Identification of Key Genes Correlated with Economic Trait Superiorities and Their SNP Screening Through Transcriptome Comparisons, WGCNA and Pearson Correlation Coefficient in the Sea Cucumber Apostichopus Japonicus

Variation in morphology-driven economic traits is a common issue hindering the development of the sea cucumber aquaculture industry. In this study, transcriptome comparisons, weighted gene correlation network analysis (WGCNA) and Pearson correlation coefficient (PCC) were first employed to identify key genes correlated with morphological variation in the sea cucumber Apostichopus japonicus, after which the relationship between identified key genes (relative expression and genotype) and economic trait phenotypes was investigated to screen potential biomarker targets for molecular-assisted breeding. The results showed that three genes (putative ficolin–2, fibrinogen c domain–containing protein 1, and angiopoietin–4) were closely associated with economic trait superiorities. Two single nucleotide polymorphisms (SNPs) were identified in the putative ficolin–2 gene as having a strong correlation with body weight and papilla number. The findings from this study will enrich breeding biomarker resources and benefit the development of molecular-assisted breeding techniques in sea cucumber aquaculture.