Genome-Wide Association Studies of Polysaccharides, Collagen, and Saponin Traits in the Sea Cucumber Apostichopus japonicus

Apostichopus japonicus is a commercially important marine species known for its high nutritional value and a range of bioactive compounds, including polysaccharides, collagen, and saponins. In this study, a genome-wide association study (GWAS) was carried out on 143 A. japonicus individuals. A total of 72 single nucleotide polymorphisms (SNPs) and 36 candidate genes were identified through the analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were then conducted, leading to the identification of 10 candidate genes related to polysaccharide, collagen, and saponin traits. These candidate genes were further validated through subsequent analyses. Five candidate genes, ALDH5A1, FAT1, KDR, ORC2, and PIGK, were identified to affect polysaccharides synthesis, among which the SNPs of ALDH5A1 had nonsynonymous substitution (S12G). BMI1 and UBR4 were identified as key candidate genes for collagen synthesis. A nonsynonymous SNP at Chr7_28028124, although not annotated to a known gene, was located within an exon and resulted in a serine-to-cysteine (S→C) substitution, which may influence collagen synthesis by affecting the function of an uncharacterized protein. CUBN and structural maintenance of Chromosomes 1B (SMC1B) were identified as candidate genes associated with saponin synthesis. The SNPs and candidate genes identified in this study serve as valuable genetic resources for selective breeding in A. japonicus and contribute to a better understanding of the genetic basis of these traits.