How to produce sufficient nutritious food to support a growing global population is a huge challenge for research and innovation right now. In 2009, the Food and Agriculture Organization estimated that the amount of food needed to feed our growing population was expected to rise by 70% by 2050.
Fundamental research in one model plant species has helped pave the way in the field of plant genomics and for the development of improved crop varieties that will support population needs in an increasingly changing climate.
Small but mighty cress
Arabidopsis thaliana, or thale cress, is a wild member of the mustard family commonly used in plant biology labs. Since the late 1980s, researchers have used it as a ‘model’ or ‘reference’ plant. It is now the most widely used model system to study plant biology and has delivered numerous breakthroughs for our understanding of biological processes, which apply to plants and life more broadly.
It is an excellent model plant because:
- it can be grown in a relatively small space, indoors and under artificial light
- the stretches of DNA between genes are relatively short, making it easier to study the genetics of the plant
- it has a short lifecycle, going from germination to seed production in the laboratory in around six weeks
- Arabidopsis plants are relatively easy to ‘transform’ in terms of inserting DNA into their genome
A genome revolution for plant research
Another advantage of Arabidopsis is that its genome is quite small. It has 17 mega base pairs over five chromosomes. In comparison, other plants have larger and more complex genomes; for example, wheat has 1000 times more DNA, organised over 42 chromosomes.
The Arabidopsis Genome Initiative sequenced the first flowering plant genome in 2000. The effort comprised several institutions and countries, including the John Innes Centre, an institute strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC). The results enabled researchers to identify the fundamental genes that are likely shared across all plant species.
The biology community was quick to see the potential of the Arabidopsis sequence, and several large studies in fundamental plant genetics followed.
One such study was led by Professor Richard Mott at the University of Oxford that defined which genes mapped to specific observable traits in Arabidopsis, leading to a key study in 2017. This work led to the creation of the MAGIC population (Multiparent Advanced Generation Inter-Cross), created by Dr Paula Kover’s team at The University of Manchester (now at the University of Bath), which has enabled easier identification of the genes responsible for specific traits, such as drought resistance.
Understanding gene function in Arabidopsis has given insight into many basic mechanisms, such as plant growth, development, and flowering. This has proven invaluable in helping interpret more complex plant genomes, such as globally important food crops.
Capitalising on the promise of Arabidopsis would not have been possible without creating resources for the plant science community to efficiently share materials and expertise.
The Nottingham Arabidopsis Stock Centre (NASC) and the Genomic Arabidopsis Resource Network (GARNet) have been pivotal over the years in shaping this plant genomics community.
NASC has supplied researchers working with Arabidopsis since 1990. BBSRC continues to fund this key infrastructure as a National and International Capability, which provides researchers with seeds with known mutations or genotypes. The collection now has over a million stocks and is widely used in the UK and further afield, underpinning the UK’s world-leading plant science research.
GARNet came about through a successful bid to BBSRC’s Investigating Gene Function initiative by Professor Dame Ottoline Leyser (then based at the University of York). The network was funded by BBSRC for 20 years in total through a series of awards. Through hosting meetings for members, regular newsletters, research round ups and provision of training, more rapid exploitation of the Arabidopsis genome was possible. Researchers have gone on to apply learning from Arabidopsis genomics to other plants and crops.
Uncovering the sequences of our food
As sequencing technology and analysis improved, researchers could turn to larger and more complex genomes found in commercially important crop species. Sequencing these genomes often involved large international consortia, with BBSRC supporting UK involvement in the sequencing of several important crop species.
Chinese cabbage (Brassica rapa) and oilseed rape (Brassica napus)
In 2011, scientists sequenced the genome of Chinese cabbage, a close relative of oilseed rape. The project included researchers in the UK from the John Innes Centre and Rothamsted Research, both institutes are strategically funded by BBSRC.
Due to genome similarities, the sequencing of Chinese cabbage has the potential to improve breeding efficiency across a much wider range of crops, too, including other important brassicas such as broccoli, sprouts, and cabbage.
Oilseed rape was sequenced in 2014 by an international consortium involving several institutions. BBSRC funding contributed to the effort via a grant awarded to Professor Ian Bancroft when he was at the John Innes Centre.
Due to their ability to germinate and grow at low temperatures, the oilseed Brassicas are one of the few oil crops that can be grown in temperate regions of the world. Oilseed crops are the third largest source of food oil behind palm oil and soyabean.
Potato (Solanum tuberosum)
Potato is the largest non-cereal food crop worldwide and ranked as the fourth most important food crop after maize, wheat and rice. The sequence of the potato genome was published in 2011. The UK component of the consortium was part-funded through grants to the University of Dundee and Imperial College London.
Tomato (Solanum lycopersicum)
This sequencing project was led by researchers at the University of Nottingham and Imperial College London in collaboration with leading scientists at:
- the Earlham Institute (then called The Genome Analysis Centre)
- the James Hutton Institute
- the University of East Anglia (UEA)
- the Natural History Museum
The project was funded in the UK by BBSRC, Department for Environment Food and Rural Affairs, and the Scottish Government, and the sequencing was undertaken by the Wellcome Trust Sanger Institute.
Tomatoes are a widely cultivated crop packed with nutrients: a primary source of lycopene (a key antioxidant), vitamin A, and vitamin C. The tomato genome sequence has assisted our understanding of the evolution and genomic basis of the Vitamin C pathway.
The full tomato genome sequence has enabled researchers to identify several genes and pathways controlling fruit ripening, including flesh and flavour-related genes that are the best targets for breeders to improve their varieties.
Nutritional benefits are also possible, with researchers at the John Innes Centre recently building on their genetics expertise to develop tomatoes that accumulate vitamin D in their fruit.
Barley (Hordeum vulgare L)
Barley is a staple food grain, also used for animal feed and in the production of beer. Around 150 million metric tonnes of barley are produced globally. It has less demanding environment, fertiliser, and climate requirements compared to wheat and maize.
A high-resolution draft sequence for barley was published in 2012. The UK component involved the James Hutton Institute and the Earlham Institute and was again part-funded by BBSRC.
Bread wheat (Triticum aestivum)
Wheat is a challenging crop to sequence. Bread wheat is a hybrid crop that formed from three ancient wheat ancestors and therefore has six sets of chromosomes (it is polyploid) and a highly complex genome. In comparison, humans have only a sixth as many DNA base pairs and only two sets of chromosomes.
The first whole-genome draft of the annotated bread wheat genome sequence was released by the International Wheat Genome Sequencing Consortium in 2014. BBSRC contributed grant funding to this international project, with the Earlham Institute contributing to the DNA sequencing effort.
Wheat is the second most important staple crop, with over 780 million metric tonnes of wheat produced worldwide last year. This genome sequencing project has helped to empower sustainable agriculture by unlocking the genome of this highly complex crop.
All of these crops are vitally important to feed our growing population, and the various sequencing projects are enabling critical new insights.
All of them build on that first flowering plant sequence, Arabidopsis.
Making sense of the data
Without the Arabidopsis data, these genomes would have been almost impossible to comprehend. The previous work on the small plant acted as a guide, or map, showing where to start looking for key genes.
Shared genes are likely to be fundamental genes, those that code for the key features of plants. Genes that weren’t found in the model plant were likely to encode more crop-specific functions, such as adaptation to specific growing conditions or relating to special features of the crop.
And it doesn’t stop at Arabidopsis. Once the mapping is complete for one plant, it goes on to inform the next. Rice and barley are grass crops with simple diploid genomes. Their genetic information can be used to help identify gene function in other grass crops, such as wheat with its more complex genome.
This expansion of knowledge demonstrates the value of fundamental research. One key result underpins a series of other findings that themselves then go on to open more opportunities for research and new fields to explore, ultimately translating into results that benefit us all.
The scientific journal article that detailed the first genome analysis for Arabidopsis now has 173,000 views on Nature and 4649 citations, according to Web of Science. According to Altmetric, the paper is placed in the top 5% of all research outputs and places in the 99th percentile compared to papers of a similar age and source. Suffice to say, the original genome paper has had a massive impact on the plant genomics sector, informing and underpinning a wide array of crop research.
Plant genomics branches out
Researchers now know that complex plant traits are affected by much more than just the genome sequence. Gene expression is a complex process, proteins read and ‘transcribe’ the DNA sequence of genes to produce lengths of RNA. This RNA is then ‘translated’ into strings of amino acids, which form proteins.
Fundamental research in Arabidopsis has exploded the possibilities in plant genomics, leading to new areas of exploration that are now being funded by BBSRC, laying the foundations for answers to future challenges.
The environment can influence heritable changes to the expression of genes even if the sequences are the same; for example, whether genes are ‘on’, ‘off’ or ‘dimmed’ from parent to offspring.
Dr Philippa Borrill, at the John Innes Centre, has been awarded a BBSRC grant to investigate this further. She is investigating how the polyploid nature of wheat affects gene expression and the genetic and epigenetic factors that influence inheritance.
By improving our understanding of how genetics and epigenetics influence polyploidy in wheat, we can better understand how the expression of desirable characteristics can be inherited. This will inform wheat breeding programmes and could help to increase productivity and other crop improvements.
Proteomics and transcriptomics
Genes code for proteins which carry out all the functions of the cell and the organism (in this case, a plant). The transcriptome is the total set of RNA instructions for making proteins produced by the genome of an organism, and the proteome is the total set of proteins produced. Work to understand RNA and proteins adds more detail into why changes in the genotype would result in variation among plants.
BBSRC is currently funding Kew Gardens and a large number of partners to sequence 50 genomes from a collection of Arabidopsis strains. The project, which is an ERA-CAPS collaboration called 1001 Genomes Plus, will also annotate these genomes with transcriptome and epigenome information. These efforts will help researchers to understand more fully the mechanisms of evolution and adaptation across varied Arabidopsis plants and will provide tools for future pan-genome research in other plant species.
Professor Ari Sadanandom has been awarded a Strategic Longer and Larger (sLoLa) grant to study and map SUMOylation in Arabidopsis. SUMOylation is a type of post-transcriptional modification, which involves the attachment of specialised proteins to other proteins, modifying the latter’s function. This process is a way plant cells take external signals and ‘code’ molecular interactions to change the way they function and is important for responding to environmental stresses.
Climate change is rapidly affecting the environment in which our crops are grown, with drought, high salinity, extremes of temperature, and exposure to new pests and pathogens, all affecting crop yield.
Understanding the mechanisms of how plants respond to environmental stressors could enable researchers and plant breeders to future-proof crops and improve their resilience to the ongoing problems of climate instability and change.
It is clear that plant genomics is certainly not done.
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