Benchmark Genetics describes the new platform as "a practical genomic resource that will support shellfish research, breeding and conservation for years to come."
Photo: Benchmark Genetics
Researchers from Benchmark Genetics and six European research institutions have developed the first high-density SNP array for two commercially important clam species, creating a new genomic tool aiming to support selective breeding, conservation and sustainable shellfish aquaculture.
The new dual-species 63K SNP array has been developed for Manila clam (Ruditapes philippinarum) and grooved carpet shell clam (Ruditapes decussatus). According to Benchmark Genetics, the platform includes 49,392 markers for Manila clam and 14,193 markers for grooved carpet shell clam. It is now available to researchers, breeding programmes and industry partners working on productivity, resilience and population management.
Manila clams from Rias Baixas, Galicia, Spain.
Photo: Adobe Stock
The SNP array was developed through a collaboration between the University of Padova in Italy, the University of Santiago de Compostela in Spain, CIIMAR in Portugal, The Roslin Institute at the University of Edinburgh in the UK, the Technical University Institute of Brest-Morlaix in France, Benchmark Genetics and Thermo Fisher Scientific.
The partners combined expertise in shellfish biology, genomics, bioinformatics, breeding programme design and genotyping technologies to address what Benchmark described as a longstanding lack of genomic resources for two economically important clam species.
The development drew on genomic resources from both wild and farmed clam populations across Europe, with researchers screening more than 300 million genetic variants before selecting approximately 63,500 high-quality SNP markers for the platform.
Manila clam and grooved carpet shell clam are among Europe’s most valuable shellfish species and support coastal communities, employment and food production, with key production areas including Italy and Spain. However, both species are facing increasing pressure from climate change, emerging diseases, habitat degradation, invasive species and declining wild populations.
Benchmark Genetics scientists Dr Carolina Peñaloza, Dr Ross Houston and Dr Shernae Woolley contributed to the SNP array design, bioinformatic analyses and validation.
“This SNP array provides researchers and breeding programmes with a genomic resource that simply didn’t exist for these species before. It opens new opportunities to accelerate genetic improvement while supporting the long-term conservation of valuable clam populations,” said Peñaloza, who is Head of Genotyping at Benchmark Genetics.
Validation of the array showed strong genotyping performance across both clam species, including high call rates, informative markers and broad genome-wide coverage, Benchmark said. The platform was also able to distinguish genetically distinct populations and support accurate parentage assignment, demonstrating its potential use in breeding programmes and population management.
Its potential applications include selective breeding, genetic improvement, parentage assignment, pedigree reconstruction, genome-wide association studies, population genetic analysis, stock discrimination, monitoring genetic diversity and inbreeding, and conservation of wild populations.
Benchmark also said the array provides researchers with a standardised genomic platform to better understand adaptation, resilience and genetic diversity in shellfish populations.
The project was carried out within the EU-funded reserach initiatives IGNITION and ShellFishBoost.
Benchmark said the work demonstrates how collaboration between academia, industry and technology providers can accelerate innovation in aquaculture.
"By bringing together complementary expertise from across Europe, the consortium has delivered a practical genomic resource that will support shellfish research, breeding and conservation for years to come," the company stated in a release.
Benchmark Genetics also said the project highlights its growing capabilities in advanced genomic technologies beyond salmon, including SNP array development, bioinformatics and genotyping services for a wider range of aquaculture species.
The full research paper, "A dual-clam species 63K SNP array for sustainable production and conservation of wild resources", is available online in the journal Aquaculture.
