After almost 20 years of research, an international group of researchers led by Brazilian scientistshas assembled the most complete genome sequence of commercial sugarcane. They mapped 373,869 genes or 99.1 percent of the total genome. This is a basis for the genetic improvement of the world’s largest crop in tonnage according to the U.N. Food & Agriculture Organization (FAO),
An article describing the study is published in GigaScience. Its lead authors are Glaucia Mendes Souza, a full professor at the University of São Paulo’s Chemistry Institute (IQ-USP) and a member of the steering committee for the FAPESP Bioenergy Research Program (BIOEN- FAPESP), and Marie-Anne Van Sluys, a full professor at the same university’s Bioscience Institute (IB-USP) and a member of FAPESP’s Life Sciences Adjunct Panel.
“It’s the first time all the genes of the sugarcane plant, or the vast majority, have been seen. In previous projects by various research groups, the sequences had to be collapsed for lack of a proper assembly tool, so they were only an approximation,” said Souza.
As the researchers explained, 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.
Although the technology available at the start of the project was capable of producing 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 idea for the whole-genome sequencing of sugarcane dates to the onset of the BIOEN Program in 2008. A presentation by Souza at a conference held by Microsoft and FAPESP in 2014 left David Hackerman, a researcher at Microsoft Research Institute in Los Angeles, fascinated with the computational challenges posed by the initiative. He proposed a collaboration with FAPESP, which took the form of the project “Development of an algorithm for the assembly of the sugarcane polyploid genome,” with Souza as the principal investigator funded by FAPESP’s program Research Partnership for Technological Innovation (PITE). The project was a collaboration with other partners, such as Bob Davidson, then a researcher with Microsoft at its Seattle unit and now with Amazon.
“Although in some cases the genes are 99.9 percent identical, we can detect differences in their promoters, and these help us determine which ancestor the copies derive from, S. officinarum or S. spontaneum,” Souza said. The achievement permits studies, for example, of how different copies contribute to increased sugar and fiber yields and which copies may be advantageous to the different genotypes selected by programs to breed sugarcane varieties for sugar and for energy.
There is always recall that research on sugarcane is one of the factors that enabled Brazil to achieve something no other country of a similar size has achieved to date, namely, producing 40 percent of its total energy from renewables and with low carbon emissions. This result confirms Brazil’s and São Paulo state’s leadership in research on sugarcane which is such an important plant for our country. It also reflects foresight on the part of the São Paulo research community and of FAPESP, regarding the challenge of learning about the sugarcane genome to extract knowledge leading to increased efficiency and productivity.