The Wheat ‘Pan Genome’.

Annual global wheat trade is higher than that of maize and rice combined. Wheat is also the most important source of protein and provides around 20% of human caloric intake globally. With a growing population, wheat production needs to increase by around 60% in the next 40 years to meet demands; therefore, the challenges for wheat breeders and growers are tremendous. Continued development of genomic resources to support wheat research and breeding are at the forefront to support this global challenge.

2017 was a remarkable year and represented a significant step forward for wheat genomics. In 2017, highly continuous genome assemblies were released for two of modern wheat’s ancestors, wild emmer wheat (accession “Zavitan”)1 and Aegilops tauschii2. Genome sequences for domesticated wheat, including both tetraploid wheat (durum cultivar “Svevo”) and hexaploid wheat (bread wheat landrace “Chinese Spring) were also well underway, with improved genome sequences being released^3,4. In July 2017, the International Wheat Genome Sequencing Consortium (IWGSC) also announced the most comprehensive and contiguous assembly of the "Chinese Spring" hexaploid wheat genome. However, these genome assemblies are only the first step towards understanding the diversity available to wheat scientists and breeders. It is likely that one of the key reasons why bread wheat has such a huge geographic range and has been adapted into so many environmental conditions is that the wheat genome is highly plastic and tolerant of a huge level of mutation and intergression.

Modern wheat cultivars carry a wide range of different genes associated with important traits, such as increased yield and disease resistance. It is impossible to capture all of these genes with a single genome sequence; therefore, additional genome sequences are required. Sequencing multiple wheat genomes will allow for the full complement of wheat genes to be identified, also called the ‘pan genome’. The ‘pan genome’ can be subdivided into two components, the ‘core genome’ and the ‘dispensable genome’. The ‘core genome’ encompasses genes that are common across most or all wheat, while the ‘dispensable genome’ includes genes that are present in only a subset of individuals or are unique to an individual. By capturing the ‘pan’, ‘core’, and ‘dispensable’ genome, wheat researchers and breeders will be better equipped to identify genes that can be used for improving wheat production and quality. It will also aid our understanding of gene-models and regulatory motifs.

References:

1) Avni, R., M. Nave, O. Barad, K. Baruch, S. O. Twardziok, H. Gundlach, I. Hale, M. Mascher, M. Spannagl, K. Wiebe, K. W. Jordan, G. Golan, J. Deek, B. Ben-Zvi, G. Ben-Zvi, A. Himmelbach, R. P. MacLachlan, A. G. Sharpe, A. Fritz, R. Ben-David, H. Budak, T. Fahima, A. Korol, J. D. Faris, A. Hernandez, M. A. Mikel, A. A. Levy, B. Steffenson, M. Maccaferri, R. Tuberosa, L. Cattivelli, P. Faccioli, A. Ceriotti, K. Kashkush, M. Pourkheirandish, T. Komatsuda, T. Eilam, H. Sela, A. Sharon, N. Ohad, D. A. Chamovitz, K. F. X. Mayer, N. Stein, G. Ronen, Z. Peleg, C. J. Pozniak, E. D. Akhunov and A. Distelfeld (2017). 'Wild emmer genome architecture and diversity elucidate wheat evolution and domestication'. Science 357(6346): 93-97.

2) Zhao, G., C. Zou, K. Li, K. Wang, T. Li, L. Gao, X. Zhang, H. Wang, Z. Yang, X. Liu, W. Jiang, L. Mao, X. Kong, Y. Jiao and J. Jia (2017). 'The Aegilops tauschii genome reveals multiple impacts of transposons'. Nature Plants 3(12): 946-955.

3) Clavijo BJ, Venturini L, Schudoma C, et al. 'An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. Genome Research'. 2017;27(5):885-896. doi:10.1101/gr.217117.116.

4) Zimin, A. V., D. Puiu, R. Hall, S. Kingan, B. J. Clavijo and S. L. Salzberg (2017). 'The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum'. GigaScience 6(11): 1-7.

The 10+ Wheat Genomes Project is a global partnership that leverages collaborative expertise and funding with the aim to characterize the wheat ‘pan genome’. In addition to assembled genomes it will also generate annotated gene models based on electronic prediction and experiment transcriptome data. This research partnership will also build the most comprehensive functional analysis of the ‘pan genome’, by comparing gene expression (transcription) networks throughout plant development. The partnership will generate at many high quality wheat genome assemblies and develop strategies and resources to compare multiple wheat genome sequences from around the globe.

Created in 2011 following endorsement from the G20 Agriculture Ministries, the Wheat Initiative provides a framework to establish strategic research and organization priorities for wheat research at the international level in both developed and developing countries. The Wheat Initiative fosters communication between the research community, funders, and global policy makers, and aims at securing efficient and long-term investments to meet wheat research and development goals. The Wheat Initiative Strategic Research Agenda recognizes the wheat genome assembly as a high priority “game-changer” that will be a cross-cutting resource to support wheat biology, genetics, and breeding. Indeed, DNA sequencing technologies and data analysis tools have advanced rapidly over the past decade and it is now possible to generate high quality genome data for large complex genomes, such as wheat.

In July of 2016, the Wheat Initiative sponsored a workshop focusing on “Wheat Genomic Resources in a Post-Reference Sequence Era”. As a result of the workshop, a number of priority areas were identified. One area that was deemed to require immediate attention was the completion of the “Wheat Ten Genome Project” and development of ‘pan genome’ resources.

As an Associated Programme of the Wheat Initiative, the 10+ Wheat Genomes Project is committed to disseminate progress quickly and share the developed pan genome resources to the broader wheat community. Although the partnership is an independent research activity, the 10+ Wheat Genomes Project is committed to the Wheat Initiative’s mission to develop global genetic resources to support a vibrant wheat research and breeding community.