Major sequencing of the commercial sugarcane genome completed

An international group led by Brazilian researchers has completed the most complete sequencing of the commercial sugarcane genome ever carried out. In total, 373.869 genes were mapped, which corresponds to 99,1% of the total.

The work is the result of almost 20 years of research supported by FAPESP and paves the way for the genetic improvement of the most produced crop in the world by tons, according to the Food and Agriculture Organization of the United Nations (FAO).

O article published in the magazine GigaScience has as its first authors Glaucia Mendes Souza, professor at the Chemistry Institute of the University of São Paulo (IQ-USP) and coordinator of the Program BIOEN from FAPESP, and Marie-Anne Van Sluys, professor at the Biosciences Institute at USP and member of the Joint Coordination of Life Sciences at FAPESP.

“This is the first time that the vast majority of sugarcane genes have been visualized. In previous projects by several research groups, the sequences were assembled in a collapsed manner, due to the lack of a suitable assembly tool. Therefore, they were just an approximation”, said Souza, who coordinates the Thematic Project “Regulatory networks and signaling associated with energy cane".

“This knowledge opens up several possibilities, from applications in biotechnology and genetic improvement to gene editing [substitution or elimination of genes with specific functions]”, said Van Sluys, who coordinates the Thematic Project “Contribution of genes, genomes and transposition elements in the interaction between plants and microorganisms: case study in sugarcane".

Challenges

As the researchers explained, sequencing the sugarcane genome is not an easy task and there is still no prediction of when it will be possible to map the part that was missing in the study (0,9%). Result of crossings carried out over a few millennia between different varieties of two species – Saccharum officinarum e S.spontaneum, the sugar cane cultivated today has a very complex genetic material.

Composed of 10 billion base pairs, distributed between 100 and 130 chromosomes, the sugarcane genome demands a large computational capacity to, on the one hand, unite the sequenced pieces of DNA and, on the other, keep the homologous chromosomes (pairs with genetic information similar to that inherited from parents). To give you an idea, the wheat genome has 17 billion base pairs divided into 46 chromosomes. The human genome, in turn, has 3,2 billion base pairs also organized into 46 chromosomes.

Although the technology available at the beginning of the project already allowed the production of long sequences, these were produced from smaller fragments. To assemble the genome from these sequences, a large computational processing capacity was required, provided by Microsoft.

The challenge of sequencing the complete sugarcane genome was determinado still at the beginning of the BIOEN Program, in 2008. After watching a lecture by Souza, at a conference promoted by Microsoft and FAPESP in 2014, David Hackerman, a researcher at the Microsoft Research Institute, in Los Angeles, became fascinated with the computational challenges involved in the initiative and proposed to the company a collaboration with FAPESP, which came in the form of the project “Development of an algorithm for assembling the sugarcane polyploid genome”, coordinated by Souza and supported within the scope of the Research in Partnership for Technological Innovation Program (PITE-FAPESP). The project allowed the entry of other partners such as Bob Davidson, at the time a Microsoft researcher based in the Seattle unit and, currently, at Amazon.

With the sequencing now published, for the first time it was possible to identify diversity in promoter sequences – regions of genes that control their expression.

“Although in some cases the genes are 99,9% identical, we can observe differences in their promoters, which help determine whether the copies originate from the ancestor S. officinarum ou S.spontaneum”, said Souza.

The revelation allows studies, for example, of the functions of different copies in increasing productivity and increasing sugar and fiber. Furthermore, it makes it possible to verify which copies may be conferring advantages to the different genotypes selected by sugarcane and energy cane variety improvement programs.

“The result confirms the leadership of Brazil and the State of São Paulo in research on this plant that is so important for the country. It also reflects the anticipation of the research community in São Paulo and FAPESP regarding the challenge of learning about the sugarcane genome, in order to extract knowledge that leads to an increase in efficiency and productivity. It is always good to remember that research on sugarcane is one of the factors that led Brazil to achieve something that no country of similar size has achieved to date: having 40% of its total energy produced in a renewable way and with low carbon emissions”, he stated. Carlos Henrique de Brito Cruz, scientific director of FAPESP.

History

The SP80-3280 variety was chosen for sequencing because it has the largest amount of data available in the scientific literature. During the Sugarcane Genome Project – known as FAPESP Success Project, which lasted from 1999 to 2002 –, 238 thousand functional gene fragments of this variety had already been partially sequenced.

Currently, SP80-3280 is among the 20 most cultivated sugarcane varieties in the State of São Paulo. Furthermore, it is part of the genealogy of several commercial varieties, as it is used in new crossings. This cultivar has good agricultural productivity and ratoon sprouting (roots that remain after cutting), being one of the options for late harvesting at the end of the harvest in the State of São Paulo.

“The knowledge obtained for this variety can be applied to the study of other genotypes, mainly in the discovery of genes that control the accumulation of biomass”, he explained. Augusto Lima Diniz, co-author of the study that is currently carrying out phase at the Cold Spring Harbor Laboratory (CSHL), in the United States, as part of its post doctoral at IQ-USP.

Recently, Souza and Van Sluys participated in an international team that sequenced the genome of S.spontaneum, an ancestor that corresponds to around 10% to 15% of the commercial sugarcane genome – S. officinarum contributed the other 80% to 85%. The remaining 5% are recombinant chromosomes from these two parents. The study was published na Nature Genetics.

In 2018, Van Sluys was one of the authors of a article with the results of mapping around half of the monoploid sugarcane genome (only one chromosome from each pair).

Based on the information obtained in the current sequencing, the USP group develops tools for the genetic improvement of sugarcane and tests different candidate genes in transgenic plants. It also carries out comparative genomics studies of large gene families, with the aim of understanding their contribution to the various sugarcane varieties used in the country's breeding programs. The objective is to find genes that can increase productivity and drought tolerance, in addition to enabling the development of new compounds from sugarcane.

“We are also making a Genome Browser available to the community, a tool that allows you to search for genes of interest and analyze the sequences in comparison with previous sequences. It will be something of great value for biotechnology projects not only involving sugarcane, but also other cultivated plants”, said Souza.