17 March 2015
'Genomics of Food Security' by Prof. Robert Henry
Professor Robert Henry is the Foundation Director of the Queensland Alliance for Agriculture and Food Innovation. On 17 March, he gave us a whirlwind tour of the astounding diversity of research in which his genomics group is involved, and a tantalising glimpse at its far-reaching potential for the productivity, quality, diversification and resilience of food plants. The technologies for genetic sequencing have advanced at a dizzying pace – the year 2000 was presented as the dark ages by comparison with today’s capacity, which will soon seem primitive in turn. We can now find all the genetic differences between two individuals quickly and cheaply, allowing rapid identification of genetic sequences responsible for specific traits: a complete convergence of genotyping and sequencing.
Diversification of crops is one area of application of these technologies, through rapid domestication of wild relatives or introduction of features from them. Globalisation is leading to a homogeneity of diets – while it increases the diversity of foods eaten by most people, this is only by exchange of each other’s foods, while total diversity is lost. Northern Australia may be the centre of origin for rice – it is certainly a centre of diversity in wild Oryza species. Whole genome sequencing has clarified the relationships between rices from different regions, with the species in Asian and African centres of domestication being more closely related than Australian and South American species. Wild species have genetic variation in areas of chromosomes where domestic species have none, and these include useful traits such as disease resistance. The starch diversity of rice species is also a potentially valuable source of improvement.
Genomics has also advanced the understanding of wheat flour traits conferring quality for bread-making or for chapatis. Genome comparisons identified a small, 40-amino acid protein associated with bread quality – a protein overlooked by biochemical studies looking at larger proteins. Understanding that bread quality is not merely linked to quantity of gluten protein may enable high-quality wheat to be produced with less protein and therefore lower environmental impact of nitrogen fertilisation.
Genome comparisons have also shed light on the mysterious basis of hybrid vigour – it appears that there is an optimum level of genetic difference between the parents, which for rice is around 250,000 base pair differences. Higher or lower diversity produces less enhanced hybrids.
Whole genome comparisons of related crops such as cherry, peach and almond have identified sources of traits such as bitterness and climacteric ripening. Such discoveries help target genetic improvement through either conventional breeding or genetic manipulation. The wild and domestic diversity in a range of high-value crops are being studied, including a major collaboration with India on mango, and a global consortium on coffee. The latter has already discovered that caffeine biosynthesis has evolved separately in coffee, tea and cocoa, suggesting an important adaptive role for caffeine in the plant.
Energy crops, including sugar cane and Eucalyptus, are also in the sights. Genome sequencing of Eucalyptus species confirms a high level of interspecific gene exchange, and an instance of two “species” differing only in a single-gene trait which confers larger size of leaves and nuts.
A climate resilient crop genome consortium has compared genomes of varieties collected from sea level to mountaintop. The surprising finding is that the variation found was not for tolerance to abiotic stresses such as temperature and drought, but to biotic stresses (diseases). The extent to which biotic stresses change with climatic change may be underappreciated.
QAAFI is also participating in DivSeek, a global project to provide access to useful biological diversity, by sequencing seven million genomes and placing the data in the public domain.
In meeting the challenge of sufficient food production for a growing population, there are two options: 1/ change the plants and animals we are producing, or 2/ change the way we manage them. Historically, each strategy has contributed about equally to productivity advances. We need to balance investment between these two areas. In discussion, the strong synergy between these two strategies was highlighted. Banana was a case in point, where Queensland production is under threat from the recent introduction of Panama disease. Where in the past breeding has been difficult, the focus has been on disease management. New technologies may harness genetic solutions to disease threats. Perhaps greater integration between genetic and agro-systems endeavours will emerge.