The wheat genome – the best thing since …

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Published on: December 4, 2012

When Anthony Hall trailed the wheat genome paper (Brenchley et al.; published on Thursday) at last week’s GARNet Tools and Technologies workshop, I knew it was excellent blog fodder. When I sat down to read the paper on Friday though, it seemed like a bad choice for a blog post. This is no restricted-access, wordy paper with obvious aspects to highlight in an accessible way; it is open access and describes the bread wheat genome, comparing it to related species concisely and clearly. However, in many ways this paper is important, even a landmark, because of what is not in it. So instead of highlighting the paper, I will attempt to explain why it was all over plant science social media and science news sites, and why it deserved far more coverage from the general media.

First, the bread wheat (Triticum aestivum) genome was, to steal a phrase from the Annals of Botany blog, the Everest of crop genomes. Sequencing it was difficult due to its enormous size. It is a hexaploid, essentially containing the genomes of three separate grass species. First of all Triticum urartu hybridized with a Sitopsis species to form tetraploid species Triticum dicoccoides, which eventually hybridized with Aegilops tauschii around 8000 years ago (for more information, see WheatBP). Both hybridization events increased the ploidy of the offspring. In 2010, the draft sequence of this huge genome was released, and analysing it must have seemed almost impossible. In the end, the genome took the team just two years to analyse – and that is what is published. It is an amazing achievement, which took a multinational team of scientists many years. The analysis showed that the genome contains 94 – 96 000 genes. The team were able to identify the parent species of many gene families and track their development over time.

Second, this work and other high profile ‘big data’ stories celebrate groundbreaking achievements in biological sciences. Sequencing technologies and analysis techniques have advanced beyond recognition since the human genome was sequenced in 2003. Many sequencing methods were used in the wheat genome project, all of which are either out of date or have been upgraded since – so sequencing more wheat genomes in a project similar to ENCODE or the 1001 Genomes project will take far less time. Similarly the computing power needed to analyse 17 gigabase-pairs of DNA sequence was unheard of in 2000, but 12 years later it is not only here, but improving. The bread wheat genome marks wheat’s entry into the ‘big science’ era.

Third, and most importantly, wheat is one of the most important plants on earth. It makes up 20% of the calories consumed by humans (statistic from Brenchley et al.). When crops fail, it affects everyone. This year saw poor weather in wheat regions across the globe, leading to warnings of unprecedented rises in the price of bread in the UK. Plant scientists are working with agriculturalists to improve crops and reduce the risk of harvest failure, but a 2011 Science paper (Lobell et al., 2011) commented that in some regions, the negative effects of climate change offset the technological advances that should increase crop yields. A fully sequenced and analysed bread wheat genome is a great asset for crop scientists working on developing breeds that may, for example, be able to withstand draughts and floods, and contain higher levels of nutrients.

The wheat genome sequence is not only a triumph for crop scientists. The more information there is out there on wheat ‘omics,’ the easier it is for Arabidopsis researchers to transfer their knowledge to wheat and improve the ‘impact’ of their projects – or find out in advance that for that particular gene or process, cross-over is impossible.

The sequencing of the Arabidopsis thaliana genome was completed in 2000, causing a paradigm shift in plant research. In 2005 Bevan and Walsh published an overview of the progress made in the first five years after the annotated genome was published, including the establishment of large stocks of the gene disruption lines now taken for granted. The sequencing of the wheat genome opens up new avenues of research for crop scientists and I am looking forward to seeing the results in the coming years.

There are instructions on how to download and use the wheat genome sequence at MIPS.

Highlighted paper: Rachel Brenchley, Manuel Spannagl, Matthias Pfeifer, Gary L. A. Barker, Rosalinda D’Amore, Alexandra M. Allen, Neil McKenzie, Melissa Kramer, Arnaud Kerhornou, Dan Bolser, Suzanne Kay, Darren Waite, Martin Trick, Ian Bancroft, Yong Gu, Naxin Huo, Ming-Cheng Luo, Sunish Sehgal, Bikram Gill, Sharyar Kianian, Olin Anderson, Paul Kersey, Jan Dvorak, W. Richard McCombie, Anthony Hall, Klaus F. X. Mayer, Keith J. Edwards, Michael W. Bevan & Neil Hall (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491, 705–710 doi:10.1038/nature11650

Image credits: Great Harvest by MMNoergaar and Challah by ladySorrow, both via stock.xchng.

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