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

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.

Translocation and Aquaculture Impact on Genetic Diversity and Composition of Wild Self-Sustainable Ostrea edulis Populations in the Adriatic Sea

“…The low global genetic differentiation of flat oyster in the Adriatic Sea (F ST = 0.0082) was similar to levels previously documented using polymorphic SNPs (F ST = 0.0061; Vera et al, 2019) and 16 microsatellite loci (F ST = 0.0079; Vera et al, 2016) on a broad sample collected from the Atlantic area. When populations from the Mediterranean and Atlantic regions were analyzed together using five microsatellite loci, interpopulation differentiation was found to be slightly increased (F ST = 0.019) and followed the isolation by distance pattern, separating populations according to geographic origin (Launey et al, 2002).…”

Biotic and abiotic factors shaping the genome of cockle (Cerastoderma edule) in the Northeast Atlantic: a baseline for sustainable management of its wild resources

“…southeast Ireland and Wales) using a classical RADseq technique (Etter et al, 2011). Genetic diversity observed for C. edule in our study was similar to that reported for the sister species C. glaucum (He: 0.078 -0.137; Sromek et al, 2019); however, both cockle species showed lower genetic diversity at genomic scale than other bivalves such as Placopecten magellanicus (He = 0.271 ± 0.133, Van Wyngaarden et al, 2017), Crassostrea virginica (He ~ 0.300; Bernatchez et al, 2019), Ostrea edulis (He ~ 0.300; Vera et al, 2019) and Crassostrea gigas (He ~ 0.300; Gutierrez et al, 2017), suggesting the lower genetic diversity to be a particular feature of the genus Cerastoderma, although we cannot discard that the different methodologies applied for SNP genotyping in those studies might explain this observation.…”

“…Moreover, genetic diversity existing in the wild is important for commercial species, such as C. edule, to support breeding programs for selecting high-value seed for intensive production in particular areas (Lallias et al, 2010;do Prado et al, 2018;Petereit et al, 2018;Vera et al, 2019). Genetic diversity was similar across all cockle beds studied in the Northeast Atlantic, especially when no polymorphic filtering criterion was applied (MAF; He range: 0.077 -0.086).…”

Bonamia infection in native oysters (Ostrea edulis) in relation to European restoration projects

“…Comparisons of gene expression profiles in Bonamia-free and -infected oysters are producing suites of candidate resistance conferring genes (e.g. Ronza et al, 2018;Vera et al, 2019) for testing and screening resistance.…”

“…Comparisons of gene expression profiles in Bonamia ‐free and ‐infected oysters are producing suites of candidate resistance conferring genes (e.g. Ronza et al, 2018; Vera et al, 2019) for testing and screening resistance. Proteomic approaches can also contribute to identify molecular markers of resistance to bonamiosis (de la Ballina, Villalba, & Cao, 2018).…”