Estimates of genetic variability and inbreeding in experimentally selected populations of European sea bass

Type Article
Date 2017-10
Language English
Author(s) Hillen J. E. J.1, Coscia I.1, 6, Vandeputte Marc2, 3, Herten K.4, Hellemans B.1, Maroso F.5, Vergnet Alain3, Allal FrancoisORCID3, Maes G. E.1, 4, 7, Volckaert F. A. M.1
Affiliation(s) 1 : Univ Leuven, Lab Biodivers & Evolutionary Genom, Ch Beriostr 32, B-3000 Leuven, Belgium.
2 : Univ Paris Saclay, GABI, INRA, AgroParisTech, F-78350 Jouy En Josas, France.
3 : IFREMER, MARBEC, UMR9190, Chemin Maguelone, F-34250 Palavas Les Flots, France.
4 : Univ Leuven, Ctr Human Genet, Lab Cytogenet & Genome Res, Genom Core, B-3000 Leuven, Belgium.
5 : Univ Padua, Dept Compared Biomed & Food Sci, I-5020 Legnaro, Italy.
6 : Sch Environm & Life Sci, Peel Bldg, Salford M5 4WT, Lancs, England.
7 : James Cook Univ, Coll Sci & Engn, Ctr Sustainable Trop Fisheries & Aquaculture, Comparat Genom Ctr, Townsville, Qld 4811, Australia.
Source Aquaculture (0044-8486) (Elsevier Science Bv), 2017-10 , Vol. 479 , P. 742-749
DOI 10.1016/j.aquaculture.2017.07.012
WOS© Times Cited 5
Keyword(s) Artificial selection, ddRAD, Fish, Genetic diversity, Genomics, Inbreeding
Abstract

The aquaculture industry has increasingly aimed at improving economically important traits like growth, feed efficiency and resistance to infections. Artificial selection represents an important window of opportunity to significantly improve production. However, the pitfall is that selection will reduce genetic diversity and increase inbreeding in the farmed stocks. Genetic tools are very useful in this context as they provide accurate measures of genetic diversity together with many additional insights in the stock status and the selection process. In this study we assessed the level of genetic variability and relatedness over several generations of two lines of experimentally selected European sea bass (Dicentrarchus labrax L.). The first line was selected for growth over three generations and the second line for both high and low weight loss under a starvation regime over two generations. We used a genomic approach (2549 single nucleotide polymorphism markers derived from double digest restriction site associated DNA sequencing) in combination with eight microsatellites to estimate genetic variation, relatedness, effective population size and genetic differentiation across generations. Individual heterozygosity estimates indicated that the selected lines showed no significant reduction in diversity compared with wild populations. There was, however, a decreasing trend in allelic richness, suggesting the loss of low frequency alleles. We compared the estimates of effective population size from genetic markers with pedigree information and found good correspondence between methods. This study provides important insights in the genetic consequences of selective breeding and demonstrates the operational use of the latest genomic tools to estimate variability, inbreeding and at a later stage domestication and artificial selection.

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