Developments to sequence capture technology from Roche Nimblegen, originally focused on human research, have enabled the technology to be transferred to rice and subsequently adapted to maize.
In January 2009, Roche Nimblegen and Biogemma announced a 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 equipped for large-scale genomic marker discovery for wheat and rapeseed.
While former capture technologies displayed insufficient performance on complex polyploid genomes, the Nimblegen Sequence Capture protocol developed by this collaboration is said to be an efficient, reliable, fast and cost-effective front-end method for targeted re-sequencing.
The Roche genomics portfolio allowed the combination of Nimblegen Sequence Capture arrays and 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 is 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 breakthrough in SNP discovery, in particular for species for which breeding efforts were thought to be slowed due to a lack of SNP markers.
The findings of this research was presented to the scientific community during the last Plant and Animal Genome Conference in San Diego in January 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 improvements of several agronomical traits including disease resistance, yield, drought and nitrogen use efficiency.
