Novel online bioinformatics tool significantly reduces time of multiple genome analysis

UK research collaboration develops a new bioinformatics pipeline that enables automated primer design for multiple genome species, significantly reducing turnaround time.

With a rising global population leading to increased pressure on food resources, it is becoming ever more essential that crop breeding programmes work to enhance the security of global food sources.

A key aspect of this is utilising breakthroughs in genomics research to guide the selection of the individuals to incorporate in breeding schemes. It is possible to relate the DNA of a species to its physical characteristics or phenotypes, and identify areas of DNA responsible for desirable traits such as high yield or disease resistance.

Crop breeding programmes can make use of this genetic information to ensure that the preferred trait is inherited by future crop yields, helping to secure future food supply. However, the majority of tools for the analysis of DNA are designed for diploid organisms, such as humans, with one set of chromosomes, and perform poorly when applied to polyploid species such as bread wheat (Triticum aestivum L.) which has multiple sets of chromosomes.

Scientists from The Genome Analysis Centre (TGAC) and John Innes Centre have developed a bioinformatics pipeline, PolyMarker that facilitates the design of genomic specific primers for polyploid species. Once identified, these primers can be used to ascertain whether or not an individual organism has the genetic variation associated with a given trait.

As an open access tool, researchers and crop breeders can submit their own data to PolyMarker and the online tool will return suggested design primers to identify genetic variations that tag vital traits in their crop samples, with a significantly reduced turnaround time compared to the current manual method.

"The process of manually designing primers to validate in hexaploid wheat is time consuming, with PolyMarker we have reduced the design time from around a week to twenty minutes," said lead author Ricardo Ramirez-Gonzalez, PhD student at TGAC.

"PolyMarker has already demonstrated its value having been developed and applied in a research project where it identified genetic markers that signal resistance to the wheat yellow rust pathogen (Puccinia striiformis f. sp. tritici). This disease is responsible for devastating bread wheat crops and has developed 'Warrior' strains capable of infecting individuals previously believed to have tolerance."

Mario Caccamo, senior author of the paper, said: "The development of PolyMarker is a great example of the benefits of multidisciplinary research. In one new software tool, we have applied expertise in advanced algorithm development, knowledge on genetics and principles of genome architecture."

This innovative online tool has been used to generate putative KASP probes for the 820K markers designed by the CerealsDB project from the BBSRC funded WISP programme (a collaboration between John Innes Centre, the University of Bristol, Rothamsted Research, NIAB and University of Nottingham). Polymarker has also been used to design probes for the 90K iSelect markers set.

The paper, titled: "PolyMarker: A fast polyploid primer design pipeline" is published in Bioinformatics.