3 Biotech

, 10:48 | Cite as

Whole-genome diversity, population structure and linkage disequilibrium analysis of globally diverse wheat genotypes using genotyping-by-sequencing DArTseq platform

  • Mojgan Mahboubi
  • Rahim Mehrabi
  • Amir Mohammad Naji
  • Reza TalebiEmail author
Original Article


In this study, 129 wheat genotypes from globally diverse origins were genotyped using DArTseq (SilicoDArT and SNP) markers. After filtering markers for quality-filtering, 14,270 SilicoDArTs and 6484 SNPs were retained and used for genetic diversity, population structure and linkage disequilibrium analyses. The highest number of SilicoDArT and SNP markers mapped on genome A and B compared to genome D. In both marker types, polymorphism information content (PIC) values ranged from 0.1 to 0.5, while > 0.80% of SilicoDArTs and > 0.44% SNPs showed PIC value more than median (0.25%). Un-weighted Neighbor Joining cluster analysis and Bayesian-based model population structure grouped wheat genotypes into three and four clusters, respectively. Principal component analysis and discriminant analysis of principal component results showed highly match with cluster and population structure analysis. Linkage disequilibrium (LD) was more extensive in both marker types, while graphical display of LD decay for both marker types showed that LD declined in the region close to 15 kbp, where r2-values corresponded to r2 = 0.16. Overall, our genetic diversity analysis showed high level of variation in studied wheat genotypes, even though there was no relationship between wheat grouping and origins. This might be attributed to admixture level that occurred during long-term natural selection of wheat genotypes in different parts of the world. Highly diverse wheat genotypes used in this study may possess unique genes and are useful sources in breeding programs to improve grain yield and quality.


Wheat Genetic diversity Population structure Linkage disequilibrium SilicoDArT SNP 



The study was conducted as a part of PhD thesis of first author and supported by Islamic Azad University, Sanandaj Branch, Iran. We are grateful to Iranian Cereal Research Institute for providing wheat genotypes used in this study.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

13205_2019_2014_MOESM1_ESM.xlsx (18 kb)
Supplementary file1 (XLSX 18 kb)
13205_2019_2014_MOESM2_ESM.xlsx (400 kb)
Supplementary file2 (XLSX 400 kb)
13205_2019_2014_MOESM3_ESM.xlsx (344 kb)
Supplementary file3 (XLSX 344 kb)
13205_2019_2014_MOESM4_ESM.xlsx (344 kb)
Supplementary file4 (XLSX 344 kb)


  1. Akbari M, Wenzl P, Caig V, Carling J, Xia L, Yang S et al (2006) Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113:1409–1420PubMedCrossRefGoogle Scholar
  2. Alam M, Neal J, O’Connor K, Kilian A, Topp B (2018) Ultra-high-throughput DArTseq-based silicoDArT and SNP markers for genomic studies in macadamia. PLoS ONE 13(8):e0203465PubMedPubMedCentralCrossRefGoogle Scholar
  3. Alipour H, Bihamta MR, Mohammadi V, Peyghambari SA, Bai G, Zhang G (2017) Genotyping-by-sequencing (GBS) revealed molecular genetic diversity of Iranian wheat landraces and cultivars. Front Plant Sci 8:1293PubMedPubMedCentralCrossRefGoogle Scholar
  4. Balfourier F, Bouchet S, Robert S, De Oliveira R, Rimbert H, Kitt J, Choulet F, International Wheat Genome Sequencing Consortium, BreedWheat Consortium, Paux E (2019) Worldwide phylogeography and history of wheat genetic diversity. Sci Adv 5:eaav0536PubMedPubMedCentralCrossRefGoogle Scholar
  5. Baloch FS, Alsaleh A, Shahid MQ, Çiftçi V, Sáenz de Miera L, Aasim M, Nadeem MA, Aktas S, Ozkan H, Hatipoglu R (2017) A whole genome DArTseq and SNP analysis for genetic diversity assessment in Durum wheat from central fertile crescent. PLoS ONE 12(1):e0167821–3486PubMedPubMedCentralCrossRefGoogle Scholar
  6. Bellucci A, Torp AM, Bruun S, Magid J, Andersen SB, Rasmussen SK (2015) Association mapping in Scandinavian winter wheat for yield, plant height, and traits important for second-generation bioethanol production. Front Plant Sci 6:1046PubMedPubMedCentralCrossRefGoogle Scholar
  7. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635CrossRefGoogle Scholar
  8. Chen X, Min D, Yasir TA, Hu Y-G (2012) Genetic diversity, population structure and linkage disequilibrium in elite Chinese winter wheat investigated with SSR markers. PLoS ONE 7(9):e44510–2830PubMedPubMedCentralCrossRefGoogle Scholar
  9. Christiansen MJ, Andersen SB, Ortiz R (2002) Diversity changes in an intensively bred wheat germplasm during the 20th century. Mol Breed 9:1–11CrossRefGoogle Scholar
  10. Cox TS (1998) Deepening the wheat gene pool. J Crop Prod 1:1–25CrossRefGoogle Scholar
  11. Cruz VMV, Kilian A, Dierig DA (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:e64062PubMedPubMedCentralCrossRefGoogle Scholar
  12. de Vicente MC, Guzmán FA, Engels J, Rao VR (2005) Genetic characterization and its use in decision making for the conservation of crop germplasm. The Role of Biotechnology, Villa Gualino, Turin, Italy, 5–7 March 2005Google Scholar
  13. Dvorak J, Zhang HK (1992) Reconstruction of the phylogeny of the genus Triticum from variation in repeated nucleotide sequences. Theor Appl Genet 84:419–429PubMedCrossRefGoogle Scholar
  14. Earl DA, Vonholdt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4(2):359–361CrossRefGoogle Scholar
  15. Edet OU, Gorafi YSA, Cho SW, Kishii M, Tsujimoto H (2018) Novel molecular marker-assisted strategy for production of wheat–Leymus mollis chromosome addition lines. Sci Rep 8:16117PubMedPubMedCentralCrossRefGoogle Scholar
  16. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620CrossRefGoogle Scholar
  17. Fayaz F, Aghaee M, Talebi R, Azadi A (2019) Genetic diversity and molecular characterization of Iranian durum wheat landraces (Triticum turgidum durum (Desf.) Husn.) using DArT markers. Biochem Genet 57(1):98–116PubMedCrossRefGoogle Scholar
  18. Ghaffari P, Talebi R, Keshavarz F (2014) Genetic diversity and geographical differentiation of Iranian landrace, cultivars and exotic chickpea lines as revealed by morphological and microsatellite markers. Physiol Mol Biol Plants 20(2):225–233PubMedPubMedCentralCrossRefGoogle Scholar
  19. Golicz AA, Batley J, Edwards D (2016) Towards plant pangenomics. Plant Biotechnol J 14:1099–1105PubMedCrossRefGoogle Scholar
  20. Govindaraj M, Vetriventhan M, Srinivasan M (2015) Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet Res Int 2015:431487PubMedPubMedCentralGoogle Scholar
  21. Greger L (2015) How wheat came to Britain. Science 347:6225Google Scholar
  22. Hammer Ø, Harper DAT, Ryan PD (2001) Paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9–18Google Scholar
  23. Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24(11): 1403–1405CrossRefGoogle Scholar
  24. Kabbaj H, Sall AT, Al-Abdallat A, Geleta M, Amri A, Filali-Maltouf A, Belkadi B, Ortiz R, Bassi FM (2017) Genetic diversity within a global panel of durum wheat (Triticum durum) landraces and modern germplasm reveals the history of allele’s exchange. Front Plant Sci 8:1277PubMedPubMedCentralCrossRefGoogle Scholar
  25. Kilian B, Özkan H, Walther A, Kohl J, Dagan T, Salamini F, Martin W (2007) Molecular diversity at 18 loci in 321 wild and 92 domesticate lines reveal no reduction of nucleotide diversity during Triticum monococcum (einkorn) domestication: implications for the origin of agriculture. Mol Biol Evol 24:2657–2668PubMedCrossRefPubMedCentralGoogle Scholar
  26. Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H, Caig V, Heller-Uszynsk K, Jaccoud D, Hopper C, Aschenbrenner-Kilian M, Evers M, Peng K, Cayla C, Hok P, Uszynski G (2012) Diversity arrays technology: a generic genome profiling technology on open platforms. Methods Mol Biol 888:67–89PubMedCrossRefPubMedCentralGoogle Scholar
  27. Laido G, Marone D, Russo MA, Colecchia SA, Mastrangelo AM, De Vita P, Papa R (2014) Linkage disequilibrium and genome-wide association mapping in tetraploid wheat (Triticum turgidum L.). PLoS ONE 9(4):e95211PubMedPubMedCentralCrossRefGoogle Scholar
  28. Lassner MW, Peterson P, Yoder JI (1989) Simultaneous amplification of multiple DNA fragments by polymerase chain reaction in the analysis of transgenic plants and their progeny. Plant Mol Biol Rep 7:116–128CrossRefGoogle Scholar
  29. Lipka AE, Tian F, Wang Q, Peiffer J, Li M, Bradbury PJ, Gore MA, Buckler ES, Zhang Z (2012) GAPIT: genome association and prediction integrated tool. Bioinformatics 28:2397–2399PubMedCrossRefGoogle Scholar
  30. Lopes MS, El-Basyoni I, Baenziger PS, Singh S, Royo C, Ozbek K, Aktas H, Ozer E, Ozdemir F, Manickavelu A, Ban T, Vikram P (2015) Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change. J Exp Bot 66(12):3477–3486PubMedCrossRefGoogle Scholar
  31. Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M, Jakobsen KS, Wulff BBH, Steuernagel B, Mayer KFX, Olsen O-A, Rogers J, el Dole J, Pozniak C, Eversole K, Feuillet C, Gill B, Friebe B, Lukaszewski AJ, Sourdille P (2014) Ancient hybridizations among the ancestral genomes of bread wheat. Science 345:1250092PubMedCrossRefGoogle Scholar
  32. Marzario S, Logozzo G, David JL, Zeuli PS, Gioia T (2018) Molecular genotyping (SSR) and agronomic phenotyping for utilization of durum wheat (Triticum durum Desf.) ex-situ collection from southern Italy: a combined approach including pedigreed varieties. Genes 9:465PubMedCentralCrossRefPubMedGoogle Scholar
  33. Mehrabi R, Makhdoomi A, Jafar-Aghaie M (2015) Identification of new sources of resistance to septoria tritici blotch caused by Zymoseptoria tritici. J Phytopathol 163:84–90CrossRefGoogle Scholar
  34. Mogga M, Sibiya J, Shimelis H, Lamo J, Yao N (2018) Diversity analysis and genome-wide association studies of grain shape and eating quality traits in rice (Oryza sativa L.) using DArT markers. PLoS One 14(2):e0212078CrossRefGoogle Scholar
  35. Monostori I, Szira F, Tondelli A, Arendas T, Gierczik K, Cattivelli L, Galiba G, Vagujfalvi A (2017) Genome-wide association study and genetic diversity analysis on nitrogen use efficiency in a Central European winter wheat (Triticum aestivum L.) collection. PLoS ONE 12(12):e0189265PubMedPubMedCentralCrossRefGoogle Scholar
  36. Morgante M, Salamini F (2003) From plant genomics to breeding practice. Curr Opin Biotechnol 14:214–219PubMedCrossRefGoogle Scholar
  37. Mwadzingeni L, Shimelis H, Rees DJG, Tsilo TJ (2017) Genome-wide association analysis of agronomic traits in wheat under drought-stressed and non-stressed conditions. PLoS ONE 12(2):e0171692PubMedPubMedCentralCrossRefGoogle Scholar
  38. Ndjiondjop MN, Semagn K, Gouda AC, Kpeki SB, Dro Tia D, Sow M, Goungoulou A, Sie M, Perrier X, Ghesquiere A, Warburton ML (2017) Genetic variation and population structure of Oryza glaberrima and development of a mini-core collection using DArTseq. Front Plant Sci 8:1748PubMedPubMedCentralCrossRefGoogle Scholar
  39. Nielsen NH, Backes G, Stougaard J, Andersen SU, Jahoor A (2014) Genetic diversity and population structure analysis of European hexaploid bread wheat (Triticum aestivum L.) varieties. PLoS ONE 9:e94000PubMedPubMedCentralCrossRefGoogle Scholar
  40. Novoselovic D, Bentley AR, Šimek R, Dvojkovic K, Sorrells ME, Gosman N, Horsnell R, Drezner G, Šatovic Z (2016) Characterizing Croatian wheat germplasm diversity and structure in a European context by DArT markers. Front Plant Sci 7:184PubMedPubMedCentralCrossRefGoogle Scholar
  41. Omari S, Kamenir Y, Benichou JIC, Pariente S, Sela H, Perl-Treves R (2018) Landraces of snake melon, an ancient Middle Eastern crop, reveal extensive morphological and DNA diversity for potential genetic improvement. BMC Genet 19:34PubMedPubMedCentralCrossRefGoogle Scholar
  42. Ovenden B, Milgate A, Wade LJ, Rebetzke GJ, Holland JB (2017) Genome-wide associations for water-soluble carbohydrate concentration and relative maturity in wheat using SNP and DArT marker arrays. G3: Genes Genomes Genet 7(8):2821–2830CrossRefGoogle Scholar
  43. Pailles Y, Ho S, Pires IS, Tester M, Negrão S, Schmöckel SM (2017) Genetic diversity and population structure of two tomato species from the Galapagos Islands. Front Plant Sci 8:138PubMedPubMedCentralCrossRefGoogle Scholar
  44. Perrier X, Jacquemoud-Collet JP (2006) DARwin software.
  45. Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Science Publishers, Enfield, pp 43–76Google Scholar
  46. R Core Team (2014) R: a language and environment for statistical computing. R Core Team, ViennaGoogle Scholar
  47. Ray DK, Mueller ND, West PC, Foley JA (2013) Yield trends are insufficient to double global crop production by 2050. PLoS ONE 8:e66428PubMedPubMedCentralCrossRefGoogle Scholar
  48. Ren R, Ray R, Li P, Xu J, Zhang M, Liu G, Yao X, Kilian A, Yang X (2015) Construction of a high-density DArTseq SNP-based genetic map and identification of genomic regions with segregation distortion in a genetic population derived from a cross between feral and cultivated-type watermelon. Mol Genet Genom 290(2):1457–1470CrossRefGoogle Scholar
  49. Rubenstein DK, Heisey P, Shoemaker R, Sullivan J, Frisvold G (2005) Crop genetic resources: an economic appraisal. United States Department of Agriculture (USDA). Economic Information Bulletin No. 2. (
  50. Rufo R, Alvaro F, Royo C, Soriano JM (2019) From landraces to improved cultivars: assessment of genetic diversity and population structure of Mediterranean wheat using SNP markers. PLoS ONE 14(7):e0219867PubMedPubMedCentralCrossRefGoogle Scholar
  51. Schuster I, Vieira ESN, da Silva GC, de Assis FF, Marchioro VS (2009) Genetic variability in Brazilian wheat cultivars assessed by microsatellite markers. Genet Mol Biol 32:557–563PubMedPubMedCentralCrossRefGoogle Scholar
  52. Smale M, Reynolds MP, Warburton M, Skovmand B, Trethowan R, Singh RP, Ortiz-Monasterio I, Crossa J (2002) Dimensions of diversity in modernspring bread wheat in developing countries from 1965. Crop Sci 42:1766–1779CrossRefGoogle Scholar
  53. Sohail Q, Manickavelu A, Ban T (2015) Genetic diversity analysis of Afghan wheat landraces (Triticum aestivum) using DArT markers. Genet Resour Crop Evol 62(8):1147–1157CrossRefGoogle Scholar
  54. Soleimani VD, Baum BR, Johnson DA (2002) AFLP and pedigree-based genetic diversity estimates in modern cultivars of durum wheat [Triticum turgidum L. ssp. Durum (Desf.) Husn.]. Theor Appl Genet 104:350–357PubMedCrossRefGoogle Scholar
  55. Soriano JM, Villegas D, Aranzana MJ, Garcıa del MoralL F, Royo C (2016) Genetic structure of modern durum wheat cultivars and Mediterranean landraces matches with their agronomic performance. PLoS ONE 11(8):e0160983PubMedPubMedCentralCrossRefGoogle Scholar
  56. Talebi R (2008) An alternative strategy in rapid DNA extraction protocol for high throughput RAPD analysis in chickpea and its wild related species. J Appl Biol Sci 2(3):121–124Google Scholar
  57. Talebi R, Fayyaz F (2012) Quantitative evaluation of genetic diversity in Iranian modern cultivars of wheat (Triticum aestivum L.) using morphological and amplified fragment length polymorphism (AFLP) markers. Biharean Biol 6:14–18Google Scholar
  58. Van de Wouw M, van Hintum T, Kik C, van Treuren R, Visser B (2010) Genetic diversity trends in twentieth century crop cultivars: a meta-analysis. Theor Appl Genet 120:1241–1252PubMedPubMedCentralCrossRefGoogle Scholar
  59. Van Raden PM (2008) Efficient methods to compute genomic predictions. J Dairy Sci 91(4):414–4423Google Scholar
  60. Vikram P, Franco J, Burgueño-Ferreira J, Li H, Sehgal D, Pierre CS, Ortiz C, Sneller C, Tattaris M, Guzman C, Sansaloni CP, Ellis M, Fuentes-Davila G, Reynolds M, Sonder K, Singh P, Payne T, Wenzl P, Sharma A, Bains NS, Singh GP, Crossa J, Singh S (2016) Unlocking the genetic diversity of Creole wheats. Sci Rep 6:23092PubMedPubMedCentralCrossRefGoogle Scholar
  61. Zaitoun SYA, Jamous RM, Shtaya MJ, Mallah OB, Eid IS, Ali-Shtayeh MS (2018) Characterizing Palestinian snake melon (Cucumis melo var.flexuosus) germplasm diversity and structure using SNP and DArTseq markers. BMC Plant Biol 18:246PubMedPubMedCentralCrossRefGoogle Scholar
  62. Zeven AC (1998) Landraces: a review of definitions and classification. Euphytica 104:127–139CrossRefGoogle Scholar
  63. Zeven AC (2000) Traditional maintenance breeding of landraces: 1. Data by crop. Euphytica 116:65–85CrossRefGoogle Scholar
  64. Zhang LY, Liu DC, Guo XL, Yang WL, Sun JZ, Wang DW, Sourdille P, Zhang AM (2011a) Investigation of genetic diversity and population structure of common wheat cultivars in northern China using DArT markers. BMC Genet 12:42PubMedPubMedCentralCrossRefGoogle Scholar
  65. Zhang Z, Belcram H, Gornicki P, Charles M, Just J, Huneau C, Magdelenat G, Couloux A, Samain S, Gill BS, Rasmussen JB, Barbe V, Faris JD, Chalhoub B (2011b) Duplication and partitioning in evolution and function of homoeologous Q; loci governing domestication characters in polyploid wheat. Proc Natl Acad Sci USA 108:18737–18742PubMedCrossRefGoogle Scholar
  66. Zohary D, Harlan JH, Vardi A (1969) The wild diploid progenitors of wheat and their breeding value. Euphytica 18:58–65Google Scholar

Copyright information

© King Abdulaziz City for Science and Technology 2020

Authors and Affiliations

  1. 1.College of Agriculture, Sanandaj BranchIslamic Azad UniversitySanandajIran
  2. 2.Department of Biotechnology, College of AgricultureIsfahan University of TechnologyIsfahanIran
  3. 3.Department of Agronomy and Plant Breeding, Faculty of AgricultureShahed UniversityTehranIran

Personalised recommendations