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New DivSeek Initiative to Encourage Genomic Characterization of Seed Bank Holdings

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NEW YORK (GenomeWeb) – A new initiative aims to foster the genomic characterization of the 7 million crop accessions currently being stored at gene banks around the world.  

Called Diversity Seek, or DivSeek, the effort brings together gene banks, researchers, plant breeders, and big data experts, all of whom intend to use genomics to unlock crop diversity, ultimately leading to greater food security and sustainable agriculture.

Though DivSeek itself will not undertake the generation of data on these holdings, it will provide an arena for different member organizations to partner on sequencing projects and to share genomic information, according to those familiar with the initiative.

"The fundamental motivation behind DivSeek is that today's technology landscape — mostly in the area of genomics and big data, but increasingly also in the area of high-throughput phenotyping — finally enables the systematic and comprehensive characterization of entire gene bank collections," said Peter Wenzl, DivSeek liaison for the Global Crop Diversity Trust. "That's something that simply wasn't technically and economically feasible until just a few years ago."

The Crop Trust is a Bonn, Germany-based organization that seeks to conserve and disseminate crop diversity for food security. It includes among its missions the funding of 11 of the world's largest gene banks, in addition to the maintenance of the Global Seed Vault, a biorepository located on a remote Norwegian island north of the Arctic Circle, where back-ups of much of the world's crop accessions are stored.

The Crop Trust instigated the formation of DivSeek earlier this year, hoping to encourage the use of approaches like next-generation sequencing to generate more data on genebank holdings, information that could later be used to broaden crop diversity. And, according to Wenzl, continued declines in the cost of NGS, plus the ability to multiplex samples, made it a compelling time to begin pooling resources within DivSeek.

"Genebanks have long wanted to fully unlock their genetic potential," said Wenzl. "Many scientists in genomics research are keen to leverage cutting-edge technologies for food security. And breeders have long wanted to more effectively utilize genetic variation in genebanks to speed up genetic gains in their programs."

DivSeek, he added, "could probably be defined as the area where the interests of these stakeholder groups intersect and reinforce each other."

The initiative first met in San Diego in January during the annual Plant and Animal Genome Conference. According to a white paper recently produced by the effort, dozens of members were present at its founding, including representatives of some of the world's largest gene banks, such as the International Center for Agricultural Research in the Dry Areas in Beirut, Lebanon; the International Rice Research Institute at Los Baños in the Philippines; and the International Crops Research Institute for the Semi-Arid Tropics in Hyderabad, India.

Ruth Bastow, executive director of the Global Plant Council in London, said that the effort has a number of core ambitions. These include facilitating an integrated approach to information management by "promoting the use of commonly used data-management standards to enable information integration and interoperability among data sets and repositories."

The Global Plant Council, together with Crop Trust, the CGIAR Consortium Office, and the Secretariat of the International Treaty on Plant Genetc Resources for Food and Agriculture make up DivSeek's joint facilitation unit, which oversees its activities.

DivSeek's plan to create a shared information management system definitely ranks among its priorities and is heavily featured in its white paper, which outlines the development of a unified information management platform to share genotypic and phenotypic data associated with gene bank germplasm.

This initiative also aims to create a system of internationally agreed-upon standards, protocols, tools, and best practices for generating and managing tools related to gene bank holdings, according to the paper.

Bastow acknowledged the need for such standards, citing a "revolutionary change" in technologies at gene banks' disposal, "such as inexpensive and rapid DNA sequencing, remote sensing, precision phenotyping, and big-data analytics." When combined with a harmonized information management system developed via DivSeek, users should be able to "enable dramatically different approaches for investigating and exploiting plant genetic variation to develop high-yielding, nutritious crops that are able to deal with a fluctuating environment," Bastow maintained.

While DivSeek plugs ahead towards those goals, Sarah Ayling, who leads the computational genomics group at The Genome Analysis Centre (TGAC) in Norwich, UK, said that the effort is still in development, and that much of the past few months have been spent ironing out organizational questions, such as how to operate, membership requirements, and how to engage broader communities.

Ayling, who sits on DivSeek’s steering committee, characterized the initiative as a forum for partners to create best practices, share experience, and work towards the goals of characterizing gene bank holdings. She noted that it seems natural that many projects discussed within DivSeek will likely rely on NGS to generate data on accessions.

"Since we are looking for genetic diversity, sequencing is the natural direction to take," said Ayling. While DivSeek will not undertake sequencing projects, it can advise on how to best carry them out. "DivSeek can help people to decide … the best way to accomplish this," she said.

DivSeek's plan to develop information management systems will overlap with NGS in the area of allele mining, where breeders will be able to query a database of gene bank holdings in order to identify accessions with particular alleles that could be used to diversify and improve future generations of a particular crop.  

"It will also help gene bank managers to manage accessions," Ayling noted of such a system, "allowing managers to understand allelic diversity in their banks and to capture more diversity from generation to generation."

And according to the Crop Trust's Wenzl, his organization will take a leading role in ensuring that DivSeek's goals will eventually be realized.

"As DivSeek gradually takes on a life of its own, the Crop Trust's continuing involvement in DivSeek will likely focus on representing the gene banks' interests within DivSeek and helping to make sure that the growing body of characterization data is linked back to the physical genetic resources conserved in gene banks," said Wenzl.

This is important for DivSeek for two reasons, he added. Echoing Ayling, he noted that genetic and phenotypic characterization data will "shed unprecedented light" on the composition of gene banks, "enabling them to identify duplicates and to more effectively structure their holdings in alignment with the diversity patterns of their holdings."

But moreover, the creation of such information management tools via DivSeek will permit the allele mining that Ayling mentioned. "By attaching characterization data to accession data, gene bank users will increasingly be able to Google gene bank accessions for any combination of genetic and phenotypic traits," said Wenzl. This ability, he noted, will enable gene bank users to "identify and use genetic resources in a more targeted and effective manner than has been possible until now."

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