Skip to main content

Genetic diversity analysis using DArTseq and SNP markers in populations of Aegilops species from Azerbaijan

Abstract

Despite a large number of Aegilops L. species and their diversity in Azerbaijan, a majority of this genetic material has not been characterized at molecular levels. The current study has implemented DArTseq technology to evaluate genetic diversity among 150 accessions of different Aegilops species from Azerbaijan. A total of 61,574 SilicoDArTseq and 30,433 SNP markers were used to assess genetic diversity in Aegilops species. Genetic diversity was measured using Shannon’s genetic diversity index, which was equal to 0.852. Dendrograms were built to establish the relationship among Aegilops species. Both the DArTseq and SNP markers could completely segregate the U genome species from those with D genome with high confidence and allowed assigning most species to separate subclusters. The pattern of clustering within the Aegilops tauschii Coss. to certain extent was related to their geographical regions. Genetic structure among the 150 Aegilops accessions was similar with the cluster analysis. Two groups were identified in the studied population, which were exactly corresponded to two clusters in the dendrogram. Principal coordinate analysis confirmed sub-grouping obtained by cluster analysis. The first two principal coordinates explained 82.34% of the total variation. The study reported a sufficient level of genetic diversity of Aegilops from different eco-geographical regions of Azerbaijan, which can be very useful for their conservation and management, as well as for profitable diversifying the gene pool of hexaploid wheat.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

References

  1. Alnaddaf LM, Moualla MY, Haider N (2012) The genetic relationships among Aegilops L. and Triticum L. species. Asian J Agr Sci 4(5):352–367

    Google Scholar 

  2. Aminov N, Aliyeva A (2012) The genetic interactions between Aegilops L. and Triticum L. genera. Elm, Baku

    Google Scholar 

  3. Amri A, Nawar M, Shehadeh A, Piggin J, Maxted N, Gill B (2016) Ex situ and in situ conservation efforts for Aegilops and wild Triticum species. In: Bonjean AP, Angus WJ (eds) The world wheat book: a history of wheat breeding, vol 3. Lavoisier, Paris, pp 1–48

    Google Scholar 

  4. Badaeva ED, Amosova AV, Muravenko OV, Samatadze TE, Chikida NN, Zelenin AV, Friebe B, Gill BS (2002) Genome differentiation in Aegilops. 3. Evolution of the D-genome cluster. Plant Syst Evol 231:163–190

    CAS  Google Scholar 

  5. Baloch FS, Alsaleh A, Shahid MQ, Çiftçi V, de Miera LES, Aasim M, Nadeem MA, Aktaş H, Özkan H, Hatipoğlu R (2017) A whole genome DArTseq and SNP analysis for genetic diversity assessment in durum wheat from central fertile crescent. PLoS ONE 12(1):e0167821

    PubMed  PubMed Central  Google Scholar 

  6. Baum BR, Edwards T, Johnson DA (2009) Phylogenetic relationships among diploid Aegilops species inferred from 5S rDNA units. Mol Phylogenet Evol 53(1):34–44

    CAS  PubMed  Google Scholar 

  7. Bordbar F, Rahiminejad MR, Saeidi H, Blattner FR (2011) Phylogeny and genetic diversity of D-genome species of Aegilops and Triticum (Triticeae, Poaceae) from Iran based on microsatellites, ITS, and trnL-F. Plant Syst Evol 291(1–2):117–131

    Google Scholar 

  8. Caldwell K, Dvorak J, Lagudah ES, Akhunov E, Luo M-C, Wolters P, Powell W (2004) Sequence polymorphism in polyploid wheat and their D genome diploid ancestor. Genetics 167:941–947

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Castillo A, Ramírez MC, Martín AC, Kilian A, Martín A, Atienza SG (2013) High-throughput genotyping of wheat-barley amphiploids utilizing diversity array technology (DArT). BMC Plant Biol 13(1):87–97

    PubMed  PubMed Central  Google Scholar 

  10. Chhuneja P, Dhaliwal HS, Bains NS, Singh K (2006) Aegilops kotschyi and Aegilops tauschii as sources for higher levels of grain iron and zinc. Plant Breed 125(5):529–531

    CAS  Google Scholar 

  11. Cui F, Fan X, Zhao C, Zhang W, Chen M, Ji J, Li J (2014) A novel genetic map of wheat: utility for mapping QTL for yield under different nitrogen treatments. BMC Genet 15(1):57

    PubMed  PubMed Central  Google Scholar 

  12. Dvorak J, Luo MC, Yang ZL (1998) Genetic evidence on the origin of Triticum aestivum L. In: Damania AB, Valkoun J, Willcox G, Qualset CO (eds) The origins of agriculture and crop domestication, proceedings of Harlan symposium. ICARDA, Aleppo, pp 235–251

  13. Earl DA, vonHoldt BM (2014) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4(2):359–361. https://doi.org/10.1007/s12686-011-9548-7

    Article  Google Scholar 

  14. Farooq S, Farooq EA (2001) Co-existence of salt and drought tolerance in Triticeae. Hereditas 135:205–210

    CAS  PubMed  Google Scholar 

  15. Fu YB, Somers DJ (2009) Genome-wide reduction of genetic diversity in wheat breeding. Crop Sci 49(1):161–168

    Google Scholar 

  16. Gandhi HT, Vales MI, Watson CJ, Mallory-Smith CA, Mori N, Rehman M, Zemetra RS, Riera-Lizarazu O (2005) Chloroplast and nuclear microsatellite analysis of Aegilops cylindrica. Theor Appl Genet 111(3):561–572

    CAS  PubMed  Google Scholar 

  17. Gill BS, Friebe B, Raupp WJ, Wilson DL, Cox TS, Sears RG, Brown-Guedira GL, Fritz AK (2006) Wheat genetics resource center: the first 25 years. Adv Agron 89:73–136

    Google Scholar 

  18. Gong HY, Liu AH, Wang JB (2006) Genomic evolutionary changes in Aegilops allopolyploids revealed by ISSR markers. Acta Phytotax Sin 44:286–295

    Google Scholar 

  19. Goryunova SV, Kochieva EZ, Chikida NN, Pukhalskyi VA (2004) Phylogenetic relationships and intraspecific variation of D-Genome Aegilops L. as revealed by RAPD analysis. Russ J Genet 40:515–523

    CAS  Google Scholar 

  20. Grzebelus D, Iorizzo M, Senalik D, Ellison S, Cavagnaro P, Macko-Podgorni A, Heller-Uszynska K, Kilian A, Nothnagel T, Allender C, Simon PW (2014) Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L) genome, as revealed by Diversity Arrays Technology (DArT) markers. Mol Breed 33(3):625–637

    CAS  PubMed  Google Scholar 

  21. Hammer K (1980) Vorarbeiten zur monographischen Darstellung von Wildpflanzensortimenten: Aegilops L. Kulturpflanze 28:33–180

    Google Scholar 

  22. Hammer K, Laghetti G (2005) Genetic erosion-examples from Italy 1, 2. Genet Resour Crop Evol 52(5):629–634

    Google Scholar 

  23. Huang S, Sirikhachornkit A, Su X, Faris J, Gill B, Haselkorn R, Gornicki P (2002) Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proc Nat Acad Sci 99(12):8133–8138

    CAS  PubMed  Google Scholar 

  24. 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

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Kilian B, Özkan H, Deusch O, Effgen S, Brandolini A, Kohl J, Martin W, Salamini F (2006) Independent wheat B and G genome origins in outcrossing Aegilops progenitor haplotypes. Mol Biol Evol 24(1):217–227

    PubMed  Google Scholar 

  26. Kilian B, Mammen K, Millet E, Sharma R, Graner A, Salamini F, Hammer K, Özkan H (2011) Aegilops. In: Kole C (ed) Wild crop relatives: genomic and breeding resources: cereals. Springer, Berlin, pp 1–76

    Google Scholar 

  27. Lelley T, Stachel M, Grausgruber H, Vollmann J (2000) Analysis of relationships between Aegilops tauschii and the D-genome of wheat utilizing microsatellites. Genome 43:661–668

    CAS  PubMed  Google Scholar 

  28. Luikart G, England PR, Tallmon D, Jordan S, Taberlet P (2003) The power and promise of population genomics: from genotyping to genome typing. Nat Rev Genet 4(12):981

    CAS  PubMed  Google Scholar 

  29. Naghavi MR, Aghaei MJ, Taleei AR, Omidi M, Hassani ME (2008) Genetic diversity of hexaploid wheat and three Aegilops species using microsatellite markers. https://ses.library.usyd.edu.au/bitstream/2123/3231/1/P028.pdf

  30. Okuno K, Ebana K, Noov B, Yoshida H (1998) Genetic diversity of Central Asian and north Caucasian Aegilops species as revealed by RAPD markers. Genet Resour Crop Evol 45(4):389–394

    Google Scholar 

  31. Pacheco A, Alvarado G, Rodriguez F, Burgueno J (2016) BIO-R (Biodiversity analysis with R for Windows) Version 1.0.1, hdl:11529/10820, CIMMYT Research Data and Software Repository Network, V6

  32. Pester TA, Ward SM, Fenwick AL, Westra P, Nissen SJ (2003) Genetic diversity of jointed goatgrass (Aegilops cylindrica) determined with RAPD and AFLP markers. Weed Sci 51:287–293

    CAS  Google Scholar 

  33. Pestsova E, Korzun V, Goncharov NP, Hammer K, Ganal MW, Röder MS (2000) Microsatellite analysis of Aegilops tauschii germplasm. Theor Appl Genet 101(1):100–106

    CAS  Google Scholar 

  34. Petersen G, Seberg O, Yde M, Berthelsen K (2006) Phylogenetic relationships of Triticum and Aegilops and evidence for the origin of the A, B, and D genomes of common wheat (Triticum aestivum). Mol Phylogenet Evol 39(1):70–82

    CAS  PubMed  Google Scholar 

  35. Pour-Aboughadareh A, Ahmadi J, Mehrabi AA, Etminan A, Moghaddam M (2018) Insight into the genetic variability analysis and relationships among some Aegilops and Triticum species, as genome progenitors of bread wheat, using SCoT markers. Plant Biosyst 152:694–703

    Google Scholar 

  36. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genet 155(2):945–959

    CAS  Google Scholar 

  37. Queen RA, Gribbon BM, James C, Jack P, Flavell AJ (2004) Retrotransposon-based molecular markers for linkage and genetic diversity analysis in wheat. Mol Gen Genom 271:91–97

    CAS  Google Scholar 

  38. Raman H, Dalton-Morgan J, Diffey S, Raman R, Alamery S, Edwards D, Batley J (2014) SNP markers-based map construction and genome-wide linkage analysis in Brassica napus. Plant Biotechnol J 12(7):851–860

    CAS  PubMed  Google Scholar 

  39. Ren J, Sun D, Chen L, You FM, Wang J, Peng Y, Nevo E, Sun D, Luo MC, Peng J (2013) Genetic diversity revealed by single nucleotide polymorphism markers in a worldwide germplasm collection of durum wheat. Int J Mol Sci 14(4):7061–7088

    CAS  PubMed  PubMed Central  Google Scholar 

  40. 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 Proc 5(Suppl 7):P54

    PubMed Central  Google Scholar 

  41. Sears ER (1956) The transfer of leaf rust resistance from Aegilops umbellulata to wheat. Brookhaven Symp Biol 9:1–22

    Google Scholar 

  42. Sharma M, Nagavardhini A, Thudi M, Ghosh R, Pande S, Varshney RK (2014) Development of DArT markers and assessment of diversity in Fusarium oxysporum f. sp. ciceris, wilt pathogen of chickpea (Cicer arietinum L.). BMC Genom 15(1):454

    Google Scholar 

  43. Singh RP, Hodson DP, Jin Y, Huerta-Espino J, Kinyua MG, Wanyera R, Njau P, Ward RW (2006) Current status, likely migration and strategies to mitigate the threat to wheat production from race Ug99 (TTKS) of stem rust pathogen. CAB Rev Perspect Agric Vet Sci Nutr Nat Resour 1(54):1–3

    CAS  Google Scholar 

  44. Sliai AM, Amer SA (2013) Molecular relationships among different Serbian Aegilops species (Poaceae). Nat Resour 4(01):76–81

    Google Scholar 

  45. Sohail Q, Shehzad T, Kilian A, Eltayeb AE, Tanaka H, Tsujimoto H (2012) Development of diversity array technology (DArT) markers for assessment of population structure and diversity in Aegilops tauschii. Breed Sci 62(1):38–45

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Trethowan RM, van Ginkel M (2009) Synthetic wheat—an emerging genetic resource. Wheat Sci Trade 29:369–385

    Google Scholar 

  47. Vikram P, Franco J, Burgueño-Ferreira J, Li H, Sehgal D, Saint Pierre C, Ortiz C, Sneller C, Tattaris M, Guzman C, Sansaloni CP (2016) Unlocking the genetic diversity of Creole wheats. Sci Rep 6:23092

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Wang J, Luo MC, Chen Z, You FM, Wei Y, Zheng Y, Dvorak J (2013) Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D-genome genetic diversity and pinpoint the geographic origin of hexaploid wheat. New Phytol 198(3):925–937

    CAS  PubMed  Google Scholar 

  49. Watanabe N, Mastui K, Furuta Y (1994) Uniformity of the alpha-amylase isozymes of Aegilops cylindrica introduced into North America. In: Wang RRC, Jensen KB, Jaussi C (eds) Comparison with ancestral Eurasian accessions. Second Int Wheat Symp, Logan, pp 215–218

    Google Scholar 

  50. Wright S (1978) Evolution and the genetics of populations, volume 3: experimental results and evolutionary deductions. University of Chicago Press, Chicago

    Google Scholar 

  51. Yamane K, Kawahara T (2005) Intra-and interspecific phylogenetic relationships among diploid TriticumAegilops species (Poaceae) based on base-pair substitutions, indels, and microsatellites in chloroplast noncoding sequences. Am J Bot 92(11):1887–1898

    CAS  PubMed  Google Scholar 

  52. Yu H, Deng Z, Xiang C, Tian J (2014) Analysis of diversity and linkage disequilibrium mapping of agronomic traits on B-genome of wheat. J Genom 2:20–30

    Google Scholar 

  53. Ziems LA, Hickey LT, Hunt CH, Mace ES, Platz GJ, Franckowiak JD, Jordan DR (2014) Association mapping of resistance to Puccinia hordei in Australian barley breeding germplasm. Theor Appl Genet 127(5):1199–1212

    CAS  PubMed  Google Scholar 

Download references

Author information

Affiliations

Authors

Corresponding authors

Correspondence to Mehraj Abbasov or Carolina Paola Sansaloni.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 137 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Abbasov, M., Sansaloni, C.P., Burgueño, J. et al. Genetic diversity analysis using DArTseq and SNP markers in populations of Aegilops species from Azerbaijan. Genet Resour Crop Evol 67, 281–291 (2020). https://doi.org/10.1007/s10722-019-00866-7

Download citation

Keywords

  • Aegilops
  • DArTseq
  • SNP markers
  • SilicoDArTseq
  • Genetic diversity
  • Species