Scientists map 99% of sugarcane genome

An international group of researchers led by Brazilian scientists has assembled the most complete genome sequence of commercial sugarcane. They mapped 373,869 genes or 99.1% of the total genome. The results are published in GigaScience.

Today’s commercial sugarcane hybrids have been bred over thousands of years by crossing different varieties of two species (Saccharum officinarum and S. spontaneum) and have a highly complex genome comprising 10 billion base pairs in 100–130 chromosomes. Sequencing the genome is no easy task, requiring substantial computing power to assemble the DNA fragments while keeping homologous chromosomes separate.

The variety chosen for sequencing was SP80-3280 because more data are available about this variety in scientific literature than about any other variety. During Project Sugarcane Genome (known as FAPESP SucEST, 1999–2002), 238,000 functional gene fragments from this variety were partially sequenced.

Although the technology available at the start of the project could produce long sequences, these long sequences had to be built from smaller fragments. Assembling the genome with these sequences required significant computing power, which was supplied by Microsoft.

The published sequence has made it possible for the first time to identify the diversity in genome segments called gene promoters—DNA regions that control gene expression. “Although in some cases the genes are 99.9% identical, we can detect differences in their promoters, and these help us determine which ancestor the copies derive from, S. officinarum or S. spontaneum,” Glaucia Mendes Souza, professor at the University of São Paulo’s Chemistry Institute (IQ-USP), in a press release.

Based on the information obtained from this latest whole-genome sequencing effort, researchers at USP are developing tools for the genetic improvement of sugarcane and testing several candidate genes in genetically modified plants. They are also conducting comparative genomics studies on large gene families with the aim of understanding their contributions to the sugarcane varieties used in Brazilian genetic improvement programs. They hope to find genes that can increase yields, enhance drought resistance, and contribute to the development of novel compounds from sugarcane.

“We’re also offering the community a genome browser that can be used to search for specific genes and analyze sequences in comparison with previous sequencing exercises. This will be valuable to biotech projects not just relating to sugarcane but also to other crops and plants,” said Souza.

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