About & citation

Please cite

If you use data or tools from this site, please cite:

1. Montenegro JD, Golicz AA, Bayer PE, Hurgobin B, Lee H, Chan C-KK, Visendi P, Lai K, Doležel J, Batley J, Edwards D (2017). The pangenome of hexaploid bread wheat. The Plant Journal 90(5): 1007–1013. doi:10.1111/tpj.13515
2. Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J, Edwards D (2012). WheatGenome.info: an integrated database and portal for wheat genome information. Plant and Cell Physiology 53(2): e2. doi:10.1093/pcp/pcr141

Each browser, dataset and tool on the Data & tools page also lists the paper that describes it.

How the data was produced

When this site began, there were two main ways to sequence a genome:

• Whole genome shotgun (WGS) sequences the whole genome at once and assembles the reads. It is fast and relatively cheap, but struggles with polyploid and highly repetitive genomes like wheat, where reads from the A, B and D sub-genomes and from repeats are hard to tell apart.
• BAC-by-BAC breaks the genome into ordered pieces of around 120 kb, which are sequenced one at a time. It gives the highest quality result, but for wheat it was extremely expensive and slow.

The UWA assemblies took a middle path. The chromosome group 7 assemblies (7A, 7B and 7D) were built from sequence of individual, flow-sorted chromosome arms. Sequencing one arm at a time greatly reduces confusion between the three sub-genomes. The wheat pangenome v1.0 extended this approach to the whole genome, combining the reference assembly with sequence from many wheat cultivars. This identified genes that are present in some cultivars and absent from others, and catalogued SNPs between them.

Since then, long-read sequencing and the IWGSC reference genome have opened up new approaches, and the site has grown with them. Newer resources such as Wheat Panache, a pangenome graph of 16 bread wheat genomes, bring together genome assemblies produced by research groups around the world.

Related publications

Selected wheat papers from the Applied Bioinformatics group.

Wheat genome assembly and diversity

• Berkman PJ et al. (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnology Journal 9: 768–775. doi
• Berkman PJ et al. (2012) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theoretical and Applied Genetics 124: 423–432. doi
• Berkman PJ et al. (2013) Dispersion and domestication shaped the genome of bread wheat. Plant Biotechnology Journal 11: 564–571. doi
• Lai K et al. (2012) Single nucleotide polymorphism discovery from wheat next-generation sequence data. Plant Biotechnology Journal 10: 743–749. doi
• Lorenc MT et al. (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology 1: 370–382. doi
• Lai K et al. (2015) Identification and characterisation of more than 4 million inter-varietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 13: 97–104. doi
• Visendi P et al. (2016) An efficient approach to BAC based assembly of complex genomes. Plant Methods 12: 2. doi
• Montenegro JD et al. (2017) The pangenome of hexaploid bread wheat. The Plant Journal 90: 1007–1013. doi
• Tulpová Z et al. (2018) Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies. New Biotechnology 48: 12–19. doi
• Feng K et al. (2020) The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat. Plant Biotechnology Journal 18: 732–742. doi
• Bayer PE et al. (2022) Wheat Panache: a pangenome graph database representing presence–absence variation across sixteen bread wheat genomes. The Plant Genome 15: e20221. doi

The wheat reference genome (IWGSC)

• International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345: 1251788. doi
• International Wheat Genome Sequencing Consortium (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361: eaar7191. doi

Databases and tools

• Duran C et al. (2009) AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants. Nucleic Acids Research 37: D951–D953. doi
• Marshall DJ et al. (2010) Targeted identification of genomic regions using TAGdb. Plant Methods 6: 19. doi
• Duran C et al. (2010) CMap3D: a 3D visualisation tool for comparative genetic maps. Bioinformatics 26: 273–274. doi
• Scheben A et al. (2019) CropSNPdb: a database of SNP array data for Brassica crops and hexaploid bread wheat. The Plant Journal 98: 142–152. doi
• Schliebs O et al. (2021) Daisychain: search and interactive visualisation of homologs in genome assemblies. Agronomy 11: 2587. doi

Reviews and book chapters

• Edwards D (2011) Wheat bioinformatics. In: Bonjean A, Angus W, Van Ginkel M (eds) The World Wheat Book, vol. 2. Lavoisier, pp. 851–875.
• Berkman PJ et al. (2012) Next-generation sequencing applications for wheat crop improvement. American Journal of Botany 99: 365–371. doi
• Edwards D et al. (2012) Bread matters: a national initiative to profile the genetic diversity of Australian wheat. Plant Biotechnology Journal 10: 703–708. doi
• Yuan Y et al. (2017) Databases for wheat genomics and crop improvement. In: Wheat Biotechnology, Methods in Molecular Biology, Springer, pp. 277–291. doi
• Scheben A et al. (2019) Progress in single-access information systems for wheat and rice crop improvement. Briefings in Bioinformatics 20: 565–571. doi
• Tay Fernandez CG et al. (2021) Application of pangenomics for wheat molecular breeding. In: Molecular Breeding in Wheat, Maize and Sorghum. CABI, pp. 236–246. doi
• Boden SA et al. (2023) Updated guidelines for gene nomenclature in wheat. Theoretical and Applied Genetics 136: 72. doi

Data access

All the data is freely available from the Data & tools page. If you need raw reads or anything that isn't listed there, please get in touch.