Development of SNP-genotyping arrays in two shellfish species

Area of Science:

• Genomics
• Aquaculture
• Marine Biology

Background:

• Single nucleotide polymorphisms (SNPs) are abundant genetic markers favored for their cost-effectiveness and high throughput in genomic studies.
• Advancements in genotyping technologies have enabled large-scale SNP discovery and application in non-model organisms.

Purpose of the Study:

• To discover single nucleotide polymorphisms (SNPs) and design medium-throughput genotyping arrays for the Pacific oyster (Crassostrea gigas) and the European flat oyster (Ostrea edulis).
• To evaluate the utility of these SNP panels for population genetics and selective breeding in aquaculture.

Main Methods:

• In vitro and in silico discovery of SNPs.
• Design of two 384-SNP Illumina GoldenGate arrays for each oyster species.
• Genotyping of over 1000 samples per species, including wild, selected, and family populations.
• Analysis of factors influencing genotyping success and simulation for parental assignment accuracy.

Main Results:

• Approximately 60% of designed polymorphic SNPs were successfully genotyped for both oyster species.
• Genotyping success was influenced by SNP origin and quality (Illumina functionality score).
• A simulation indicated that at least 150 markers are necessary for accurate parental assignment in Crassostrea gigas.

Conclusions:

• Developed SNP genotyping arrays provide valuable tools for oyster research.
• These tools can enhance understanding of population connectivity and support selective breeding programs in aquaculture.