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Jury :

- Zulma VITEZICA ; Professor, INP Toulouse ; Rapporteur & Examinator
- Bertrand BED'HOM; Professor, MNHN ; Rapporteur & Examinator
- François ALLAL ; Scientist, Ifremer ; Examinator
- Pascale LEROY ; Senior Scientist, INRAE (Bretagne-Normandie) ; Examinator
- Xavier ROGNON; Professor, AgroParisTech (University Paris-Saclay) ; Examinator
- Florence PHOCAS ; Senior Scientist, INRAE (University Paris-Saclay) ; PhD supervisor
Title : Evolution of genetic diversity in farmed rainbow trout populations

Abstract:

Genetic improvement of rainbow trout populations has increased production efficiency, but has contributed to a sharp decrease in genetic variability. This loss of genetic diversity may induce inbreeding depression but has also compromised long-term genetic progress and population adaptation to environmental changes. The inbreeding levels observed (through genomic indicators) in our French trout populations, question their causes and impacts. These questions are the subject of the thesis work presented.

In addition to the effects of selection and genetic drift due to the small size of breeding populations, the loss of genetic diversity in rainbow trout populations may also be explained by an imbalanced contribution of mothers to the next generation associated with excess of embryonic mortality observed from fertilization to hatching in the offspring of some mothers. The study of the local effects of inbreeding on the size, reproduction and survival performance of trout, shows that inbreeding, which is localized in certain regions of the genome, may have significant effects, without necessarily observing a genome-wide effect. While these local effects may be negative, they may also be positive in some genomic regions. The main phenomenon observed is a negative impact of recent inbreeding, explained by the accumulation of recessive alleles with unfavorable effects, directly related to the estimation of important dominance effects on reproduction and survival traits. However, inbreeding, especially accumulated in past generations, also generates positive effects. Thus, nine regions of strong homozygosity have been identified under positive selection common to three French trout lines and one American population. Genes annotated in these regions are related to domestication (growth, reproduction, behavior and immunity functions) as well as to natural fitness related to individual survival (embryogenesis, cell organization).

Therefore, understanding the impact and role of local genetic diversity is essential to better manage it in breeding programs. The use of genomic indicators of inbreeding will allow breeders to better control the trade-offs between genetic values of the breeding stock and the undesirable effects of inbreeding on their progeny. This will also allow exploiting heterosis effects, and thus improve the performance of production stocks in a sustainable way.

Keywords : Aquaculture, domestication, selection, inbreeding, dominance, genetic variability