Wheat

Wheat is a major human staple used for the production of bread, pasta, noodles, beer and even ethanol biofuel. The hexaploid genome of bread wheat is extremely large, 16,000 million basepairs (Mbp), making it difficult to characterise and confounding many traditional bioinformatics analysis tools. We are developing bioinformatics tools for the analysis of this complex crop genome with the aim of supporting applied crop research and improvement.

Wheat is probably the most important crop in the world, yet it has one of the most challenging genomes. Bread wheat is a hexaploid, with three complete genomes termed A, B and D in the nucleus of each cell. Each of these genomes is almost twice of the human genome and consists of around 5,500 million letters. Several groups around the world are working towards sequencing wheat. Details of individual efforts can be found on the wiki below.

Genome sequencing projects can be generally divided into whole genome shotgun (WGS) methods or BAC by BAC methods.

WGS attempts to sequence the genome in one go, by generating a large amount of sequence data and then assembling this to produce a representation of the string of letters which make up the genome. WGS has the benefit in that it is quick and relatively inexpensive, but it is often confounded by the inability to stitch the individual sequence reads together, resulting in a poor quality assembly. This is particularly problematic for polyploids, where more than one genome is present in each cell, or where there is a substantial quantity of repetitive sequences. Wheat is a polyploid with 3 genomes, each of which is 80% repetitive, making WGS unattractive.

The alternative BAC by BAC approach requires breaking the genome down to relatively small pieces (c. 120 kbp), ordering these as a minimal tiling path, then sequencing each of the BACs in the tiling path. While sequence assembly or repetitive regions remains problematic, this approach offers the potential to produce the best quality finished genome. However, BAC by BAC sequencing of wheat is hugely expensive, time consuming and is still not guaranteed to produce a complete genome due to some regions being underrepresented in BAC libraries.

We have taken an alternative approach, combining their experience of second generation sequencing technology with the ability of the Dolezel group in the Czech Republic to isolate individual chromosome arms. We have demonstrated that we can produce sequence data and assemble all genes for a specific chromosome arm. By including comparative genomic and molecular genetic marker data, we can produce an assembled sequence representing all known genes, including gene promoters and surrounding genome sequence. This syntenic build is the basis for studies of genome evolution and function with the aim of improving this important crop plant. As we assemble and annotate wheat chromosome arms, they are made publically available using the genome viewer GBrowse2.

The results are presented in the publications below.

1. International Wheat Genome Sequencing Consortium. (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345:1251788-1251788
2. Marcussen T., Sandve S.R., Heier L., Spannagl M., Pfeifer M., Jakobsen K.S., Wulff B.B.H., Steuernagel B., Mayer K.F.X., Olsen O.-A., International Wheat Genome Sequencing Consortium. (2014) Ancient hybridizations among the ancestral genomes of bread wheat. Science 345:1250092-1250092
3. Pfeifer M., Kugler K.G., Sandve S.R., Zhan B., Rudi H., Hvidsten T.R., Mayer K.F.X., Olsen O.-A., International Wheat Genome Sequencing Consortium. (2014) Genome interplay in the grain transcriptome of hexaploid bread wheat. Science 345:1250091-1250091
4. Berkman, P.J., Visendi, P., Lee, H.C., Stiller, J., Manoli, S., Lorenc, M.T., Lai, K., Batley, J., Fleury, D., Šimková, H., Kubaláková, M., Weining, S., Doležel, J. and Edwards, D. (2013) Dispersion and domestication shaped the genome of bread wheat. Plant Biotechnology Journal 11 (5): 564-571
5. Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubaláková M, Šimková H, Batley J, Doležel J, Pilar Hernandez P, and Edwards D. (2012) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theoretical and Applied Genetics 3: 423-432
6. Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubaláková M, Šimková H, Batley J, Fleury D, Doležel J and Edwards D. (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnology Journal 9 (7): 768-775

In addition to chromosome arm shotgun sequencing, we contribute to the IWGSC assembly of the BAC minimum tiling path led by Jaroslav Dolezel.

A major effort of the group is the translation of genomics for crop improvement. We led an Australian consortium to resequence a set of diverse Australian bread wheat line and have identified more than 20 million SNP molecular markers across teh bread wheat genome. Related papers are listed below.

1. Lai K, Lorenc MT, Lee H, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan CK, Manoli S, Stiller J, Batley J and Edwards D. (2015) Identification and characterisation of more than 4 million inter-varietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 13 (1), 97-104
2. Visendi P, Batley J, Edwards D. (2013) Next generation characterisation of cereal genomes for marker discovery. Biology 2: 1357-1377 Biology 2: 1357-1377
3. Deng P, Nie X, Wang L, Cui L, Liu P, Tong W, Biradar SS, Edwards D, Berkman P, Šimková H, Doležel J, Luo M, You F, Batley J, Fleury D, Appels R, Weining S. (2013) Computational Identification and Comparative Analysis of miRNAs in Wheat Group 7 Chromosomes. Plant Molecular Biology Reporter. 1-14
4. Edwards D, Batley J and Snowdon, R. (2013) Accessing complex crop genomes with next-generation sequencing. Theoretical and Applied Genetics 126 (1): 1-11
5. Lorenc MT, Hayashi S, Stiller J, Lee H, Manoli S, Ruperao P, Visendi P, J. Berkman PJ, Lai K, Batley J and Edwards D. (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology 1(2): 370-38
6. Lai K, Duran C, Berkman PJ, Lorenc MT, Stiller J, Manoli S, Hayden M, Forrest K, Fleury D, Baumann U, Zander M, Mason A, Batley J, Edwards D. (2012) Single Nucleotide Polymorphism Discovery from Wheat Next Generation Sequence Data. Plant Biotechnology Journal. 10 (6): 743-749
7. Edwards D, Wilcox S, Barrero RA, Fleury D, Cavanagh CR, Forrest KL, Hayden MJ, Moolhuijzen P, Keeble-Gagnère G, Bellgard MI, Lorenc MT, Shang CA, Baumann U, Taylor JM, Morell MK, Langridge P, Appels R, Fitzgerald A. (2012) Bread matters: A national initiative to profile the genetic diversity of Australian wheat. Plant Biotechnology Journal. 10 (6): 703-708
8. Nie X, Li B, Wang L, Liu P, Biradar SS, Li T, Dolezel J, Edwards D, Luo M, Weining S. (2012) Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology. American Journal of Botany. 99 (9) e369-e371
9. Berkman PJ, Lai K, Lorenc MT and Edwards D. Next generation sequencing applications for wheat crop improvement. (2012) American Journal of Botany 99 (2): 365-371
10. Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J and Edwards D. (2012) WheatGenome.info: An integrated database and portal for wheat genome information. Plant and Cell Physiology 53(2): e2(1–7)
11. Edwards D and Batley J. (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnology Journal 8: 2–9

Further information on our wheat research is available at wheatgenome.info

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