Comparative analysis of chromosome 2A molecular organization in diploid and hexaploid wheat


Diploid A genome wheat species harbor immense genetic variability which has been targeted and proven useful in wheat improvement. Development and deployment of sequence-based markers has opened avenues for comparative analysis, gene transfer and marker assisted selection (MAS) using high throughput cost effective genotyping techniques. Chromosome 2A of wheat is known to harbor several economically important genes. The present study aimed at identification of genic sequences corresponding to full length cDNAs and mining of SSRs and ISBPs from 2A draft sequence assembly of hexaploid wheat cv. Chinese Spring for marker development. In total, 1029 primer pairs including 478 gene derived, 501 SSRs and 50 ISBPs were amplified in diploid A genome species Triticum monococcum and T. boeoticum identifying 221 polymorphic loci. Out of these, 119 markers were mapped onto a pre-existing chromosome 2A genetic map consisting of 42 mapped markers. The enriched genetic map constituted 161 mapped markers with final map length of 549.6 cM. Further, 2A genetic map of T. monococcum was anchored to the physical map of 2A of cv. Chinese Spring which revealed several rearrangements between the two species. The present study generated a highly saturated genetic map of 2A and physical anchoring of genetically mapped markers revealed a complex genetic architecture of chromosome 2A that needs to be investigated further.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3


  1. 1.

    Hawkesford MJ, Araus JL, Park R, Calderini D, Miralles D, Shen T, Zhang J, Parry MAJ (2013) Prospects of doubling global wheat yields. Food Energy Secur 2:34–48

    Article  Google Scholar 

  2. 2.

    Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46

    Article  CAS  Google Scholar 

  3. 3.

    Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100

    Article  CAS  Google Scholar 

  4. 4.

    Akhunov E, Nicolet C, Dvorak J (2009) Single nucleotide polymorphism genotyping in polyploidy wheat with the illumina golden gate assay. Theor Appl Genet 119:507–517

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. 5.

    Kassa MT, You FM, Hiebert CW, Pozniak CJ, Fobert PR, Sharpe AG, Menzies JG, Humphreys DG, Harrison NR, Fellers JP, McCallum BD, McCartney CA (2017) Highly predictive SNP markers for efficient selection of the wheat leaf rust resistance gene Lr 16. BMC Plant Biol 17:45

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. 6.

    Wu J, Wang Q, Kang Z, Liu S, Li H, Mu J, Dai M, Han D, Zeng Q, Chen X (2017) Development and validation of KASP-SNP markers for QTL underlying resistance to stripe rust in common wheat cultivar P10057. Plant Dis 101:2079–2087

    Article  Google Scholar 

  7. 7.

    Rimbert H, Darrier B, Navarro J, Kitt J, Choulet F, Leveugle M, Duarte J, Rivière N, Eversole K, LeGouis J, Davassi A, Balfourier F, Le Paslier MC, Berard A, Brunel D, Feuillet C, Poncet C, Soudielle P, Paux E (2018) High throughput SNP discovery and genotyping in hexaploid wheat. PLoS ONE 13:e0186329

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Mourad AMI, Sallam A, Belamkar V, Wegulo S, Bowden R, Jin Y, Mahdy E, Bakheit B, El-Wafaa AA, Poland J, Baenziger PS (2018) Genome-wide association study for identification and validation of novel SNP markers for Sr6 stem rust resistance gene in bread wheat. Front Plant Sci 9:380

    Article  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Paux E, Sourdille P, Mackay I, Feuillet C (2012) Sequence-based marker development in wheat: advances and applications to breeding. Biotechnol Adv 30:1071–1088

    Article  CAS  Google Scholar 

  10. 10.

    Winfield MO, Wilkinson PA, Allen AM, Barker GL, Coghill JA, Burridge A, Hall A, Brenchley RC, D’Amore R, Hall N, Bevan MW, Richmond T, Gerhardt DJ, Jeddeloh JA, Edwards KJ (2012) Targeted re-sequencing of the allohexaploid wheat exome. Plant Biotechnol J 7:733–742

    Article  CAS  Google Scholar 

  11. 11.

    Akhunov E, Sehgal S, Liang H, Wang S, Akhunova AR, Kaur G, Li W, Forrest KL, See D, Šimková H, Ma Y, Hayden MJ, Luo M, Faris JD, Doležel J, Gill BS (2013) Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat. Plant Physiol 161:252–265

    Article  CAS  Google Scholar 

  12. 12.

    Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, International Wheat Genome Sequencing Consortium, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E (2014) Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol J 12:787–796

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. 13.

    International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345:e1251788

    Article  CAS  Google Scholar 

  14. 14.

    International Wheat Genome Sequencing Consortium (2018) Shifting the limits in wheat research and breeding through a fully annotated and anchored reference genome sequence. Science 361:eaar7191

    Article  CAS  Google Scholar 

  15. 15.

    Singh K, Ghai M, Garg M, Chhuneja P, Kaur P, Schnurbusch T, Keller B, Dhaliwal HS (2007) An integrated molecular linkage map of diploid wheat based on a Triticum boeoticum × T monococcum RIL population. Theor Appl Genet 115:301–312

    Article  CAS  Google Scholar 

  16. 16.

    Dubcovsky J, Luo MC, Zhong GY, Brandsteitter R, Desai A, Kilian A, Kleinhofs A, Dvorak J (1996) Genetic map of diploid wheat, Triticum monococcum L. and its comparison with maps of Hordeum vulgare L. Genetics 143:983–999

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Boyko EV, Gill KS, Mickelson-Young L, Nasuda S, Raupp WJ, Ziegle JN, Singh S, Hassawi DS, Fritz AK, Namuth D, Lapitan NLV, Gill BS (1999) A high-density genetic map of Aegilops tauschii, the D genome progenitor of bread wheat. Theor Appl Genet 99:16–26

    Article  CAS  Google Scholar 

  18. 18.

    Luo M, Deal KR, Yang Z, Dvorak J (2005) Comparative genetic maps reveal extreme crossover localization in the Aegilops speltoides chromosomes Theor. Appl Genet 111:1098–1106

    Article  CAS  Google Scholar 

  19. 19.

    Chhuneja P, Kaur S, Garg T, Ghai M, Kaur S, Prashar M, Bains NS, Goel RK, Keller B, Dhaliwal HS, Singh K (2008) Mapping of adult plant stripe rust resistance genes in diploid A genome wheat species and their transfer to bread wheat. Theor Appl Genet 116:313–324

    Article  CAS  Google Scholar 

  20. 20.

    Tiwari VK, Rawat N, Chhuneja P, Singh N, Aggarwal R, Randhawa GS, Dhaliwal HS, Keller B, Singh K (2009) Mapping of quantitative trait loci for grain iron and zinc concentration in A genome diploid wheat. J Heredity 100:771–776

    Article  CAS  Google Scholar 

  21. 21.

    Singh K, Chhuneja P, Singh I, Sharma SK, Garg T, Garg M, Keller B (2010) Molecular mapping of cereal cyst nematode resistance in Triticum monococcum L and its transfer to the genetic background of cultivated wheat. Euphytica 176:213–222

    Article  CAS  Google Scholar 

  22. 22.

    Chhuneja P, Kumar K, Stirnweis D, Hurni S, Keller B, Dhaliwal HS, Singh K (2012) Identification and mapping of two powdery mildew resistance genes in Triticum boeoticum L. Theor Appl Genet 124:1051–1058

    Article  CAS  Google Scholar 

  23. 23.

    Chhuneja P, Yadav B, Stirnweis D, Hurni S, Kaur S, Elkot AFA, Keller B, Wicker T, Sehgal S, Gill BS, Singh K (2015) Fine mapping of powdery mildew resistance genes PmTb7A1 and PmTb7A2 in Triticum boeoticum (Boiss) using the shotgun sequence assembly of chromosome 7AL. Theor Appl Genet 128:2099–2111

    Article  CAS  Google Scholar 

  24. 24.

    Elkot AFA, Chhuneja P, Kaur S, Saluja M, Keller B, Singh K (2015) Marker assisted transfer of two powdery mildew resistance genes PmTb7A1. PLoS ONE 10:e0128297

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. 25.

    Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA apacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018

    Article  CAS  Google Scholar 

  26. 26.

    Sears ER, Sears LMS (1978) The telocentric chromosomes of common wheat In S Ramanujams, ed. Proc 5th Int Wheat Genetics Symp, p 389–407 New Delhi, Indian Agricultural Research Institute

  27. 27.

    Kubaláková M, Vrána J, Číhalíková J, Šimková H, Doležel J (2002) Flow karyotyping and chromosome sorting in bread wheat (Triticum aestivum L.). Theor Appl Genet 104:1362–1372

    Article  Google Scholar 

  28. 28.

    Šimková H, Svensson JT, Condamine P, Hřibová E, Suchánková P, Bhat PR, Bartoš J, Šafář J, Close TJ, Doležel J (2008) Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley. BMC Genom 9:294

    Article  CAS  Google Scholar 

  29. 29.

    Wicker T, Matthews DE, Keller B (2002) TREP: a database for Triticeae repetitive elements. Trends Plant Sci 7:561–562

    Article  CAS  Google Scholar 

  30. 30.

    Paux E, Faure S, Choulet F, Roger D, Gauthier V, Martinant JP, Sourdille P, Balfourier F, Le Paslier MC, Chauveau A, Cakir M, Gandon B, Feuillet C (2010) Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat. Plant Biotechnol J 8:196–210

    Article  CAS  Google Scholar 

  31. 31.

    Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newberg LA (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  CAS  Google Scholar 

  32. 32.

    Lincoln SE, Daly MJ, Lander ES (1993) Constructing genetic maps with MAPMAKER/EXP version 30: a tutorial and reference manual Whitehead Inst Biomed Res Tech Rpt, 3rd edn Whitehead Institute for Biomedical Research, Cambridge, p 97

  33. 33.

    Haldane JBS (1919) The combination of linkage values and the calculation of distance between the loci of linked factors. J Genet 8:299–309

    Article  Google Scholar 

  34. 34.

    Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. 35.

    Krzywinski M, Schien JE, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetics for comparative genomics. Genome Res 19:1639–1645

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. 36.

    Kaur P, Yadav IS, Yadav B, Mahato A, Gupta OP, Doležel J, Singh NK, Khurana JP, Singh K (2019) In silico annotation of 458 genes identified from comparative analysis of Full length cDNAs and NextGen sequence of chromosome 2A of hexaploid wheat. J Plant Biochem Biotechnol 28:25–34

    Article  CAS  Google Scholar 

  37. 37.

    Roder MS, Korzun V, Wendehake K, Plaschke J, Tixier MHN, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023

    CAS  PubMed  PubMed Central  Google Scholar 

  38. 38.

    Johnson BL, Dhaliwal HS (1976) Reproductive isolation of Triticum boeoticum and Triticum urartu and the origin of the tetraploid wheat. Am J Bot 63:1088–1094

    Article  Google Scholar 

  39. 39.

    Doležel J, Vrána J, Šafář J, Bartoš J, Kubaláková M, Šimková H (2012) Chromosomes in the flow to simplify genome analysis. Funct Integr Genom 12:397–416

    Article  CAS  Google Scholar 

  40. 40.

    Akpinar BA, Lucas S, Budak H (2017) A large-scale chromosome-specific SNP discovery guideline. Funct Integr Genom 17(1):97–105

    Article  CAS  Google Scholar 

  41. 41.

    Dobrovolskaya O, Boeuf C, Salse J, Pont C, Sourdille P, Bernard M, Salina E (2011) Microsatellite mapping of Ae. speltoides and map-based comparative analysis of the S, G, and B genomes of Triticeae species. Theor Appl Genet 123:1145–1157

    Article  CAS  Google Scholar 

  42. 42.

    Molnár I, Vrána J, Burešová V, Cápal P, Farkas A, Darko E, Cseh A, Kubaláková M, Molnár-Láng M, Doležel J (2016) Dissecting the U, M, S and C genomes of wild relatives of bread wheat (Aegilops spp) into chromosomes and exploring their synteny with wheat. The Plant J 88:452–467

    Article  CAS  Google Scholar 

  43. 43.

    Lucas SJ, Salantur A, Yazar S, Budak H (2017) High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis. Funct Integr Genom 17(6):667–685

    Article  CAS  Google Scholar 

  44. 44.

    Sharma P, Bawa P, Yadav B, Kaur P, Jindal S, Yadav I, Kaur S, Singh K, Chhuneja P (2019) Physical mapping of an adult plant stripe rust resistance gene from Triticum monococcum. J Plant Biochem Biotech.

    Article  Google Scholar 

Download references


Contribution of all members of International Wheat Genome Sequencing Consortium (IWGSC) is highly acknowledged. Authors are grateful to the Director, School of Agricultural Biotechnology, PAU, Ludhiana, India for providing facilities. Funding provided by INSPIRE (Innovation in Scientific Pursuit for Inspired Research) Fellowship by Department of Science and Technology (DST), Government of India, India to Parampreet Kaur (Inspire fellow, IF 110226) for pursuing her Ph.D. is highly acknowledged. We thank Dr. Marie Kubaláková for assistance with chromosome flow sorting. Authors also thank other members of our research groups and collaborators for technical assistance and discussions.


The core funding for the work was provided by Department of Biotechnology, New Delhi, India under grant No. BT/IWGSC/03/TF/2008. J.V., H.Š and J.D. were supported by the ERDF project "Plants as a tool for sustainable global development" (No. CZ.02.1.01/0.0/0.0/16_019/0000827).

Author information




KS, PK and SJ designed and executed the experiments; JV, HŠ and JD flow sorted 2AS and 2AL telosomes and prepared DNA for sequencing; PK and SJ identified and developed gene based markers and SSR/ISBPs markers, respectively; PK, SJ, BY, ISY, AM did the bioinformatics work; PS, OPG provided technical assistance; SK and PC maintained the genetic material; JD, BSG, KM are IWGSC consortium members; PK and SJ wrote the manuscript; KS and PC conceived the study, provided genetic material, arranged funding and helped in manuscript writing. All authors have critically read and approved the final manuscript.

Corresponding author

Correspondence to Parampreet Kaur.

Ethics declarations

Conflicts of interest

The authors declare no competing financial interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the author.

Additional information

Publisher's Note

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

Sequence Submission: 513 genic sequences (partial sequences) of T. monococcum and T. boeoticum submitted to GenBank (KP240087-KP240600).

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Kaur, P., Jindal, S., Yadav, B. et al. Comparative analysis of chromosome 2A molecular organization in diploid and hexaploid wheat. Mol Biol Rep 47, 1991–2003 (2020).

Download citation


  • Genetic map
  • Chromosome 2A
  • Diploid wheat
  • Linkage map
  • Physical map
  • Anchoring