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Last update: May 2021

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A powerful new tool for identifying genes of interest in farmed fish: a high-density chip with 665,000 genetic markers for rainbow trout

@INRAE M. Dupont-Nivet
The knowledge of the variations of the DNA sequence which constitutes the genome of an individual is a central information in genetic research. If it is possible to sequence the entire genome to know all these variations, it remains very expensive. Genotyping chips, which are much less expensive, make it possible to work with an intermediate density of information (corresponding to a selection of positions, or "markers", judiciously distributed over the genome). However, their efficiency is directly related to the number of available markers. For rainbow trout, the leading farmed fish species in France, INRAE and its partners have just developed a new high-density genotyping chip (665,000 markers, i.e. about 15 times more than the best tools available so far), which greatly increases the analysis power obtained. By providing access to much more precise genomic information, this chip will make it easier to identify the genes responsible for differences between individuals and to develop more effective selection procedures to adapt animals to changing environmental conditions.

To identify the areas of the genome involved in variations in a trait of interest (for example, resistance to a disease), it is possible to sequence the entire DNA of individuals evaluated for this trait, and then to look for statistical associations between the genetic variations detected and the variations in the trait observed between individuals. However, this approach is very expensive, especially since in order to find such associations, it is necessary to study several hundred to several thousand individuals. Therefore, instead of analyzing the information at each position of the genome (sequencing), we study the information reduced to a given number of positions or "genetic markers". These markers, judiciously distributed throughout the genome and chosen to maximize the chances of observing differences between individuals, "summarize" the information present in the entire genome in an inexpensive way. This technique is called pan-genomic genotyping, and all the genetic markers selected are analyzed using a chip called a "genotyping chip".

In aquaculture, as for other farmed animal species, access to a small number of complete genomic sequences and the development of low (a few thousand markers) or medium density (a few tens of thousands of genetic markers) genotyping tools have, since the 2010s, already made it possible to implement genomic selection and improve important traits in farming, such as fillet quality or disease resistance. In trout, the first research work used low to medium density genotyping that identified the main regions of the genome linked to resistance to two major diseases, flavobacteriosis (caused by a bacterium) and infectious pancreatic necrosis (caused by a virus). However, with this number of markers, the localization of the regions of interest remains too imprecise to allow the identification of genes precisely associated with resistance/susceptibility to the infectious agent.

To develop a reliable, accurate and versatile genotyping tool (i.e. adapted to trout populations of diverse genetic origins), it is essential to identify markers in the genome that are as representative as possible of this diversity. To this end, researchers from INRAE's GABI unit collaborated with American researchers from the USDA's Agricultural Research Service to sequence the complete genome of 159 trout of as diverse origins as possible. The sequencing allowed them to identify more than 32 million markers, from which they carefully selected the 665,000 most informative markers in both French and North American trout populations to develop the first "high density" genotyping chip. This new tool was developed with the help of ThermoFisher Scientific and used by the INRAE Gentyane genotyping platform, in partnership with the French Poultry and Aquaculture Breeders' Union (SYSAAF), as part of a research project* on trout resistance to increased temperature and hypoxia (oxygen deficit). With this high-density chip, the localization of genomic regions of interest for these two climate change adaptation traits is 25 times more accurate than with previously available tools. This major advance will considerably facilitate the identification of genes of interest in trout, and thus accelerate the fine understanding of the determinism of traits and the improvement of the efficiency of selection for breeding by combining more effectively genetic progress and preservation of the genetic diversity of populations.

*Hypotemp project supported by FEAMP (European Maritime Affairs and Fisheries Fund), n° P FEA470019FA1000016

  

EU_FeAMP

See also

Maria Bernard, Audrey Dehaullon, Guangtu Gao, Katy Paul, Henri Lagarde, Mathieu Charles, Martin Prchal, Jeanne Danon, Lydia Jaffrelo, Charles Poncet, Pierre Patrice, Pierrick Haffray, Edwige Quillet, Mathilde Dupont-Nivet, Yniv Palti, Delphine Lallias, Florence Phocas (2022). Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping. Frontiers in Genetics 13 : 941340. https://doi.org/10.3389/fgene.2022.941340