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Theses

Intérêt et optimisation de la sélection génomique chez la truite arc-en-ciel

Abstract : The French rainbow trout breeding programs are using since 2004 a family selection method based on pedigrees established by molecular markers and performance measured on one to two thousand sibs of the candidates for selection. Genomic selection (GS) is an obvious development for these companies if it can be efficiently implemented technically and economically. A first medium density (MD) genotyp-ing tool, including 57,000 markers, being available since 2015, the aim of the thesis was to assess the interest of SG for three French lines of rainbow trout. A prerequisite was to assess whether the density of the MD chip was sufficient for the linkage desequi-librium between successive markers to allow effec-tive GS with regard to the genetic diversity of the French lines. The effective sizes of the lines were estimated at values from 50 to 70 and the linkage desequilibrium between successive markers at val-ues (r² ~ 0.30) compatible with a good GS efficiency. These results were confirmed by cross-validation studies of GS for various traits of reproduction, resistance to infectiouspancreatic necrosis (IPN), growth, cutting yield and quality flesh. With estimat-ed heritability at low (NPI) to high values (eviscer-ated and headed weight), all these traits are very polygenic: few genomic regions explain more than 1% of the genetic variance and no major effect re-gion (> 10% of the variance) has not been identified. The results obtained make it possible to conclude on an accuracy of GS superior of 10 to 30% (ac-cording to the studied traits) compared to the selec-tion based on the pedigree. They open up avenues for reflection on an economic optimization of GS by using low density chips to obtain a GS accuracy close to that obtained in MD (loss of efficiency <5% above 6000 markers) and reduction in the number of phenotyped sibs. Indeed, 700 sibs of the candi-dates for selection seem sufficient to obtain accura-cy of GS superior to the pedigree-based one. French breeding companies can therefore imple-ment a technically efficient and quickly profitable GS in rainbow trout.
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Submitted on : Tuesday, April 27, 2021 - 9:59:09 AM
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  • HAL Id : tel-03209220, version 1

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Jonathan d'Ambrosio. Intérêt et optimisation de la sélection génomique chez la truite arc-en-ciel. Génétique animale. Université Paris-Saclay, 2020. Français. ⟨NNT : 2020UPASB030⟩. ⟨tel-03209220⟩

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