Updating Magic Universe
The genetic code of wheat
Last night the UK’s Biotechnology and Biological Sciences Research Council made available online a draft of the largest genetic code of an organism ever tackled – the genome of wheat, which is five times larger than the human genome and more than 30 times larger than that of rice, revealed back in 2002. But well worth the effort, for a crop with virtues that have shaped human history since its domestication more than 10,000 years ago.
Chinese Spring wheat is the variety now read. Leading the work is the British team of Neil Hall and Anthony Hall at the University of Liverpool, Keith Edwards and Gary Barker at the University of Bristol. and Mike Bevan at the John Innes Centre. Most of the actual gene-reading was done with a “platform” developed in the USA by a subsidiary of Swiss company Roche.
The implications are big. Although the genome isn’t yet organised into its chromosomes, plant breeders now have access to 95 per cent of all wheat genes. That should shorten by some years the time required to develop viable new varieties of wheat that can thrive in marginal conditions – adapted for example to face drought, salty soil, or disease.
Here’s the most relevant extract from the story in Magic Universe called “Cereals: genetic boosts for the most cosseted inhabitants of the planet.”
A treasure house of genes
Reading the rice genome lit a beacon of hope for the poor and hungry. When the first drafts of indica and japonica rice became available in 2002, sixteen ‘future harvest centres’ around the world sprang into action to exploit the new knowledge. An immediate question was how useful the rice data would be, for breeders working with other cereals.
‘Wheat is rice,’ said Mike Gale of the UK’s John Innes Centre. By that oracular statement, first made in 1991, he meant that knowledge of the rice genome would provide a clear insight into the wheat genome, or that of any other cereal. Despite the daunting fact that wheat chromosomes contain 36 times more of the genetic material (DNA) than rice chromosomes do, and even though the two species diverged from one another 60 million years ago, Gale found that the genes themselves and the order in which they are arranged are remarkably conserved between them.
The comparative figures for DNA, reckoned in millions of letters of the genetic code, are 430 for rice and 16,000 for wheat. No wonder the geneticists decided to tackle the rice genome first. Maize is intermediate, at 3000 million, the same as the human complement of genetic material.
These huge variations reflect the botanical and agricultural histories of the cereals, in which the duplication of entire sets of genes was not unusual. Since wheat is not thirty-six times smarter than rice, most of its genetic material must be redundant or inert. Until such time as someone should shotgun wheat and maize, as the Beijing Genomics Institute promised to do, the rice genome was a good stopgap.
When valuable genes are pinpointed in rice — for accommodation to acid soils, for example — there are two ways to apply the knowledge in other cereals. One is directly to transfer a gene from species to species by genetic engineering. That is not as quick as it may sound, because years of work are then needed to verify the stability and safety of the transplanted gene, and to try it out in various strains and settings. The other way forward is to look for the analogue of the rice acid-soil gene (or whatever it be) within the existing varieties of your own cereal. The reading of plant genomes adds vastly to the value of the world’s seed banks.
Recall that Cambodia was desperately hungry after the devastation of the Pol Pot era. Farming communities had lost, or at death’s door eaten, all of the deepwater rice seeds of traditional Khmer agriculture. In 1989, a young agronomist Chan Phaloeun and her Australian mentor Harry Nesbitt initiated a 12-year effort that restored Cambodian agriculture. From the International Rice Research Institute, Nesbitt brought Cambodian seeds that had been safely stored away the outskirts of Manila.
Even in the steamy Philippines, you need a warm coat to visit the institute’s gene bank. The active collections are kept at 2 degrees Celsius and the base collections at minus 20. The packets and canisters of seeds represent far more than a safety net. With more than 110,000 varieties of traditional cultivated rice and related wild species held in the gene bank, the opportunities for plant breeders are breathtaking.
The sub-species and varieties of Oryza sativa have all been more or less successful within various environments and farming practices. The wild species include even forest-dwelling rice. Adaptations to many kinds of soil chemistry, to different calendars of dry and rainy seasons, and to all kinds of hazards are represented. Rice in the gene bank has faced down pests and diseases that farmers may have forgotten, but which could reappear.
Until the 21st Century, scientists and plant breeders could do very little with the Manila treasure house. They had no way of evaluating it, variety by variety, in a human lifetime. Thanks to the reading of the rice genome, and to modern techniques of molecular biology that look for hundreds or thousands of genes in one operation, the collection now becomes practical. Identify any gene deemed to be functionally important, and you can search for existing variants that may be invaluable to a plant breeder.
Hei Leung of the Manila institute likened the rice genome to a dictionary that lists the all the words, but from which most of the definitions are missing. He was optimistic both about rapid progress in filling in the definitions, and about finding undiscovered variants in the gene bank. Even so, he warned that breeding important new varieties of rice was likely to take a decade or more.
‘Like words in poetry, the creative composition of genes is the essence of successful plant breeding,’ Leung remarked. ‘It will come down to how well we can use the dictionary.’ For a sense of the potential, note that among all the tens of thousands of genes in the cereal dictionary, just two made the Green Revolution possible. The dwarf wheat and rice grew usefully short because of mutant genes that cause malfunction of the natural plant growth hormone gibberellin. Rht in wheat and sd1 in rice saved the world from mass starvation.
Another eight years were to elapse before a first draft of the genome of wheat became available, in 2010. Being three times larger than the human genome, it had to wait for progress in technology. Eventually British researchers from Liverpool, Bristol and the John Innes Centre were able to subject Chinese Spring wheat to advanced DNA reading machines from 454 Life Sciences in the USA. Richard Summers of the British Society of Plant Breeders, commented: “The team brought together world class skills in sequencing and wheat genetics to deal with a major barrier in wheat breeding. This is an excellent example of how to achieve technology transfer from research lab through to practical deployment.”
BBSRC press release http://www.alphagalileo.org/ViewItem.aspx?ItemId=83492&CultureCode=en
Financial Times article http://www.ft.com/cms/s/0/13857ac8-b132-11df-b899-00144feabdc0.html
N. Calder, Magic Universe, pp. 131-133, Oxford UP, 2003