United Kingdom
November 4, 2015
The second Wheat Breeders’ Workshop entitled, “Towards A Sustainable Future for Wheat Genomics” was held at The Genome Analysis Centre (TGAC) on 20-21 October 2015 to show new and upcoming resources to wheat breeders and involve them in future development of the tools they stand to benefit from.
Supported by a BBSRC ‘strategic longer and larger’ (sLoLa) grant the workshop gathered experts in genomics and bioinformatics from five world-leading, UK-based institutes to give presentations and provided tuition to help breeders improve crop yields using genomic analysis resources. Some hands-on exercises were provided, to help attendees get to grips with use cases to highlight the value of what is available.
Day one began with an introductory update on the improved upcoming wheat genome resources, from Matt Clark (Project Co-PI and Group Leader at TGAC) and Jon Wright, (Scientific Programmer, Algorithms Research and Development at TGAC). A new Chinese Spring wheat genome assembly is due for public release in November 2015.
Day one’s principle topic, though, was genetic variation in the wheat plant family (Triticeae) and access to improved seed stock from Seedstor presented by Ksenia Krasileva (Group Leader, TGAC), Cristobal Uauy (John Innes Centre (JIC)) and Andy Philips (Rothamsted Research (RRes)). Another useful resource for breeders to use these variation data is Polymarker, a tool for designing primers that allow the verification of sub-genome-specific gene variants in breeding stock.
Mark Winfield (University of Bristol) gave a presentation about CerealsDB, a public resource that focuses upon wheat SNP diversity and haplotypes. Keywan Hassani-Pak (RRes) presented QTLNetMiner a web application that can interrogate plant and animal knowledge networks. Then there was also a walk-through of many of the featured plant genomic tools on Ensembl, from Dan Bolser and Denise Carvalho-Silva (EMBL-EBI).
Day two tackled more in-depth genomic tools and workflows, including Ensembl Plants, Compara and Biomart and then a recap of the upcoming wheat genome assembly from Bernardo Clavijo, (Leader of Algorithms Research and Development at TGAC).
It is impossible to overstate the importance of high-quality wheat genome assemblies to breeders – there is a synergistic improvement as marker maps, genetic maps and physical maps are combined.
The new assembly was created de novo in a Whole Genome Shotgun approach, which is significant because the technique can subsequently be applied to further wheat cultivars of more direct relevance to the breeders – candidate wheat lines were proposed. TGAC is working to bring down the cost to make this approach cost-effective and accessible to all crop breeders.
The event closed with an open discussion, chaired by Cristobal Uauy (JIC), focused upon how wheat breeders rate the current wheat resources, and what they want to see in the immediate (and more distant) future.
Feedback from participants on the workshop included:
“I now feel much more up to date with the tools that are available to me to use which is great, I no longer feel like I was living in the dark ages!”
“Excellent workshop on the top of the latest developments.”
“Have already planned meetings to provide feedback to the larger wheat breeding community in our company.”
On the genome browser Ensembl: “Excellent database for access to genomic information. The variant space can still be improved, I think.”
On the CerealsDB browser: “Excellent and holistic information source for assays available to the breeding.”
“The TILLING resource obviously provides opportunities we did not have before. The information on the DISCOVAR assembly has also changed my mindset on the feasibility of full genome sequencing in wheat.”
“Despite the fact that I might not be using the different, described tools, I found the workshop very interesting and I am glad to know that those kinds of tools exist.”
The workshop provided a unique opportunity to put opinions, questions and ideas to influential researchers, and emphasis was placed on the availability of ongoing training and support after the event.
Mike Bevan (Project Co-PI, JIC), said: “The workshop was very timely as it facilitated discussion of the new wheat genome sequence assemblies and how they can be used for crop improvement. Linked to the new functional genomics resources generated in the sLoLa, the genome assemblies promise to transform wheat biology and breeding activities.”
Christine Fosker, Workshop lead and Head of Research Faculty Office at TGAC, said: “TGAC is proud to host such a progressive and practical demonstration of the value of genomic technology for those who are best placed to build upon it.”
The workshop trainers represented the following institutions: TGAC, JIC, University of Bristol, RRes, EMBL-EBI.
TGAC is strategically funded by BBSRC and operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.
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