024_G19_FoodSecurity

Global

Global Insight Food Security the first step in decoding a gene’s secrets. Scientists must then work out what the genes actually do, how they’re related and how various parts of the genome are co-ordinated. These studies have been carried out by the Genome Analysis Centre (GAC), which is funded by BBSRC. A second phase, funded by the Vietnamese government, began a year ago, using data to develop ‘molecular markers’ and employing these for breeding purpose. At the same time, TGAC will sequence 600 rice varieties with high productivity and resistance to biotic and abiotic stresses. “We’ll be doing a sequence of the whole genome but to a low depth… light touch,” says Sarah Ayling, TGAC’s computational genomics group leader. “If you have large numbers, it’s very expensive. There’ll be some missing points but you can impute things. We’re looking for traits that will suggest resistance to disease and pests, salt, drought, blight; and that show quality. “Tests on the physical characteristics will be done in Vietnam. It’s important that it’s done well – a lot of time and labour is involved in getting high quality data about the physical side, which can then be used in breeding.” Similar research – on a much bigger scale – is being run by the Philippines-based International Rice Research Institute (IRRI), where 3,000 rice varieties have been sequenced to an “intermediate depth… very much less than our first pilot but to more than our phase two will be,” says Ayling. With so much work still to be done, she’s wary about guessing how soon it may lead to new varieties being bred – “it will take several years… it could be five or ten”. Anyone with a cursory understanding of the complex de-coding process will understand her caution. The IRRI project, led by scientists in China and the Philippines, is building a database of rice genomes using samples from 89 countries – rice is known for its tremendous within-species genetic diversity and varietal group differentiation. Researchers hope for “a new round of accelerated discoveries in rice science” and have called for an “international effort to analyse and mine the dataset” – 13.4 terabytes of data. In May, coinciding with World Hunger Day, they released all this on an open-access database. The long-term goal is to provide resources specifically for “poverty-stricken farmers in Africa and Asia”, and reach 20 million of these in 16 target countries. Financial backers include the Bill and Melinda Gates Foundation. Research into the wheat genome is taking a similar path. In January a whole-genome dataset for bread wheat was made available to all on the Ensembl Plants database – information that will provide researchers and breeders with valuable tools to improve yields in different environments. The bread wheat genome is hugely complex: at least five times larger than the human genome. Bread wheat derives from three different grasses that hybridised during domestication and the three separate ancestral genomes have been retained in the modern crop. Trying to sequence and assemble each of these individually is said to be “as difficult as sequencing the genomes of a human, chimp and gorilla all at once”. This project, run by the International Wheat Genome Sequencing Consortium (IWGSC), represents the most complete version of the wheat genome to date. IWGSC, with more than 1,000 members in 57 countries, was established in 2005 by wheat growers, plant scientists and breeders. It aims to provide a publicly available genome sequence of bread wheat that will enable breeders to develop improved varieties, while also laying a foundation for basic research in wheat, cereals and plants. Much of the work was carried out in the UK by TGAC. The three wheat sub-genomes were sequenced one chromosome at a time, which made it possible for the first time to assign each chromosome fragment to the correct sub-genome. As with rice, this work will give insights into traits important for pest resistance, drought tolerance and other stresses. IWGSC aims to accelerate its genome sequencing effort and complete physical maps for all 21 wheat chromosomes. It expects to obtain a complete reference sequence of the hexaploid bread wheat genome by 2016-17. Professor Mike Bevan of the UK’s John Innes Centre, who has long been involved in this field of research, is encouraged. “There’s been a huge increase in the development of genome markers – they detect different DNA sequences and this information is being used by breeders worldwide,” he says. “Also, next generation resequencing technology, which makes measuring genetic variation and diversity much easier, has developed rapidly since it first appeared in 2008.” Bevan is currently working with a team to make mapping the genome sequence of one wheat line “very accurate” and then to develop methods of re-sequencing the other lines. “We filter out all the DNA that encodes the genes and sequence this, but that’s only 10-20 per cent of the genome – the business end.” Away from wheat and rice research, BBRSC-funded scientists have made quite a different discovery, but one of potentially great significance – that small amounts of water in soil can influence the structure of plant roots. Root branching determines the efficiency of water uptake and acquisition of nutrients, so understanding how this happens is crucially important. Using X-ray imaging, researchers from the University of Nottingham, working with several international groups, discovered that new lateral roots form on the side of the main root in contact with water, but rarely on the dry side. This ‘hydropatterning’ is common to important food crops such as maize and rice. UK team leader Professor Malcolm Bennett, from Nottingham University’s school of biosciences, believes that identifying the genes and signals that control this process opens up new possibilities to improve water and nutrient foraging. Hunger and food demand will not be solved next year, the year after or even within the decade. But in such fundamental discoveries, hope lies. The more research there is of high quality – from whatever angle – the better our chances of somehow feeding the extra millions. four 24 l www.global -br ief ing.org th quar ter 2014 global 


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