The projects "Sequencing the Aegilops tauschii genome" and "TRTech-PGR: Improvement of the genome sequence assembly of Chinese Spring wheat" release sequences, pseudomolecules, and associated information (Luo et al. 2013, 2017; Zhu et al. 2020) and unannotated wheat pseudomolecules as a service to the research community. The Ae. tauschii genomic resources have now been published and are provided with no restriction. The Triticum aestivum bread wheat ‘Chinese Spring’ sequence v2.1 release of unannotated wheat pseudomolecules does not constitute a scientific publication. Permission of the principal investigator should be obtained before publishing any analyses of the wheat pseudomolecules.

This website and its associated databases and services are for academic, non-commercial use only. Neither project has liability for the use of results, data, or information, which have been provided at this site.

Sequence and physical map data

The Ae. tauschii pseudomolecules plus the unassigned scaffolds have been deposited into GenBank as Aet v4.0 under BioProject PRJNA341983. TE annotation and all high and low confidence genes can be downloaded from here.   Click me!


1. Masked and unmasked Aegilops tauschii (accession AL8/78) pseudomolecules v4.0. Currently searches will provide coordinates of the subject sequence on the pseudomolecule. The coordinates can be used to find high confidence gene models, low confidence gene models, or transposable elements in the Aegilops tauschii JBrowse.

2. Unmasked hexaploid wheat (Triticum aestivum cultivar Chinese Spring DV418) pseudomolecules v1.0. Currently searches will provide coordinates of the subject sequence on this set of pseudomolecules.

3. Unmasked hexaploid wheat (Triticum aestivum cultivar Chinese Spring DV418) pseudomolecules v2.1. Currently searches will provide coordinates of the subject sequence on this set of pseudomolecules.

BAC clones and contigs   

A database of SNP markers, contigs, and individual BAC clones of the so-called phase II FPC contig assemblies can be accessed through this BAC clone and contig portal from a previous project.

SSR search database   

This portal allows searching the masked or unmasked pseudomolecules for SSRs in genes or in intergenic regions. The output gives the characteristics of the SSR and the gene name and pseudomolecule coordinates of the gene in or near which it resides. The user can then click on the Download sequence icon at this portal and download sequence including the SSR of selected length for primer design or blast searches in wheat or Ae. tauschii.

Meta QTL probability    

Portal for computing p-values for meta-QTL hypothesis testing. This portal was constructed to facilitate the computation of σ ̂ adjusted for recombination rate and p-values for the three hypotheses about QTLs projected onto the Ae. tauschii genome sequence (Xu et al. 2019). The tab “Test1: QTL vs QTL” was designed for testing the null hypothesis that two QTLs are independent estimates of a single locus. The tab “Test2: QTL vs Mendelian locus” was designed for testing the null hypothesis that a QTL is an estimate of variation in QTL mapping of a specific locus annotated on or projected onto the Aet v4.0 sequence. The tab “Test3: QTL vs Cluster” was designed to test the null hypothesis that a projected QTL is a member of an existing QTL cluster. QTL cluster should be based on biological evidence that the QTLs are independent estimates of the same locus, albeit of unspecified location on an Aet v4.0 peudomolecule.


Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, Van SL, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang S, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW, Müller HG, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu FH, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, and Dvořák J. (2017) Genome sequence of the progenitor of the wheat D-genome Aegilops tauschii. doi:10.1038/nature24486

Luo MC, Gu YQ, You FM, Deal KR, Ma Y, Hu Y, Huo N, Wang Y, Wang J, Chen S, Jorgensen CM, Zhang Y, McGuire PE, Pasternak S, Stein JC, Ware D, Kramer K, McCombie WR, Kianian SF, Martis MM, Mayer KFX, Sehgal SK, Li W, Gill BS, Bevan MW, Simková H, Dolezel J, Weining S, Lazo GR, Anderson OD, Dvorak J (2013) A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. PNAS 110:7940–7945.

Xu J, Dai X, Ramasamy RK, Wang L, Zhu T, McGuire PE, Jorgensen CM, Dehghani H, Gulick PJ, Luo MC, Müller HG, and Dvorak J (2019) Aegilops tauschii genome sequence: A framework for meta-analysis of wheat QTLs. G3 Genes Genomes Genetics 9:841–853. Doi:10.1534/g3.118.200921

Zhu T, Wang L, Rimbert H, Rodriguez JC, Deal KR, De Oliveira R, Choulet F, Keeble-Gagnère G, Tibbits J, Rogers J, Eversole K, Appels R, Gu YQ, Dvorak J, Luo M-C (2020) Advances in the assembly of the bread wheat Triticum aestivum cv. Chinese Spring genome. The Plant J, submitted

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.