Archaeogenomics of Sorghum domestication and adaptation

Our understanding of evolution and the genomic level has progressed substantially over the last decade in the post genomic era. To the surprise of many, it has typically been found that strong selective sweeps have been few, and it is becoming apparent that evolution generally progresses as a symphony of small changes over many loci. The evolution of domestication of plants, and subsequent evolution under domestication, is also showing the same pattern as crop genomes are sequenced. This also has been a surprise for many because until recently it had been assumed the selection of traits associated with domestication, the domestication syndrome, had been very strong and the transition between wild and domesticated forms and rapid. In corroboration of genomic evidence, the strength of selection of domestication syndrome traits has also been estimated directly from the archaeological record and found to be much weaker than previously supposed, well within the range normally found under natural selection. Further corroboration is found with model-based evidence for weak selection of the domestication syndrome.

A consequence of weak selection is that the signatures of selection in the genome are also weak. So weak, in fact, that we may not be able to detect them all because they have decayed too much since the time of domestication. Furthermore, the patterns of genetic diversity seen in domesticated crops can also be complicated by introgressive gene flow between the wild and domesticated populations after domestication. Ideally, we would like to have genetic information from a time before these weak signatures of selection had decayed, and before introgression events had occurred. Technological advance is such that we can now generate genomes from archaeological samples, which would go a long way to achieving these ideal goals. In this study we will reconstruct archaeological genomes of the crop Sorghum from time points that stretch almost half way back to the time of domestication using third generation single molecule sequencing technology. We will contrast these to modern genomes, which we will also reconstruct in this project.

Sorghum is the crop of choice for this study for many reasons. It is one of the most recent crops to be domesticated, and so relatively easy to obtain archaeological samples of good biomolecular preservation that are significantly close to the time of domestication. It is an inbreeder and has a small genome, which makes genome reconstruction not too ambitious. Sorghum is also a crop of major importance in arid areas that has an evolutionary history of adaptation to drought tolerance. Interestingly, the cultivated races of Sorghum sowed a progressively increased tolerance to drought and pests, and it has been suggested that this was a consequence of repeated introgressions with the different wild varieties. By comparing archaeological genomes with modern genomes of all five cultivated races and four wild varieties of Sorghum we will understand better how the evolution of domestication of Sorghum occurred and how it became adapted to drought conditions.

This study will establish important principles in the evolution of domestication, which will likely prove important for studies in evolution in general. It will also provide insight into one of the most important issues of food security facing the world today, how a crop evolved drought tolerance, and whether that is something that could be translated to other crops.

Who might benefit from this research?
How might they benefit from this research?

We can imagine several groups of people outside the immediate conference-attending, journal-reading community who we address through the usual academic channels outlined in the case for support and academic beneficiaries section. These include RCUK (NERC specifically amongst the individual councils) the public, schools, breeders of Sorghum and the UK nanopore industry at a crucial time.

The nature of the project described is likely to have high profile outputs that are likely to be of media interest. We believe this to be the case because several aspects make this project generally interesting. Firstly, it has an archaeology component, which the general public seem to have a tendency to engage with. Secondly, the project will be one of the first to use nanopore technology, which is not yet generally available for commercial use. It will therefore be an interesting demonstration of an important new technology. Thirdly, this will be the first project that attempts the reconstruction of entire plant genomes from ancient DNA. That this would happen eventually has already been heralded by the various hominin genomes reconstructed from ancient DNA, all of which have received a great deal of media attention. Fourthly, the subject of the research project has very clear links to issues of food security that are easy to grasp - there are good biological reasons other than general interest to carry out the work proposed. We believe these four aspects give the project a flagship quality that will be both visible and valuable.

We envisage that this flagship quality will benefit to profile of UK science to the world, and specifically RCUK and the nanopore will benefit. Both these institutions need exemplars to advertize their achievements and value. In the case of the nanopore industry, this is a crucial time. There are a number of third generation (single molecule) sequencing technologies that are controlled by private enterprise. Nanopore is notable, for several reasons, but a major one for this impact summary is that it is British. There are three principal technologies (others exist) in the running at the moment: Helicos, PacBio and Oxford Nanopore. Two of these are U.S. based. While it is possible that these technologies are sufficiently divergent from each other in end product that they may co-exist, it is more likely that one will dominate. Obviously, it is in the UK's interest that the nanopore technology prevails. As it stands, nanopore technology is the only one that has not yet opened its shop doors. In terms of performance, as outlined in the case for support, nanopore compares favourably against the other technologies. This is not a guarantee of commercial success - remember beta max. Consequently, image and market share are everything right now, so flagship projects make an essential component of the technology's portfolio.

The public and schools could also benefit from this project. Both would benefit in an educational sense, as the project would make a good vehicle for understanding the latest approaches to evolution and issues of food security. The public is also tax paying and therefore invested in the science that UK universities produce. It is therefore important to garner their support as this ultimately impacts through to government policy.

Finally, we envisage that breeders of Sorghum could benefit from the findings of the project through a better understanding of the origins of the cultivated races in terms of where desirable qualities came from, and some steer on where improvements could be made.