SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP-array

Thermal Selection Shifts Genetic Diversity and Performance in Blue Mussel Juveniles

Exploring evolutionary and physiological responses to environmental stress is crucial for assessing the effects of climate change on wild populations. Mussels, key inhabitants of the benthos with high ecological and economic value, are a particularly vulnerable species that may be pushed to their ecological limits as warming threatens their survival and population stability. Species within the Mytilus edulis complex are commonly found in temperate regions globally; in the Baltic Sea, populations are formed by M. edulis and M. trossulus hybrids with low levels of M. galloprovincialis introgression. This study investigates the mechanisms through which resilience towards global warming may be fast-tracked in Baltic mussels (Kiel, Germany). For this, we studied two cohorts of juvenile mussels (recently settled animals), one exposed to an extreme heat event early in life and one naïve to this stressor. Both cohorts were later exposed to experimental temperatures ranging from 21°C to 26°C, with animal performance measured after 25 days. Impacts of thermal stress on the genetic composition of each cohort was then assessed by genotyping 50 individuals using a blue mussel 60 K SNP-array. We observed a significant increase in M. edulis genotypes together with a decrease in M. trossulus in the challenged cohort, compared to naive juveniles. We also found exposure to high temperature affected performance of mussel cohorts, reducing dry tissue weight of selected individuals. Results from this study provide insights on how selection through thermal stress impacts performance and genetic composition of key globally distributed intertidal species, with important implications for understanding and managing mussel populations under future warming scenarios.

The mytilin gene cluster: Shedding light on the enigmatic origin of mussel dispensable genes

Mussels exhibit a sophisticated innate immune response characterized by many highly variable molecules responsible for recognizing and killing potential pathogenic microorganisms. The complexity of this molecular arsenal is marked by the occurrence of gene presence-absence (PAV), a phenomenon that targets numerous expanded lineage-specific gene families. This phenomenon enhances inter-individual sequence variability, further enriching the diversity of the repertoire of molecules involved in the immune response. Until now, the origin of mussel dispensable genes, which, unlike core genes, are not shared by all individuals, has remained elusive. In this study, by analyzing the resequenced genomes of more than 160 individuals in four distinct species of the Mytilus complex, we characterize the repertoire of mytilin genes encoding hemocyte-specific antimicrobial peptides (AMPs). We define a canonical gene architecture comprising four protein-coding genes and two pseudogenes in most haplotypes. However, the organization of the locus displays a marked intra-specific diversity due to the presence of variable alleles, the frequent pseudogenization of mytilin G1 and structural variants associated with additional dispensable mytilin genes, which often retain features that support functional preservation. Molecular phylogeny supports an ancient origin for dispensable mytilin genes, predating the radiation of modern Mytilus species. This suggests that most widespread extant haplotypes derive from a larger and more complex ancestral mytilin gene cluster and that dispensable mytilin genes are vestigial AMPs that have been retained only in a few populations where their presence may have contributed to fitness advantages and local adaptation.

Genome-wide association mapping for heat shock tolerance in Mercenaria mercenaria through SNP microarray analysis

BACKGROUND

The northern quahog Mercenaria mercenaria is a major aquaculture species on the US East Coast, and heat resistance is the most sought trait for aquaculture. This study aimed to establish a genome-wide association for heat tolerance using a 66K SNP array for M. mercenaria. Quahogs from three farms were combined for a heat challenge at 1 °C per day from 24 °C to 35 °C and stay for two days (Phase I), decreasing to 27 °C in 24 h, to 24 °C in another 24 h, and maintaining at 24 °C (Phase II) until no one dead within 48 h at 24 °C (Phase III). Dead and live quahogs were sampled for genotyping using the SNP array.

RESULTS

During the heat challenge, different mortalities among the quahogs from the three farms were identified at 38, 46, and 55% at Phase I, and 36, 30, and 29% at Phase II. For the survivors (Phase III), no changes were found in body weight before and after the heat shock challenges (p < 0.265). The PCA analyses of SNP frequencies indicated significant genetic differences associated with quahog survival under heat stress across the different farms. The heritability of the heat tolerance was 0.680 ± 0.063. GWAS analysis indicated that one SNP exhibited a significant association with the time-to-death trait on chromosome 7 (p = 1.98 × 10- 5). More significant SNPs (p < 10- 3.5) were inside genes that have been reported to function in heat tolerance such as serine/threonine-protein kinase 31 and carbohydrate sulfotransferase 11, and some genes found within 50 K bp far from SNP sites have a relationship with heat tolerance such as toll-like receptors 4 and 6 (TLRs 4 and TLRs 6), uracil-DNA glycosylase, and a disintegrin and metalloproteinase with thrombospondin motifs gon-1 (ADAMTs).

CONCLUSION

The fastStructure analysis revealed the proportions of different ancestral components within the quahogs from different farming stocks, highlighting that the genetic factors may contribute to their varying survival rates under heat stress. The associated genes have potential roles in immune response, cellular stress, and tissue repair. The findings highlighted the power of high-throughput approaches for the identification of superior quahog genotypes for further breeding.

Decoding Local Adaptation in the Exploited Native Marine Mussel Mytilus chilensis: Genomic Evidence from a Reciprocal Transplant Experiment

Local adaptations are important in evolution as they drive population divergence and preserve standing genetic diversity essential for resilience under climate change and human impacts. Protecting locally adapted populations is essential for aquaculture species. However, high larval connectivity and frequent translocations challenge this in Chilean blue mussel (Mytilus chilensis) aquaculture, a world-class industry in Chiloé Island. This study examined local adaptations in two ecologically distinct natural beds, Cochamó (northernmost inner sea of Chiloé) and Yaldad (southernmost tip), through a 91-day reciprocal transplant experiment and genomic evidence. Cochamó mussels grew faster in their native environment (0.015 g/day) than Yaldad (0.004 g/day), though growth declined upon transplantation. Mussels transplanted within and between beds displayed distinctive adaptive transcriptomic responses, with differentially expressed genes involved with immune function, osmoregulation, metabolism, and cellular balance. Additionally, 58 known outlier SNPs mapped over the species' genome sequence were linked with adaptive genes involved with osmoregulation, oxidative stress, and oxygen management, revealing selection-targeted specific genome regions. This study highlights how translocations affect the adaptive genomic response of M. chilensis and the impact of local environments in counterbalancing its genetic connectivity, concluding that the genomic differences in natural beds should be monitored and conserved for sustainable aquaculture practices.

Genomic selection for resistance to one pathogenic strain of Vibrio splendidus in blue mussel Mytilus edulis

Introduction

The blue mussel is one of the major aquaculture species worldwide. In France, this species faces a significant threat from infectious disease outbreaks in both mussel farms and the natural environment over the past decade. Diseases caused by various pathogens, particularly Vibrio spp., have posed a significant challenge to the mussel industry. Genetic improvement of disease resistance can be an effective approach to overcoming this issue.

Methods

In this work, we tested genomic selection in the blue mussel (Mytilus edulis) to understand the genetic basis of resistance to one pathogenic strain of Vibrio splendidus (strain 14/053 2T1) and to predict the accuracy of selection using both pedigree and genomic information. Additionally, we performed a genome-wide association study (GWAS) to identify putative QTLs underlying disease resistance. We conducted an experimental infection involving 2,280 mussels sampled from 24 half-sib families containing each two full-sib families which were injected with V. splendidus. Dead and survivor mussels were all sampled, and among them, 348 dead and 348 surviving mussels were genotyped using a recently published multi-species medium-density 60K SNP array.

Results

From potentially 23.5K SNPs for M. edulis present on the array, we identified 3,406 high-quality SNPs, out of which 2,204 SNPs were successfully mapped onto the recently published reference genome. Heritability for resistance to V. splendidus was moderate ranging from 0.22 to 0.31 for a pedigree-based model and from 0.28 to 0.36 for a genomic-based model.

Discussion

GWAS revealed the polygenic architecture of the resistance trait in the blue mussel. The genomic selection models studied showed overall better performance than the pedigree-based model in terms of accuracy of breeding values prediction. This work provides insights into the genetic basis of resistance to V. splendidus and exemplifies the potential of genomic selection in family-based breeding programs in M. edulis.

SNPs Analysis Indicates Non-Uniform Origins of Invasive Mussels (Mytilus galloprovincialis Lamarck, 1819) on the Southern African Coast

Understanding the origins of invasive species is necessary to manage them and predict their potential for spreading. The mussel genus Mytilus forms an important component of coastal ecosystems in the northern and southern hemispheres. M. galloprovincialis is an important invasive species globally, first appearing on the South African coast in the 1970s. Studies using nuclear and mitochondrial DNA indicated that the invasion probably originated from the north-east Atlantic. We used fifty-five polymorphic SNPs to genotype mussels from sites across the coast of South Africa with reference samples from the Mediterranean, the Atlantic, and New Zealand to test for possible introgression of the northern and southern taxa. Low levels of genetic differentiation were confirmed, and all samples grouped with reference samples of the Atlantic form of M. galloprovincialis, supporting previous studies. The SNP genotyping, however, allowed the detection of some individuals with genotypes typical of the Mediterranean, indicating that introduced populations in South Africa do not have a uniform origin. The initial population introduced to South Africa may have been genetically heterogenous from the start, coming from a region influenced by both the Atlantic and Mediterranean. Alternatively, multiple introductions may have taken place, originating from different regions, specifically North Africa, southern Europe, and the Mediterranean, building up the final heterogeneity.

Development and validation of a 66K SNP array for the hard clam (Mercenaria mercenaria)

BACKGROUND

The hard clam (Mercenaria mercenaria), a marine bivalve distributed along the U.S. eastern seaboard, supports a significant shellfish industry. Overharvest in the 1970s and 1980s led to a reduction in landings. While the transition of industry from wild harvest to aquaculture since that time has enhanced production, it has also exacerbated challenges such as disease outbreaks. In this study, we developed and validated a 66K SNP array designed to advance genetic studies and improve breeding programs in the hard clam, focusing particularly on the development of markers that could be useful in understanding disease resistance and environmental adaptability.

RESULTS

Whole-genome resequencing of 84 individual clam samples and 277 pooled clam libraries yielded over 305 million SNPs, which were filtered down to a set of 370,456 SNPs that were used as input for the design of a 66K SNP array. This medium-density array features 66,543 probes targeting coding and non-coding regions, including 70 mitochondrial SNPs, to capture the extensive genetic diversity within the species. The SNPs were distributed evenly throughout the clam genome, with an average interval of 25,641 bp between SNPs. The array incorporates markers for detecting the clam pathogen Mucochytrium quahogii (formerly QPX), enhancing its utility in disease management. Performance evaluation on 1,904 samples demonstrated a 72.7% pass rate with stringent quality control. Concordance testing affirmed the array's repeatability, with an average agreement of allele calls of 99.64% across multiple tissue types, highlighting its reliability. The tissue-specific analysis demonstrated that some tissue types yield better genotyping results than others. Importantly, the array, including its embedded mitochondrial markers, effectively elucidated complex genetic relationships across different clam groups, both wild populations and aquacultured stocks, showcasing its utility for detailed population genetics studies.

CONCLUSIONS

The 66K SNP array is a powerful and robust genotyping tool that offers unprecedented insights into the species' genomic architecture and population dynamics and that can greatly facilitate hard clam selective breeding. It represents an important resource that has the potential to transform clam aquaculture, thereby promoting industry sustainability and ecological and economic resilience.

Patterns of admixture and introgression in a mosaic Mytilus galloprovincialis and Mytilus edulis hybrid zone in SW England

The study of hybrid zones offers important insights into speciation. Earlier studies on hybrid populations of the marine mussel species Mytilus edulis and Mytilus galloprovincialis in SW England provided evidence of admixture but were constrained by the limited number of molecular markers available. We use 57 ancestry-informative SNPs, most of which have been mapped genetically, to provide evidence of distinctive differences between admixed populations in SW England and asymmetrical introgression from M. edulis to M. galloprovincialis. We combine the genetic study with analysis of phenotypic traits of potential ecological and adaptive significance. We demonstrate that hybrid individuals have brown mantle edges unlike the white or purple in the parental species, suggesting allelic or non-allelic genomic interactions. We report differences in gonad development stage between the species consistent with a prezygotic barrier between the species. By incorporating results from publications dating back to 1980, we confirm the long-term stability of the hybrid zone despite higher viability of M. galloprovincialis. This stability coincides with a dramatic change in temperature of UK coastal waters and suggests that these hybrid populations might be resisting the effects of global warming. However, a single SNP locus associated with the Notch transmembrane signalling protein shows a markedly different pattern of variation to the others and might be associated with adaptation of M. galloprovincialis to colder northern temperatures.

SNP genotyping revealed a hybrid zone between Mytilus chilensis and M. platensis in southern South America (the Strait of Magellan, Isla Grande de Tierra del Fuego and the Falkland Islands)

Hybrid zones among mussel species have been extensively studied in the northern hemisphere. In South America, it has only recently become possible to study the natural hybrid zones, due to the clarification of the taxonomy of native mussels of the Mytilus genus. Analysing 54 SNP markers, we show the genetic species composition and admixture in the hybrid zone between M. chilensis and M. platensis in the southern end of South America. Bayesian, non-Bayesian clustering and re-assignment algorithms showed that the natural hybrid zone between M. chilensis and M. platensis in the Strait of Magellan, Isla Grande de Tierra del Fuego and the Falkland Islands shows clinal architecture. The hybrid zone can be divided into three different areas: the first one is on the Atlantic coast where only pure M. platensis and hybrid were found. In the second one, inside the Strait of Magellan, pure individuals of both species and mussels with variable degrees of hybridisation coexist. In the last area at the Strait in front of Punta Arenas City, fjords on the Isla Grande de Tierra del Fuego, and at the Beagle Channel, only M. chilensis and a low number of hybrids were found. According to the proportion of hybrids, bays with protected conditions away from strong currents would give better conditions for hybridisation. We do not find evidence of any other mussel species such as M. edulis, M. galloprovincialis, M. planulatus or M. trossulus in the zone.