Hélène Bergès

The Centre conducts research projects, provides tools, resources, and expertise for plant genome analyses. CNRGV genomic resources are used in a wide variety of research projects, from obtaining fundamental knowledge on DNA content to characterization of genes that code for certain agronomically important properties (plant yield, gustatory quality, disease resistance, etc.).

The IWGSC is the first international Consortium in which the CNRGV has been involved and Hélène has been a member of the IWGSC Coordinating Committee since the inception of the Consortium. Wheat resources figure prominently in the Center’s library, with more than 7 million samples, they represent 35% of the total resources available.

How did you get involved with the IWGSC?

At my first PAG in 2005, I was lucky enough to meet Catherine Feuillet and Kellye Eversole who gave me the opportunity to present the Centre to the IWGSC members.

This initial meeting really launched the CNRGV at the international level. Now, the Centre has hundreds of contacts and collaborations worldwide within the wheat community were we are seen as the resource center for wheat genomics.

What IWGSC resources are available at the CNRGV?

Today, all chromosomes-specific BAC libraries, as well as Minimum Tiling Path chromosome specific BAC libraries and all pools used to construct MTPs created within the IWGSC projects are available at the Centre. This represents more than 5 million samples.

Depending on their specific research goals, scientists interested in these resources can either order them for use in their lab or ask the Centre to perform a specific screen or to construct a BAC library on their specific genotype of interest. Thanks to this approach, we were able to determine for example the genomic sequence of the wheat Fusarium head blight resistance QTL Fhb1 in the resistant donor cultivar CM-82036 and compare it with the Chinese Spring susceptible reference sequence. We have highlighted candidate genes in the Fhb1 locus, among which four clearly expressed genes are absent in the susceptible reference.

We also provide training services for lab members interested in learning methods we developed at the Centre. Over the last years, we had 60 trainees that visited us to learn how to construct dedicated BAC libraries, to screen for regions of interest and to sequence BAC clones using Next Generation Sequencing (NGS), assemble, and annotate sequence data.

Has there been significant interest in using the libraries?

Over the last couple of years, we saw a shift in the kind of requests we receive. Most scientists are no longer interested in the resource itself but ask us to perform specific screens or develop BACs for their specific genotype of interest.

Based on the IWGSC resources, we created more than 20 new BAC libraries from various wheat genotypes, aiming at physically characterizing various loci involved in the resistance to abiotic or biotic stresses. These projects are established in collaboration with public or private international partners.

Aside from BAC resources, in what other services would researchers like to have access to?

Most researchers are interested in their own genotype, and, in particular, in a specific region of the genome. Having a reference genome is an invaluable tool but there could be huge differences between two genotypes, with certain regions being totally different. More often than not, regions with gaps in the reference assembly end up being regions of interest for some researchers.

Resequencing the entire genome is of no interest for them; they would rather have a better assembly and higher quality annotation available for the specific region in which they have an interest. Even though BAC libraries could be used to resolve this, we are currently developing an alternative approach using CRISPR Cas9 in vitro – called CRISPR-CATCH (Cas9-Assisted Targeting of CHromosomal segments). The aim of this approach is to avoid some time-consuming steps and lack of representation of some genomic regions observed with the BAC library strategy. The originality is to use the CRISPR-Cas9 enzyme to capture large gDNA fragments. The flanking markers of the QTL are used as guide RNA to target the specific region in the genome.

As soon as we validate all the steps of this approach, this tool will be made available for the scientific community and for the wheat community, in particular. We are convinced that this method will permit a better use of genetic diversity and will facilitate the exploitation of traits related to various phenotypes.

What do you think should be the role of the IWGSC in the future?

The value of the IWGCS is its network and ability to coordinate projects. The IWGSC should continue to coordinate projects to generate resources for the wheat community; and guarantee that these resources are accessible to all.

Projects such as resequencing of elite varieties – a wheat pangenome project – would greatly benefit from the coordination strengths of the IWGSC.

Publication date: 04/18/2017