Scientists develop a new tool for studying the sugarcane genome

Researchers from Brazil and the United States describe the construction of a bacterial library containing sugarcane genomic DNA. This library could be used as a tool to further several lines of study.

By Fábio de Castro

Agência FAPESP – A tool developed by a group of researchers from Brazil and the United States should help the scientific community study numerous aspects of the complex sugarcane genome.

An article published in the open access BioMed Central Research Notes described the construction and sequencing of a Bacterial Artificial Chromosome (BAC) library of an important commercial sugarcane variety.

BAC libraries are considered fundamental tools for the detailed characterization of chromosome regions that contain genes of interest. These libraries make the large-scale physical mapping of the genome possible.

The study’s participants included scientists from the Universidade Estadual de Campinas (Unicamp) Molecular Biology and Genetic Engineering Center (CBMEG) and the Biology Institute of the Department of Genetics and Evolution, as well as researchers from the Embrapa Informática na Agricultura and the Arizona Genomics Institute at the University of Arizona.

According to the lead author of the study, IB-Unicamp professor and CBMEG Laboratory on Regulation of Gene Expression Studies coordinator, Paulo Arruda, the sequencing of a complex genome like that of sugarcane could help the scientific community identify useful genes and compare them to those of other plants.

“We used the library as a tool to understand the phylogenetic relationship – that is, the evolutionary lineage – among sugarcane, sorghum and corn. The article describes how the library was prepared, from the fragmentation of a portion of the genome to the cloning and analysis. This library could be used by groups that study different aspects of the sugarcane genome,” Arruda explained in an interview with Agência FAPESP.

The group headed by Arruda has worked for years on several aspects of the sugarcane genome. Currently, one of their major research interests involves the genetic relationship among sugarcane and other important species, such as corn and sorghum, throughout evolution.

For some time, the group has been working with the hypothesis that corn originated from a cross between two species of the same family.

“Our hypothesis is that a sugarcane ancestor could be involved in this process. But, in order to answer this question, we needed to sequence at least part of the sugarcane genome,” explains Arruda.

The sugarcane genome, however, contains roughly 750 million nucleotides – the “letters” that form a genetic code – which make its sequencing extremely complex.

“One of the possible approaches to address this is to construct a BAC library. First, we ‘slice’ the genome into smaller pieces of roughly 125,000 nucleotides on average. Then, we clone these segments in bacteria. With a collection of bacteria containing these fragments of the sugarcane genome, we can rapidly produce a large quantity of DNA for study,” explains Arruda.

Available tool

In the article, the scientists describe how they prepared a collection of 36,000 bacteria, each of which contains a sugarcane genome fragment of approximately 125,000 nucleotides.

“We obtained a sample from this library and sequenced some of these fragments of 125,000 nucleotides so that we could compare them to sorghum genome,” said Arruda.

The researchers discovered regions of microsynteny between the cloned inserts of the sugarcane genome and the sorghum genome.

“It was a quick first analysis, showing that these fragments are well distributed and reveal that it is possible – from a nucleotide content perspective – that the corresponding sugarcane haploid genome is a little smaller than the sorghum genome,” explains Arruda.

According to Arruda, other groups could utilize the tool to study completely different aspects of the sugarcane genome, such as specific fragments that control the development of the plant, or cytological studies focused on the organization of the chromosomes in the nucleus.

“Once constructed, these libraries could be useful for innumerous types of studies,” he said.

The article, BAC Library of the sugarcane variety (Saccharum sp.) and its inferred microsynteny with the sorghum genome, by Paulo Arruda et al., can be read at www.biomedcentral.com/1756-0500/5/185/abstract.