Roche NimbleGen and Biogemma Develop Enhanced Sequence Capture technology for Wheat and Canola

Sequence Capture technology was pioneered by Roche NimbleGen with the initial products focused on human research. Subsequent developments have enabled the technology to be successfully transferred to rice and then adapted to maize. In January 2009, Roche NimbleGen and Biogemma announced their collaboration to develop a NimbleGen Sequence Capture protocol adapted to crops containing more complex genomes including polyploid crops such as wheat and rapeseed (canola). The goal of this partnership was to enhance capture performance on these complex species in order to achieve an enrichment rate that makes downstream sequencing more effective. The new NimbleGen Sequence Capture procedure was implemented and evaluated at Biogemma, and researchers are now well equipped for large-scale genomic marker discovery for wheat and rapeseed.

While former capture technologies displayed insufficient performance on complex polyploid genomes, the new NimbleGen Sequence Capture protocol developed by this collaboration has proven to be an efficient, reliable, fast, and cost-effective front-end method for targeted re-sequencing. The combined power of the Roche genomics portfolio was shown by employing the combination of NimbleGen Sequence Capture arrays with the GS FLX Titanium sequencing technology from 454 Life Sciences, a Roche company. Routine use of this complete target enrichment and sequencing solution by researchers at Biogemma has revealed that post-capture sequencing data are reliably comprised of sequences of interest, and that the long reads from the 454 Sequencing System facilitate discovery. Along with these enhancements, Biogemma has devised a downstream bioinformatic pipeline intended for read assembly and to efficiently deal with homeologs and paralogs for robust SNP identification.

NimbleGen Sequence Capture enabled this significant breakthrough in SNP discovery, in particular for species for which breeding efforts were thought to be slowed due to a lack of SNP markers, with the findings of this research presented to the scientific community during the last Plant and Animal Genome Conference in San Diego in January of 2010. Since then, several projects employing this enhanced Sequence Capture technology have been launched by Biogemma for the above-mentioned species. The development effort has also proven valuable for other species, as the protocol refinements also appear to make maize sequence capture more attainable. For these new research projects at Biogemma, several candidate genes are now under investigation for better understanding and future improval of several agronomical traits including disease resistance, yield, drought, and nitrogen use efficiency.

“We have been impressed by the speed with which Roche NimbleGen has performed the technical development expected” said Pascual Perez, CEO of Biogemma. “This improved capture technology is now used at Biogemma to optimize our marker development strategy for candidate genes from genomic and functional genomic studies, especially those from our detailed transcriptomic studies. We are now able to saturate genomic regions associated with agronomical traits with novel markers. As a suitable upstream step for current marker and marker assisted selection technologies, this breakthrough is very attractive for Biogemma’s shareholders, especially regarding species that haven’t been fully sequenced to date.”

“We also found improved capture, associated with long read sequencing of the 454 Sequencing System, allowed us to uncover intronic sequences while targeting only exons with an EST-based design. This provides researchers with access to previously uncharacterized genomic sequences that harbor higher rates of polymorphisms.” said Jean-Philippe Pichon, scientist at Biogemma.

‘We are excited with this collaboration that extends sequence capture technologies into research on complex plants such as wheat and canola,’ said Dr. Frank Pitzer, CEO of Roche NimbleGen. ‘This specific study truly shows the flexibility to quickly adapt our NimbleGen Sequence Capture technology to assist in unraveling researchers understanding of the genetic makeup of poorly characterized species and organisms.’