Researchers from the Quadram Institute and the University of York have developed a novel approach that will help unlock the genetic secrets of plant cell walls, which form the basis of many biological products.
A field trial conducted by members of the RIPR programme in Lincolnshire, showing considerable variation between members of the same species which can be mined for novel genetics. Image courtesy of Alison Frasier (RIPR programme member, University of Nottingham).
Plant cell walls are made up of sugars, which can be arranged into a myriad of different carbohydrates that determine the wall’s properties in subtly different but significant ways. Variations in these sugars also alter the properties of the plant, by affecting how it grows, or how it defends against pests and diseases. After harvest, they also affect the properties of materials that we derive from plants. This includes, for foods, nutritional quality, storage longevity, as well as usability of plant waste matter in emerging areas of biotechnology such as biofuel and biopolymer production.
Because of the central importance of the cell wall to agronomy and bioindustry, there has been a lot of interest in the plant genes that control cell wall composition. With a better understanding of the genetic controls of plant cell wall synthesis we can make more effective improvements. Recent developments in genome sequencing technology have provided detailed information about the genetics of crop plants, but what has been lacking to date is the technology needed to collect comparable cell wall data to locate, assign and signpost these important genes for plant breeders.
To overcome this, researchers working on the Renewable Industrial Products from Rapeseed (RIPR) Programme, funded by the Biotechnology and Biological Sciences Research Council, developed high density carbohydrate microarrays containing carbohydrates from cell walls from 331 genetically different varieties of oilseed rape.
Using a microarray, sometimes called a lab-on-a-chip, enables many thousands of different samples to be analysed simultaneously. This allowed researchers to harvest a huge amount of data relevant to carbohydrate structural arrangements, which was then linked back to particular changes in genetic information between the different varieties, using a technique called association mapping. This identifies genetic markers that enable breeders to determine which gene variants are present and hence predict even at the seedling stage what the properties of the plant will be at maturity. It also enables a greater understanding of the science by enabling the identification of causative genes.
Association mapping is a powerful tool but requires a large amount of data. The approach for cell wall components, described in the Proceeding of the National Academy of Sciences, provides a high-throughput, robust and scalable way of generating such data.
“By helping to reveal the genetic basis of cell wall biosynthesis, this approach should contribute to the development of nutritious food, and sustainable materials.” said Professor Keith Waldron.
“High-density carbohydrate microarrays are a really powerful method to obtain precise, robust and scalable data suitable for GWAS. We hope that this rapid methodology can be adapted for use in both science and industry” said Dr Ian Wood.
“The advances reported underline the importance of collaborative, inter-disciplinary research conducted at the scale necessary to be internationally-competitive. The RIPR project includes both academic partners conducting the fundamental research and industry partners who will be involved in the next stages of commercialisation for the production of sustainable bio-products from crop waste materials such as straw from oilseed rape”, said Professor Ian Bancroft from the University of York.
The authors are already exploiting their approach to open new opportunities for cell wall improvement in plants and other organisms with carbohydrate-rich cell walls.
Carbohydrate microarrays and their use for the identification of molecular markers for plant cell wall composition Ian Wood, Bruce Pearson, Enriqueta Garcia-Gutierrez, Lenka Havlickova, Zhesi He, Andrea Harper, Ian Bancroft, and Keith W Waldron PNAS (2017)doi:10.1073/pnas.1619033114