Identification of Key Biomarkers of Growth-Related Traits in the Bay Scallop Argopecten irradians irradians via Multi-omics Analysis Strategies

Abstract

In an attempt to promote and advance molecular-assisted selective breeding of shellfish, in this study, gills from selected (shell color as the marker trait and growth performance as the target trait) and unselected Argopecten irradians irradians were sampled. 2b-restriction site-associated DNA sequencing, genome-wide association study, comparative transcriptome, comparative small RNA transcriptome, miRNA-mRNA integrated analysis, quantitative real-time reverse transcription-polymerase chain reaction, and weighted gene co-expression network analysis were used to identify candidate SNPs, mRNAs, miRNAs, and miRNA/mRNA pairs with potential selective breeding value at a genomic scale in A. irradians irradians. The results revealed that a total of 6 significant SNPs were correlated closely with at least two examined growth-related traits. In addition, a total of 10 mRNAs and 7 miRNAs were identified to have positive correlations with shell length, shell height, shell width, total weight, and shell color. These candidate mRNAs and miRNAs may form 11 miRNA-mRNA pairs, which have great potential for developing molecular markers for molecular-assisted selective breeding of A. irradians irradians. The findings of this study will benefit the development of molecular-assisted breeding techniques in bay scallop aquaculture.