GENOMICALLY ASSISTED RECONSTRUCTION OF THE ANCESTRAL Dicentrarchus labrax L. MEDITERRANEAN LINEAGE

Introduction

Whole-genome sequences studies of sea bass have recently revealed two ancestral lineages that diverged in allopatry for 270,000 years in the Atlantic and the Mediterranean. A postglacial contact between those lineages resulted in an asymmetrical introgression from the Atlantic to the Mediterranean background (Figure 1 - Duranton et al. 2018). In our study the base western population (WM) is introgressed at 49% by Atlantic genome, while our east-Med population (EM) at 23%. We explored different strategies to reconstruct the ancestral Mediterranean lineage by local ancestry deconvolution.

Material and Methods

A candidate population (G1) of 605 individuals was obtained after a backcross between (WM × EM) females and EM sires. Every animal was genotyped on a 57k SNP chip. We used APIS to recover the pedigree, Lep-MAP3 to construct a genetic map, and Beagle 5.1 for the phasing of the genotypes. The local ancestry for each haplotype of admixed individuals was inferred with Loter. Haplotype-resolved Atlantic genomes and Mediterranean desintrogressed haplotype-resolved genomes were used as reference for both ancestral lineages (Duranton et al. 2018). A custom-made R script was used to simulate generations of selection across different breeding strategies (backcross, BC, intercross, IC, or combinations of those). Six selection criteria were tested on each type of crossing: whole genome admixture (further referred as Med-ratio), chromosome-based Med-ratio, rarefaction of homozygous Atlantic tracts or combinations of those. For each scenario, factorial matings of 24♀×24♂ across 8 generations were simulated and repeated 20 times.

Results and Discussion

The Figure 2 display the evolution of the Med-ratio and the genomic-based inbreeding (f) across the generation for the different scenarios tested. We showed that from the candidate generation G1, displaying a Med-ratio level of 71%, a classical BC (Scenario 1) induced a stagnation at a Med-ratio level of 86% from G6. Other BC scenarios with selection of the Med-ratio (Scenarios 2 and 3) allowed to overcome the mean Med-ratio observed in the present Eastern Mediterranean population, maintaining a low level of inbreeding (below 7%), but did not allowed to reach the ancestral Mediterranean target. Pure IC strategies (Scenarios 4, 5 and 6) did not allow to reach the 98% Med-ratio target and induced a high level of inbreeding especially for Scenarios 4 and 6. The best performing strategies were those using the selection criteria on whole genome Med-ratio and including 1, 2 or 3 generations of BC followed by IC (for respectively Scenarios 7, 8 and 9). These strategies allowed to overcome the Med-ratio level of the actual EM population after just one extra generation, and to reach the breeding goal of a 98% pure Mediterranean strain at G6 for Scenario 7.

This recovered ancestral line will be key to understand the dynamics of speciation and secondary admixture in Mediterranean and Atlantic sea bass, and may represent a key resource for sea bass aquaculture in extreme environments.

Acknowledgement

This study was supported by AQUAEXCEL2020 project which received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 652831, and by the French Ministry of Environment under grant CRECHE2020.

References

Duranton, M., Allal, F., Fraïsse, C., Bierne, N., Bonhomme, F., Gagnaire, P.A. (2018). The origin and remolding of genomic islands of differentiation in the European sea bass. Nat. Commun. 9: 2518.