Crop Biotech Update

Software Locates Sugarcane Genes of Interest

May 22, 2019
The sugarcane grown today is a hybrid from two species, Saccharum officinarum – the original sugarcane domesticated in India 3,000 years ago – and S. spontaneum. The genome of sugarcane which was completed a few months ago contains 10 billion base pairs in 100-130 chromosomes, three times the size of the human genome.

According to Marcelo Falsarella Carazzolle, bioinformatics coordinator in the Genomics and Bioenergy Laboratory at the University of Campinas's Biology Institute (IB-UNICAMP) in São Paulo, Brazil, the sugarcane genome has grown to be a giant, and working on it with current genomic methods is difficult. Carazzolle and his team developed a different strategy which is much less costly and time consuming, designed to map specific portions of the genomes of polyploid plants.

The research team developed Polyploid Gene Assembler (PGA), a software that will help reconstruct complex genomes such as the sugarcane's. PGA focused on small portions of the genome, corresponding to about 1%-2%, exactly where the genes of interest are located. Carazzolle's team identified a total of 39,234 genes, 60.4% of which were clustered into known grass gene families.

"Our findings for the genome of S. spontaneum highlighted for the first time the molecular basis of certain significant characteristics, such as high productivity and resistance to biotic and abiotic stress. These results can be used in future functional and genetic studies. They will also support the development of new sugarcane varieties."

For more details, read the news article in Agência FAPESP.