The sweetest secret revealed

Core Facilities: Genomics Unit

For the first time ever, CRG researchers have sequenced and analysed the genome of the sugar beet, one of the most recent crop plants, accounting for nearly 30% of the world’s sugar production

Sugar has a really bittersweet story, full of slavery, abuse, addiction and colonisation. Sugarcane was first cultivated on the island of New Guinea approximately 8,000-10,000 years ago. There, people just picked the cane and ate it raw; they considered it a kind of elixir, improving the mood and health-related conditions. Millennia later that sweet secret passed to the Persians and from them to the Arabs, who immediately fell in love with it and turned it into an industry. As making sugar was a very hard job, it was considered suitable work only for the lowest of labourers: slaves and prisoners of war.

British and French crusaders were probably the first Europeans to fall at sugar’s feet and bring it to the old continent. But, however much they tried to grow cane, they found it was not very productive in temperate climes; in fact, it needs tropical, rain-drenched fields to flourish. So, for centuries Europe had to be content with trading the precious item with Muslims, until the spread of the Ottoman Empire, in the 15th century, made this impossible. By that time, the Western wealthy classes were so completely at the mercy of sugar that they started to think of ways to develop new sources of this sweet food.

And, maybe by chance, that is when our protagonist sprang into action: the sugar beet, one of the most recent crop plants. Only 200 years ago in Europe trials were started to cross chards with beets, which at that time were only used to feed cattle. Surprisingly, it was discovered that the new crop plant emerging from this hybridisation was really sweet and could be used to obtain the beloved sugar.


One of the most recent crop plants

In the beginning, sugar beet accounted for only 5% of the world’s annual sugar production, whereas nowadays, according to the United Nations Food and Agriculture Organisation (FAO), it is more like 30%. Now, researchers from the Centre for Genomic Regulation (CRG), the Max Planck Institute for Molecular Genetics in Berlin and the University of Bielefeld have, for the first time, been able to sequence and analyse its genome.

This achievement is hugely important for two main reasons: firstly, a financial one, as sugar beet production plays a crucial role in Central and Eastern Europe, the United States and also Canada, where it is the predominant source of sweetness. And, secondly, a biological reason, as Heinz Himmelbauer, head of the Genomics Unit at the CRG in Barcelona and leader of this work, which has been published in Nature, points out.

“The sugar beet is part of a group of flowering plants called ‘Caryophyllales’, comprising 11,500 species, among which are spinach, quinoa and also carnivorous and desert plants. Until now, no genome sequence of any of these species had been generated. So, as we have been able to obtain and analyse the genome of the sugar beet, we now have an evolutionary model that can shed light onto plant evolution”, considers this researcher.

Compared to the human genome, sugar beet has many more genes, 27,421, although, in the end, all these genes probably encode for less different proteins than the 21,000 human genes. In addition to protein-coding genes, the genome of sugar beet is full of mobile elements. These sequences are not considered to be genes, even though many of them have retained features that resemble genes. In particular, many of these sequences have the ability to copy themselves and integrate into other parts of the genome.

“This behaviour somehow drives the evolution of the sugar beet’s genome because by integrating into the genome, they can influence the activity of nearby genes. Or they can integrate within a gene, and become part of its sequence. In this way, the genome’s repertoire of genes can change, perhaps in some cases leading to new functions. Although this is not a mechanism specific to plants, these mobile elements make up a big proportion of the plant’s genome and they are more active than in humans, for instance”, Himmelbauer explains.


Towards improved crop plants

Another notable finding of this research was the low number of sugar beet transcription factor genes. These are proteins that bind to the regulatory regions of genes and drive or modulate their expression. Apparently, in sugar beet the number of genes encoding transcription factors is the lowest of any higher plant that has so far been analysed.

CRG researchers have also sequenced and compared additional sugar beet genotypes, to characterise the variation and show how artificial selection has shaped the genome. “Domestication by humans has created a plant with completely different properties when compared to its wild relatives”, Himmelbauer highlights.

As has happened with most crop plants and domesticated animals, throughout history humans have chosen to breed individuals with desired properties, artificially selecting from one generation to the next. This becomes obvious when comparing, for example, the wild sea beet found on the shore with the sugar beet crop plant. They are the same species but look completely different.

They have also sequenced sea beet as the progenitor of all beet crops and spinach as a close relative of sugar beet for extended comparative studies.

Knowing the complete genome of the sugar beet can lead to improvements in the crop plant. The genome provides a foundation for identifying genes and gene variants that confer resistance to all kinds of stress, such as high or low temperatures, drought, or salt in the soil, and, in particular, resistance against diseases and pathogens. These traits can be studied in order to breed improved plants that are better adapted to their environment.

Reference work:

Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H, Rupp O, Sörensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF, Schmidt T, Gabaldón T, Lehrach H, Weisshaar B, Himmelbauer H.
“The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).”
Nature, doi: 10.1038/nature12817. Epub 2013 Dec 18.