1. Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding
- Author
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D’Ambrosio, Jonathan, Phocas, Florence, Haffray, Pierrick, Bestin, Anastasia, Brard-Fudulea, Sophie, Poncet, Charles, Quillet, Edwige, Dechamp, Nicolas, Fraslin, Clémence, Charles, Mathieu, Dupont-Nivet, Mathilde, European Maritime and Fisheries Fund, FranceAgrimer (2015-0638 RFEA47 0016 FA 1000016 2017-0239), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), FranceAgrimer 2015-0638 RFEA47 0016 FA 1000016 2017-0239, AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), FranceAgrimer2015-0638, RFEA47 0016 FA 1000016, and 2017-0239
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[SDV.GEN]Life Sciences [q-bio]/Genetics ,Run of homozygosity ,Heterozygosity ,lcsh:QH426-470 ,Trout ,[SDV]Life Sciences [q-bio] ,Inbreeding coefficient ,Autozygosity ,SNP ,Polymorphism, Single Nucleotide ,lcsh:Genetics ,[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,Effective population size ,Fish ,Linkage disequilibrium ,Animals ,Inbreeding ,lcsh:Animal culture ,ComputingMilieux_MISCELLANEOUS ,Research Article ,Selective Breeding ,lcsh:SF1-1100 - Abstract
Background Selective breeding is a relatively recent practice in aquaculture species compared to terrestrial livestock. Nevertheless, the genetic variability of farmed salmonid lines, which have been selected for several generations, should be assessed. Indeed, a significant decrease in genetic variability due to high selection intensity could have occurred, potentially jeopardizing the long-term genetic progress as well as the adaptive capacities of populations facing change(s) in the environment. Thus, it is important to evaluate the impact of selection practices on genetic diversity to limit future inbreeding. The current study presents an analysis of genetic diversity within and between six French rainbow trout (Oncorhynchus mykiss) experimental or commercial lines based on a medium-density single nucleotide polymorphism (SNP) chip and various molecular genetic indicators: fixation index (FST), linkage disequilibrium (LD), effective population size (Ne) and inbreeding coefficient derived from runs of homozygosity (ROH). Results Our results showed a moderate level of genetic differentiation between selected lines (FST ranging from 0.08 to 0.15). LD declined rapidly over the first 100 kb, but then remained quite high at long distances, leading to low estimates of Ne in the last generation ranging from 24 to 68 depending on the line and methodology considered. These results were consistent with inbreeding estimates that varied from 10.0% in an unselected experimental line to 19.5% in a commercial line, and which are clearly higher than corresponding estimates in ruminants or pigs. In addition, strong variations in LD and inbreeding were observed along the genome that may be due to differences in local rates of recombination or due to key genes that tended to have fixed favorable alleles for domestication or production. Conclusions This is the first report on ROH for any aquaculture species. Inbreeding appeared to be moderate to high in the six French rainbow trout lines, due to founder effects at the start of the breeding programs, but also likely to sweepstakes reproductive success in addition to selection for the selected lines. Efficient management of inbreeding is a major goal in breeding programs to ensure that populations can adapt to future breeding objectives and SNP information can be used to manage the rate at which inbreeding builds up in the fish genome. Electronic supplementary material The online version of this article (10.1186/s12711-019-0468-4) contains supplementary material, which is available to authorized users.
- Published
- 2019
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