Transcriptome and MassARRAY analysis for identification of transcripts and SNPs for growth traits of the swimming crab Portunus trituberculatus

• High-throughput transcriptome sequencing was first performed in Portunus trituberculatus with different growth rates.
• 117 differentially expressed genes were detected between small and large size crabs.
• Eight important pathways associated with growth regulation were identified.
• One growth associated SNPs were detected.

Portunus trituberculatus is an important farmed crustacean in China. Growth traits are important economic traits that are controlled by many genes. The aim of this study was to screen growth-related genes using Illumina paired-end sequencing technology, and to identify growth-related SNPs in P. trituberculatus by association analysis. A total of 36,599,712 and 29,247,160 qualified Illumina read pairs for small size (SG) and large size crabs (LG) were obtained, giving rise to total clean bases of 7.14 and 5.72 G, respectively. A gene expression comparison showed that a total of 117 unigenes were differentially expressed between SG and LG, including 49 up-regulated and 68 down-regulated unigenes in SG and LG, respectively. GO functional enrichment analysis results showed up-regulated genes in LG were involved in three biological processes. These were cell communication, ovarian follicle cell development and cell division. Down-regulated genes in LG were involved in five biological processes, which were chitin metabolism, carbohydrate metabolism, ATP hydrolysis coupled proton transport, the steroid hormone mediated signaling pathway and fatty acid biosynthesis. Association analysis identified one growth-associated SNP, which was located in hemocyanin (comp58070-R31). This research has provided information on key genes, SNPs and biological processes related to growth, which will increase the efficiency of selective breeding programs for this important species.