BAC-Pool Sequencing and Analysis Confirms Growth-Associated QTLs in the Asian Seabass Genome

The Asian seabass is an important marine food fish that has been cultured for several decades in Asia Pacific. In this study, a 3D BAC pool set was generated and further screened using 22 SSR markers located on linkage group 2 which contains a growth-related QTL region. Seventy-two clones corresponding to 22 FPC contigs were sequenced by Illumina MiSeq technology. We co-assembled the MiSeq-derived scaffolds from each FPC contig with error-corrected PacBio reads, resulting in 187 sequences covering 9.7 Mb. Eleven genes annotated within this region were found to be potentially associated with growth and their tissue-specific expression was investigated. Correlation analysis demonstrated that SNPs in ctsb, skp1 and ppp2ca are likely to be used as markers for selecting fast-growing fingerlings. Conserved syntenies between seabass LG2 and five other teleosts were identified. This study i) demonstrated NGS of BAC pools as a potential approach for mining candidates underlying QTLs of this species; ii) detected eleven genes potentially responsible for growth in the QTL region; and iii) identified useful SNP markers for selective breeding program of Asian seabass.