Barley genotyping: a path to the sustainable production of food and drink

Barley is the world’s fourth most important cereal crop ­– now geneticists think that with the elucidation of its genetic code and a powerful new genotyping assay we are closer to food and drink security

Researchers at the James Hutton Institute have developed two new tools that will assist breeders.  The publication of a high-resolution draft map of the genetic code of barley, and a new genotyping assay will improve the process of developing new varieties of barley to maintain the production and availability of meat and dairy – as well as of your favourite tipple.

Using the recently released barley genome sequence and the new genotyping assay will enable breeders to develop barley varieties with traits such as enhanced nutritional value, higher yields, and improved pest and disease resistance.

Barley, a key ingredient in beer and spirits, is the world's fourth most important cereal crop both in terms of area of cultivation and in quantity of grain produced, behind only wheat, rice and maize. It is also a major component of animal feed for the meat and dairy industries. Barley straw is a source of nutrition for ruminants, is used for animal bedding and frost protection in the winter and is a potential feedstock for emerging bioprocessing and biofuel industries.

It is also the most important crop in Scotland, occupying half of all the arable land in the country, from which 50 to 70% goes to make whisky. This translates into approximately £4.2bn in revenues for the Exchequer. It is not only a key crop, but a complex one too: with 32,000 genes, its genome is nearly double the size of the human genome and 12 times that of rice.

Professor Robbie Waugh, lead crop geneticist at the James Hutton Institute in Scotland, and recently elected a Fellow of the Royal Society of Edinburgh, led the UK team that took part in the international effort to unravel the barley genome. He has also worked with colleagues Pete Hedley and Joanne Russell in the development of a new, low cost genotyping assay in partnership with US company Eureka Genomics. This new tool consists of a series of diagnostics of the genome of a given barley variety, which allows breeders to differentiate traits and identify their genetic origin.

Professor Waugh explains: “When breeding barley we want to achieve an improvement over the current best varieties. So we make crosses between different varieties to obtain an offspring and then hope to identify something that is better when compared to the current best. When we do this using the genotyping assay as a tool to identify better performing lines - this is called molecular breeding.

It is not only a key crop, but a complex one too: with 32,000 genes, its genome is nearly double the size of the human genome and 12 times that of rice.

“What happens when we make a cross between two barley varieties is that the two genomes recombine. All of the different versions of genes in each parent are shuffled during this process which results in each of the progeny being completely different. Rather than doing this blindly, the genotyping assay allows us to follow, in the progeny, which bits of the genome come from which parent. Thus, if one of the parents is a tall plant and the other is more resistant to pests and diseases or has better nutritional content, the genotyping assay allows us to predict which of these characteristics will be combined in each of the offspring – without having to go through the costly and lengthy process of growing and testing all of the plants in the field.”

The new assay is carried out in a laboratory. Leaf material is collected and ground to allow extraction of DNA. After some further purification, the assay is applied and information about precisely how the genome of the plant has been shuffled is returned.

“One of the most important aspects of this assay is its low cost. There are a lot of different traits, and an affordable assay is needed to cover the entire genome, not just bits of it. This assay is not just used as a comparison between two endpoints; it is a key tool in breeding to identify things that are better. Breeding has been responsible for approximately a one per cent increase per year in UK barley yields during the past 50 years,” Professor Waugh added.

The new assay allows scientists and breeders to look at 400 points in the barley genome but research is already underway to increase the number of points that can be looked at and the number of individuals that can be genotyped in the same assay. This would offer yet more insight into the barley genome, while driving costs down further.

The James Hutton Institute has been involved in developing these types of assay for the past 20 years. Professor Waugh said: “Previously we worked with the technology developed by a company called Illumina. This was similar in scale to our current assay, as it looked at around 400 markers, but did so one genotype at a time. The new assay looks at many genotypes simultaneously, has more than halved the cost and uses current instrumentation - a significant factor now the equipment needed for the Illumina assay has been discontinued.”

“Our challenge is now twofold: to increase the number of markers in the assay and to multiply the number of individuals that can be compared at the same time. The result will be a further reduction in cost making the assay more attractive for high throughput applications. This assay is a step in the right direction: it is highly effective and cheap, so it can be applied to lots and lots of plants and enable breeders to select plants containing the versions of genes they are interested in.”

The International Barley Genome Sequencing Consortium (IBSC) published a genetically anchored sequence assembly of the barley genome in the journal Nature in October 2012. Decoding the barley genome presented a major challenge because it contains a large proportion of closely related sequences that are difficult to piece together into a true linear order.

By developing and applying a series of innovative strategies that allowed them to circumvent these difficulties the IBSC team managed to construct a DNA sequence assembly that contains the majority of barley genes in linear order.

Commenting on the implications for barley breeding Professor Waugh said: “Access to the assembled catalogue of gene sequences will streamline efforts to improve barley production through breeding for varieties better able to withstand pests and disease and deal with adverse environmental conditions such as drought and heat stress.

“It will accelerate research in barley, and its close relative, wheat. Armed with this information breeders and scientists will be much better placed to deal with the challenge of effectively addressing the food security agenda under the constraints of a rapidly changing environment.”

The UK contribution to the barley genome research was funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and Scottish Government.