013. FISHIS: Fluorescence In situ hybridization in suspension and chromosome flow sorting made easy. PLoS ONE 8: e57994. doi: 10.1371/journal.pone.0057994 23469124

23. Ma X, Zhang XQ, Zhou YH, Bai SQ, Liu W. Assessing genetic diversity of Elymus sibiricus (Poaceae: Triticeae) populations from Qinghai-Tibet Plateau by ISSR markers. Biochem System Ecol. 2008;36(7): 514–22. doi: 10.1016/j.bse.2008.03.003

24. Yan JJ, Bai SQ, Zhang XQ, You MH, Zhang CB, Li DX, et al. Genetic diversity of wild Elymus sibiricus L. germplasm from Qinghai-Tibetan Plateau in China detected by SSR markers (In Chinese with English abstract). Acta Prataculturae Sinica. 2010;19(1): 173–183. doi: 10.3724/SP.J.1142.2010.40491

25. Zhang J, Xie W, Wang Y, Zhao X. Potential of start codon targeted (SCoT) markers to estimate genetic diversity and relationships among Chinese Elymus sibiricus accessions. Molecules. 2015;20(4): 5987–6001. doi: 10.3390/molecules20045987 25853316; PubMed Central PMCID: PMC6272172.

26. Badaeva ED, Badaev NS, Gill BS, Filatenko AA. Intraspecific karyotype divergence in Triticum araraticum (Poaceae). Plant System Evol. 1994;192(1/2): 117–145. doi: 10.1007/bf00985912

27. Badaeva ED, Jiang J, Gill BS. Detection of intergenomic translocations with centromeric and noncentromeric breakpoints in Triticum araraticum: mechanism of origin and adaptive significance. Genome, 1995;38(5): 976–981. doi: 10.1139/g95-128 18470221

28. Kato A, Lamb JC, Birchler JA. Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. P Nat Acad Sci USA. 2004;101(37): 13554–9. doi: 10.1073/pnas.0403659101 15342909; PubMed Central PMCID: PMC518793.

29. Wicker T, Taudien S, Houben A, Keller B, Graner A, Platzer M, et al. A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley. Plant J. 2009;59(5): 712–22. doi: 10.1111/j.1365-313X.2009.03911.x 19453446.

30. Jiang J. Fluorescence in situ hybridization in plants: recent developments and future applications. Chromosome Res. 2019; doi: 10.1007/s10577-019-09607-z 30852707

Článek vyšel v časopise


2020 Číslo 1
Nejčtenější tento týden