Benchmark Genetics team helps build 'powerful resource' for clam industry

Researchers from Benchmark Genetics and six leading European research institutions including Edinburgh University’s Roslin Institute have developed the first high-density SNP array for the Manila clam (Ruditapes philippinarum) and the grooved carpet shell clam (Ruditapes decussatus), providing a powerful new genomic resource to accelerate selective breeding, strengthen conservation efforts, and support the long-term sustainability of shellfish aquaculture.

Benchmark Genetics scientists played a key role in developing and validating the dual-species 63K SNP array, which contains 49,392 markers for Manila clam and 14,193 markers for grooved carpet shell clam. The platform is now available to researchers, breeding programmes, and industry partners seeking to improve productivity, resilience, and population management through advanced genomics.

The SNP array was developed through a collaboration between the University of Padova (Italy), the University of Santiago de Compostela (Spain), CIIMAR (Portugal), The Roslin Institute (Scotland), the Technical University Institute of Brest-Morlaix (France), Benchmark Genetics, and Thermo Fisher Scientific. The partners combined their expertise in shellfish biology, genomics, bioinformatics, breeding programme design, and genotyping technologies to address a longstanding gap in genomic resources for commercially important clam species.

The development was built upon extensive genomic resources generated from both wild and cultured clam populations across Europe. Researchers screened more than 300 million genetic variants before selecting approximately 63,500 high-quality SNP markers, creating the first standardised high-density genomic platform for these two economically important species.

Manila clam and grooved carpet shell clam are among Europe’s most valuable shellfish species, supporting coastal communities, employment, and food production across the region. However, both species face growing challenges from climate change, emerging diseases, habitat degradation, invasive species, and declining wild populations. These pressures have increased the need for genomic technologies that support both sustainable aquaculture and conservation initiatives.

A practical platform

Benchmark Genetics said three of its scientists - Dr Carolina Peñaloza, Dr Ross Houston and Dr Shernae Woolley - led key aspects of the SNP array design, bioinformatic analyses, and validation, helping transform extensive genomic datasets into a practical platform for breeding, conservation and research.

“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, head of genotyping at Benchmark Genetics.

Validation demonstrated excellent genotyping performance across both clam species, including high call rates, informative markers, and uniform genome-wide coverage. The array also successfully distinguished genetically distinct populations and enabled highly accurate parentage assignment, valuable for both breeding programmes and population management.

Providing a standard

Beyond breeding, the array provides researchers with a standardised genomic platform to better understand adaptation, resilience, and genetic diversity in shellfish populations. Benchmark Genetics said that as environmental pressures continue to increase, genomic tools such as this are expected to play an increasingly important role in supporting sustainable aquaculture production while safeguarding valuable marine genetic resources.

The project has been published in the journal Aquaculture in the paper A dual-clam species 63K SNP array for sustainable production and conservation of wild resources.