AUTHOR=Pampín M. , Casanova A. , Fernández C. , Blanco A. , Hermida M. , Vera M. , Pardo B. G. , Coimbra R. M. , Cao A. , Iglesias D. , Carballal M.J. , Villalba A. , Martínez P. 

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

JOURNAL=Frontiers in Marine Science

VOLUME=Volume 10 - 2023

YEAR=2023

URL=https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2023.1057206

DOI=10.3389/fmars.2023.1057206

ISSN=2296-7745

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 Ría 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 its production. For this, we carried out a population genomics approach, where naive samples from two beds of Ría de Arousa (i.e., before the first detection of M. cochillia in 2012) were compared with samples collected in 2018/2019 in Lombos do Ulla (affected: after several years of marteiliosis in the area), collected either before (non-exposed) or during (exposed) the marteiliosis outbreak occurring in that period. Among 9,154 SNPs genotyped using 2b-RADseq on a sample of 77 individuals, 110 consistent outliers for divergent selection were detected when comparing naive (38 samples) vs 2018/19 affected (39 samples) or exposed (24) vs non-exposed (53) samples. This set of SNPs was able to discriminate between the samples according with their marteiliosis status (naive vs affected; exposed vs non-exposed). Additionally, an evaluation of 767 differentially expressed genes (DEG) from a previous transcriptomic study performed in the aforementioned 2018/19 marteiliosis outbreak, enabled identifying 123 SNPs linked to DEGs associated with the level of infection across a temporal series. Lastly, combining the population genomics and transcriptomics approaches, we selected the 60 most reliable SNPs, taking the new chromosome-level assembled cockle’s genome as a reference. These markers were close to or within DEGs, many of them related to immune response (phagocytosis and cell adhesion), defense, such as apoptosis mechanism, stress, and cellular cycle, among other functions. This set of SNPs will be eventually validated to develop a cost-effective genotyping tool for their application for obtaining cockle resilient strains to marteiliosis.