December 21, 2011
You can't bluff nature. Diseases, droughts, floods and pests all take their toll on crop yields and, when choosing which cereal varieties to plant almost a year before they will be harvested, growers can never be certain which cards they are going to be dealt.
It is December and those UK arable farmers who have finished their planting for the year ahead are praying for a mild winter so that their crops can get a head start next spring. Should they have delayed planting until after the worst of the frosts? Have they selected a winning variety? Only time will tell.
Nevertheless, recent BBSRC investments in crop genomics research could help stack the deck in favour of arable farmers by helping to significantly accelerate barley and wheat breeding programmes. This work is crucial if we are to increase yields by 70% by 2050 to feed our growing global population while reducing inputs and environmental impact.
Place your bets
While growers have to make a judgement call as to which varieties are likely to meet their individual needs (see box, Aces high), one thing is certain – there is no such thing as an ideal crop variety. As Chris Tapsell, global wheat breeding lead for the international seed business KWS, explains, "People have looked to develop a single wheat ideotype – one with an idealised appearance across a range of characteristics – for the whole of the UK. But we are always going to need lots of varieties to meet different market requirements, to cope with different weather conditions, soil types and diseases in different parts of the country."
That said, there are always some desired traits that are common across all varieties and, according to Peter Jack, cereal genotyping manager for RAGT Seeds, when it comes to developing new wheat varieties for market, yield is always the ace in the hand.
"However, there is no point having good yield if the crop becomes diseased or lodges [falls over] before it can be harvested," says Jack. "Our aim is to combine the best performing wheat varieties across all characteristics.
"It's a bit of a lottery to do this all in one go, so breeders take a step-wise approach: selecting for one trait of interest, such as yield, and then complementing for deficiencies in other traits by crossing parent lines."
Beating the odds
This iterative process has been responsible for an increase in wheat yields of 0.6% per year over the past 60 years and this rate of increase is not diminishing (ref 1). A fantastic achievement, but one that falls well short of the 2% per year yield increase that has been predicted as vital to meet global demands by 2050 (ref 2).
"It's going to be extremely challenging to meet this greater target," says Jack. "It's fair to say that this would be impossible by conventional breeding alone.
"DNA-based approaches are already helping to speed up the process. For example marker analysis of seedlings allows us to skip laborious field testing, which makes selection more efficient."
Tapsell agrees, "We're going to need all of the available technologies at our disposal to breed, select and modify varieties, and we need better knowledge on markers for the traits we are interested in."
Advances in cereal genomics research are helping scientists and breeders to map the functions and locations of increasing numbers of relevant crop genes and, aided by recent investments from BBSRC, this could, in turn, open the door to new platforms for precision cereal breeding, such as the development of single nucleotide polymorphism (SNP) markers.
In August 2010, BBSRC-funded researchers announced the public release of the first stage sequence coverage of the wheat genome. Since then scientists and breeders around the world have been mining this data to identify DNA markers and to locate genes of interest.
According to Professor Mike Bevan from the John Innes Centre (JIC), who was part of the BBSRC-supported team, this work will lead shortly to a landmark paper in wheat genomics.
"This work has been pivotal," says Bevan. "Placing a large amount of data into the public domain has spurred on scientists working on wheat, and provides a good foundation for new research."
Prof. Bevan is also part of a new £5.5M, multi-institution research project aimed at producing definitive, high-quality wheat sequence data that will have longer term value for breeding experiments. The project, a strategic longer, larger grant from BBSRC, involves researchers at JIC, The Genome Analysis Centre (TGAC), Rothamsted Research (RRes), which all receive strategic funding from BBSRC, and the European Bioinformatics Institute (EBI) near Cambridge.
"This new five-year project gives us time to implement a better strategy for producing reference sequence for four chromosomes of Chinese Spring 42," explains project leader Dr Jane Rogers, Director of TGAC.
Yet the challenge facing the team is still immense. Even when armed with the latest next generation sequencing technologies, only relatively short fragments of DNA can be sequenced. This means that lots of overlapping fragments are needed to get coverage of the genome at the accuracy required, and this takes time and money. There is also a computational challenge in managing and interpreting the large amounts of sequence data produced.
As part of a much larger international sequencing programme to find all of the genes across the whole of the wheat genome, Rogers believes that this research will have a catalytic effect on sequencing different varieties which, ultimately, will lead to a more complete picture of the genetic basis of a wide range of traits in wheat such as yield, quality and disease resistance.
"With this information available, it will be possible to develop efficient marker-selected breeding strategies for wheat and reduce the time to produce new varieties with improved traits," she says. "For crops like wheat that are harvested once a year, strategies that improve breeding outcomes can have an enormous impact – it's not like the fruit fly or mouse where you can produce offspring within a few days or weeks."
New cards please
And research into barley – the UK's second most widely grown crop after wheat – is at a similar stage, for good reason: "Although barley has a simpler genome when compared to wheat, both crops are very closely related so it makes sense for us to study them together," says Rogers.
As part of a recent £1.6M BBSRC award, Rogers is working with researchers from EBI and the James Hutton Institute (JHI) near Dundee to take forward the findings from previous BBSRC-supported research on barley genetics.
According to project leader Professor Robbie Waugh from JHI, this new funding will help the UK team to coordinate international efforts to transform genomic information into a platform to understand barley genetic traits at a higher resolution and, ultimately, to isolate the genes responsible.
Waugh is hopeful that this could open up new opportunities and markets for barley growers, "Only a small portion of barley is currently sold for human consumption, mostly as pearl barley, and yet the health benefits from eating barley are well-known.
"There is scope to use barley more widely as a food ingredient, for example as a partial replacement for wheat flour in bread or as a thickening agent in processed foods. However, some of the qualities that make barley desirable as a food are essentially the opposite of those that breeders are currently focused on to meet the needs of the large, premium malting and distilling markets."
And yet, barley is more tolerant than wheat when it comes to producing reliable yields in the face of drought and poorer soils.
"Basically, focusing on the cereals, where you can't grow wheat, you grow barley," says Waugh. "However, despite its ability to grow well on lower quality land, the area dedicated to barley production is decreasing. This is a big concern to the highly profitable brewing and malting industries that consume around a third of the highest quality grain every year."
That's another reason why breeders are trying to select varieties that will give increased yields while maintaining quality on decreasing amounts of land.
"I'm confident that over the next few years we will see a great acceleration in progress for barley and wheat breeding that we have already seen for maize and rice," says Rogers. "Aided, in no small part, by the sharing of knowledge, costs and resources between researchers around the world."
It's a winning approach that is favoured by both academics and breeders: "One of the most exciting things I have observed in recent years is the closer integration between researchers in different countries," says Tapsell.
In June 2011, Agriculture Ministers from the G20 group of nations reached an historic agreement to endorse an international research initiative for wheat improvement. The Wheat Initiative is supported by research and funding organisations from many countries which have, or intend to develop, national programmes to improve wheat genetic resources. Coordination, which will be supported by BBSRC, INRA (France) and CIMMYT (Mexico) will ensure that information from these national programmes is available for application globally.
"This initiative will help wheat research on a global scale, initially through development of a shared science vision from an international science board" says BBSRC Deputy Chief Executive Steve Visscher, "It provides an interesting framework for closer collaboration in global food security between private and public researchers, and between research funding organisations, who share a common interest."
"Importantly," Tapsell continues, "the relationship between academic researchers and those in industry is how a pipeline of new genetic material passes into the genepools used by breeders. BBSRC and other research funding bodies provide the resources for developing this new material and the breeders are best placed to utilise it to achieve the targets required to feed the world in the future, whilst sustainably maintaining the environment."
Ensuring a fair deal
While the needs of the marketplace usually meet the needs of society, there are exceptions.
For example, barley yellow dwarf virus, which is endemic across all cereals, is spread by aphids. It is easy to control with cheap insecticides (about £1 per hectare) but these can be damaging to wildlife. So while it would be better from an environmental point of view to produce lines with genetic resistance to the disease, from a business point of view this is significantly outweighed by the cost of developing a new variety (approximately £1M).
This is another reason why collaboration between commercial breeders and the public sector is so important: researchers can identify and develop novel resistant material, and breeders can efficiently incorporate it without the risk or costs associated with trait discovery and characterisation. In February 2011, BBSRC awarded a £7M grant to a consortium of researchers to address just such targets. Heralded as the first comprehensive UK wheat pre-breeding programme in over 20 years (ref 3), the programme aims to increase the diversity of traits available in wheat, led by the JIC's Professor Graham Moore, and also involving researchers from the Universities of Bristol and Nottingham, RRes and the National Institute of Agricultural Botany. All the information generated in the programme will be stored in a central database, and seed stored centrally in the UK, both being freely available to both academics and breeders alike.
And genetic modification, which offers a high certainty of achieving genetic stability for disease traits, could also be an important tool in overcoming some of the economic constraints facing breeders: "Conventional breeding, allied with DNA selection methods and accelerated diversity mining approaches, offer much but to meet the 2% required yield increase, bigger step changes are needed," says Jack. "This is where GM could help, for example in providing resistance to intransigent pests and diseases, increasing photosynthetic efficiency and better fertiliser use – things which are very difficult if not impossible through non-GM routes."
Making better predictions
It is obvious that sequencing is not the end of the line. Compare with the human genome project for example: the complete sequence became available in 2003 but science and medicine have still to deliver on their promise of revolutionary new drugs.
Over the coming years it will be critical to mine genome data for useful characteristics using a comparative approach, and here crop researchers and breeders have significant genetic advantages over their medical peers, such as the ability to make controlled matings and to develop families of huge size, even if not the same resources.
Extracting useful information requires two major data sets to be developed: inherited, genotypic data together with observable, phenotypic data for the traits of interest. New genomics technologies are accelerating the speed at which the former is generated. Breeders, in addition, collect vast amounts of phenotypic data as part of their everyday activities, and this is now being complemented by new high throughput phenotyping technologies, like those being established at the Institute of Biological, Environmental and Rural Sciences at Aberystwyth University, which receives strategic funding from BBSRC. The next step, of course, is then the careful statistical analysis of very large datasets to provide the tools which breeders need for everyday use.
Ultimately, a good genepool is essential to any breeding programme. Breeders are always looking to add to this, and as all good card players know, having a good starting hand and knowing how and when to play it is key to long-term success.
Farmers' decisions about what, and when, to plant are based on experience – varieties that have grown well in the past are likely to do well again – as well as advice from agronomists and their own analysis of information such as the HGCA recommended lists, which provide sets of data showing how old and new varieties compare. For example, expected yields in different climates and soil types, disease resistance and quality.
Varieties usually stay on a recommended list for 3-5 years, unless they are exceptionally performing, to be replaced by new varieties. Breeders are continually adding new varieties with improved yield whilst maintaining characteristics that are suited to different markets, from bread wheats through to wheats that are suitable for animal feed, export, distilling and bioethanol.
- Mackay I, Horwell A, Garner J, White J, McKee J, Philpott H (2011) Reanalyses of the historical series of UK variety trials to quantify genetic gain and variety sensitivity. Theoretical & Applied Genetics, 122: 225-238
- FAO: How to Feed the World in 2050 (PDF, external link)
- BBSRC press release: £7M for public wheat pre-breeding programme announced