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Optical maps to improve our understanding of genome complexity

Plant genomes are particularly complex because of their size and the presence of numerous repeat elements. A clearer understanding of them will enable many of the agronomic improvements that are essential in a context of climate change. The French Plant Genomic Resources Centre (CNRGV) has just acquired an innovative technology that offers a global vision of genome organisation using optical maps. This project obtained funding from the European Union and the Occitanie Regional Council.

. © INRA
Updated on 07/24/2018
Published on 04/26/2018

A clearer understanding of plant biology is essential in order to characterise and preserve genetic resources, optimise cultivation practices or design new products. More specifically, the study of plant genomes is fundamental in a context of climate change as it improves our understanding of plant’s behaviours under different conditions, as well as their evolution and adaptive capacities.

In plants, a large number of agronomic traits result from genetic variations in specific regions of the genome. The complexity in terms of the size and repetition of these variations requires the development of innovative approaches that can clarify them in terms of their structure and link them to traits of agronomical interest.

The mission of the CNRGV, which is based at the INRA Occitanie-Toulouse Research Centre, is to supply resources and technological solutions to support a variety of genomic research programmes. In this context, it has acquired a technology that enables the generation of optical maps using DNA with a very high molecular weight (Irys® from BioNano Genomics http://bionanogenomics.com/).

This technology offers a global vision of genome organisation. Optical mapping generates a physical map of a genome thanks to the production of specific fingerprints left by very large DNA molecules. It is based on the direct visualisation of long DNA molecules labelled fluorescently with an enzyme recognising a specific sequence. The DNA images thus labelled are separated on a chip in nanometric channels (nanochannels) and then analysed in order to obtain a “bar code” specific to each molecule. By comparing their bar codes, the DNA molecules can then be assembled to produce a physical map of the genome under study.

The principal applications of this technology concern completion of the assembly of genomic sequences. New generation sequencing has become an essential tool in genomics research, but the short readings generated by this technique are not able to organise highly repeated zones. Even the long readings obtained by third generation sequencing leave some zones unknown in the assemblies. Combining the two approaches (third generation sequencers and optical maps) makes it possible to obtain a reference genome of very high quality. In the context of several projects being carried out in collaboration with different laboratories, a hybrid assembly combining Bionano optical maps and sequencing data obtained with the most recent technologies has improved the quality of the final assembly. This work was carried out in a number of plant species (lupin, maize, petunia, apricot, sunflower, melon, etc.).

Optical maps also enable the study of structural differences between genotypes. By comparing the optical maps of several genotypes, it is thus possible to observe structural variations between them and link them to traits of interest.