Signatures of selection for bonamiosis resistance in European flat oyster (Ostrea edulis): New genomic tools for breeding programs and management of natural resources.

Román Vilas,Antonio Villalba,Asunción Cao,Ross D Houston,Tim P Bean,Alejandro P Gutierrez,Belén G Pardo,Carlos Fernández,Paulino Martínez,Manuel Vera,Andrés Blanco

doi:10.1111/eva.12832

Abstract

The European flat oyster (Ostrea edulis) is a highly appreciated mollusk with an important aquaculture production throughout the 20th century, in addition to playing an important role on coastal ecosystems. Overexploitation of natural beds, habitat degradation, introduction of non‐native species, and epidemic outbreaks have severely affected this important resource, particularly, the protozoan parasite Bonamia ostreae, which is the main concern affecting its production and conservation. In order to identify genomic regions and markers potentially associated with bonamiosis resistance, six oyster beds distributed throughout the European Atlantic coast were sampled. Three of them have been exposed to this parasite since the early 1980s and showed some degree of innate resistance (long‐term affected group, LTA), while the other three were free of B. ostreae at least until sampling date (naïve group, NV). A total of 14,065 SNPs were analyzed, including 37 markers from candidate genes and 14,028 from a medium‐density SNP array. Gene diversity was similar between LTA and NV groups suggesting no genetic erosion due to long‐term exposure to the parasite, and three population clusters were detected using the whole dataset. Tests for divergent selection between NV and LTA groups detected the presence of a very consistent set of 22 markers, located within a putative single genomic region, which suggests the presence of a major quantitative trait locus associated with B. ostreae resistance. Moreover, 324 outlier loci associated with factors other than bonamiosis were identified allowing fully discrimination of all the oyster beds. A practical tool which included the 84 highest discriminative markers for tracing O. edulis populations was developed and tested with empirical data. Results reported herein could assist the production of stocks with improved resistance to bonamiosis and facilitate the management of oyster beds for recovery production and ecosystem services provided by this species.

Highlights

The flat oyster Ostrea edulis has been one of the most appreciated seafood products since the Roman times and represented an important aquaculture species in Europe throughout the 20th century
European flat oyster production is severely threatened by B. ostreae in the European Atlantic area and, despite the connectivity among oyster populations mainly through larvae advection (Vera et al, 2016), the presence of this parasite is apparently restricted to specific Atlantic areas (Engelsma et al, 2014)
We took advantage of the restricted parasite distribution and the low genetic structure of flat oyster in the Atlantic area and selected three long-term affected one (LTA) and three naïve one (NV) beds from the three different genetic units previously reported (Vera et al, 2016) trying to identify genomic regions showing signatures of selection related to bonamiosis resistance

Summary

Introduction

The flat oyster Ostrea edulis has been one of the most appreciated seafood products since the Roman times and represented an important aquaculture species in Europe throughout the 20th century. Detection of quantitative trait loci (QTL) and markers associated with resistance to bonamiosis could greatly accelerate the selection of breeders making the process much more efficient Such resistance markers have been successfully found for some diseases in mollusks (He, Yu, Bao, Zhang, & Guo, 2012; Schmitt, Santini, Vergnes, Degremont, & de Lorgeril, 2013; Meistertzheim et al, 2014; Nikapitiya et al, 2014; Normand et al, 2014; Raftos, Kuchel, Aladaile, & Butt, 2014; Nie, Yue, & Liu, 2015), and several QTL for resistance to bonamiosis have been identified in flat oyster (Lallias et al, 2009; Harrang et al, 2015). The detected QTL should be considered as suggestive, since they were identified at chromosome level (P < 0.05) and in only one or two families

Methods

Results

Conclusion