Genetic markers associated with divergent selection against the parasite Marteilia cochillia in common cockle (Cerastoderma edule) using transcriptomics and population genomics data

Abstract

The common cockle (Cerastoderma edule) plays an important role in marine ecosystems and represents a valuable socioeconomic resource for coastal communities. In 2012, the cockle beds from Rı́a de Arousa (Galicia, NW Spain) were seriously decimated by the protozoan Marteilia cochillia responsible for marteiliosis. We aimed to identify single nucleotide polymorphisms (SNP) markers potentially associated with resilience to marteiliosis to be used in marker-assisted selection programs for restoring affected cockle beds and recovering their production. For this, we carried out a population genomics approach using 2b-RADseq, where 38 naive samples (before the first detection of M. cochillia in 2012) from two beds of Rı́a de Arousa were compared with 39 affected samples collected in 2018/2019 (after several years of marteiliosis occurring in the area), collected either before (15 non-exposed samples) or during (24 exposed samples) the marteiliosis outbreak. Additionally, 767 differentially expressed genes (DEG) from a previous transcriptomic study addressed during the aforementioned 2018/19 marteiliosis outbreak, were evaluated to identify SNPs showing signals of selection. Using 2b-RADseq, 9,154 SNPs were genotyped and among them, 110 consistent outliers for divergent selection were identified. This set of SNPs was able to discriminate the samples according to their marteiliosis status (naive vs affected; exposed vs non-exposed), while another 123 SNPs were identified linked to DEGs associated with the level of infection across a temporal series. Finally, combining the population genomics and transcriptomics information, we selected the 60 most reliable SNPs associated with marteiliosis resilience. These SNPs were close to or within DEGs, and many of them were related to immune response (phagocytosis and cell adhesion), defence, such as apoptosis, stress, and cellular cycle, among other functions. This set of SNPs will eventually be validated to develop a cost-effective genotyping tool for their application for obtaining cockle-resilient strains for marteiliosis.

A common garden experiment supports a genetic component underlying the increased resilience of common cockle (Cerastoderma edule) to the parasite Marteilia cochillia

“…results confirm the previous observations byPampín et al (2023) in the 2018/2019 marteiliosis outbreak in Ría de Arousa and endorse the SNP strategy performed to identify genetic markers and candidate genes associated with marteiliosis resilience. However, while most selected SNPs (68.3%) showed significant differentiation between both naïve and affected stocks after Bonferroni correction (F ST range 0.030-0.265; p < 0.0013), other SNPs, mostly coming from the transcriptomic approach, showed no differentiation and could be false positives.…”

“…Understanding the genetic basis of disease resilience can be tackled through different genomic approaches, such as the identification of outlier loci associated with resilience against the neutral genomic background through a population genomics approach or the identification of differentially expressed genes (DEG) and SNP markers associated with the infection degree, which can eventually lead to the identification of the causal mutations (Potts et al, 2021;Vera et al, 2019). In a previous study, Pampín et al (2023) The common garden design enabled us to validate the association of the selected SNPs with marteiliosis resilience in a new sampling scenario and to ascertain their role both in the long term, by comparing the genetic differentiation between naïve and affected stocks, as well as in the short term, by analyzing the growing-out stage in the naïve stock in two shellfish beds. It is important to point out that no genetic differentiation was detected between samples from Ría de Muros-Noia and Ría de Arousa, where shellfish beds of naïve and affected stocks are, respectively, located using a genomic screening with ~9000 SNPs (F ST not ≠ 0; Vera et al, 2023).…”

“…However, their application for disease management and breeding programs requires their technical validation as well as checking their ability to discriminate resilient and susceptible phenotypes. Pampín et al (2023) suggested that these candidate SNPs could underlie marteiliosis resilience and to test this hypothesis, we designed a common garden experiment in Ría de Arousa, where cockle marteiliosis occurs, using a naïve cockle stock and a cockle stock affected by marteiliosis over several generations. The specific objectives of our study were (1) to confirm that marteiliosis resilience of cockles increased through natural selection after several outbreaks and (2) to assess if allelic variants of candidate SNPs could explain the resilience to the parasite.…”

“…These experiments can be conducted in a more controlled environment at indoor facilities, or in the wild, where environmental variation is greater and less predictable. In the case of marteiliosis¸ a presumable complex trait according to previous data (Pampín et al, 2023), infection at indoor facilities is not feasible because direct transmission from SNPs putatively associated with marteiliosis resilience were fitted for MassARRAY genotyping to check their role in the differential resilience detected between both stocks. Though no significant differentiation was found between the naïve and the affected stocks with neutral markers, 28 SNPs showed significant divergence between them, suggesting that these SNPs were involved in directional selection during eight generations (to the most) of marteiliosis pressure (long-term selection).…”

“…A previous genome scan in common cockle identified a set of 233 candidate SNP markers associated with resilience to marteiliosis using population genomics and transcriptomics approaches in samples with different degree of infection or exposure status collected in Ría de Arousa (Pampín et al, 2023). A total of 45 SNPs were selected as the most confident markers: 12 showing signals of divergent selection from 9154 2b-RAD genotyped SNPs (Vera et al, 2022), and 33 associated with differentially expressed genes (DEG) through RNAseq from the enriched digestive gland transcriptome (Pardo et al, 2022).…”