Development and validation of a 40 K Liquid SNP array for ark shell (Scapharca subcrenata)

The ark shell ( Scapharca subcrenata ), a commercially valuable marine bivalve, is widely distributed in both southern and northern China. In recent years, this species has been facing problems including a decline in germplasm resources, potential population admixture, and sluggish progress in breeding. SNP arrays have emerged as a cornerstone technology in genetic profiling, owing to their capacity for large-scale analysis, cost-effective operation, and exceptional precision. These attributes render them indispensable in modern genomics. To promote molecular breeding initiatives for this species, we first developed and validated a 40 K SNP genotyping array for S. subcrenata named “Hanxin No. I”. A total of 520 individuals were sampled from five wild populations in China, and 5684,437 high-confidence SNPs were obtained after stringent filtering of the whole genome resequencing data. Then we selected a panel of 40,558 SNPs exhibiting even genomic coverage across the entire genome to develop this array, including 898 markers associated with putative growth-related traits selected using a relaxed GWAS threshold and 1895 markers associated with population differentiation, respectively. Our SNP array demonstrated robust genotyping capabilities, achieving an overall calling rate of 97.68% and loci with MAF > 0.1 accounted for 94.77% of the total across 65 ark shells. In addition, to verify the effectiveness and accuracy of this array in population genetics, we examined genetic diversity and population structure across eight different populations. Our findings indicated a distinct genetic stratification between northern and southern populations. In summary, the SNP array provides a reliable, high-resolution platform for genotyping in S. subcrenata , and it has significantly advanced the process of germplasm resource conservation and may provide a useful marker resource for future genomic selection or breeding studies.