Abstract
The Asian seabass is an important marine food fish that has been cultured for several decades in Asia Pacific. However, the lack of a high quality reference genome has hampered efforts to improve its selective breeding. A 3D BAC pool set generated in this study was 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 can be potentially used as markers for selecting fast-growing fingerlings. Conserved syntenies between seabass LG2 and five other teleosts were identified. This study i) provided a 10 Mb targeted genome assembly; ii) demonstrated NGS of BAC pools as a potential approach for mining candidates underlying QTLs of this species; iii) detected eleven genes potentially responsible for growth in the QTL region; and iv) identified useful SNP markers for selective breeding programs of Asian seabass.
Highlights
Approaches that target subgenomic regions have been explored
This study aims to: (i) test the strategy of sequencing and assembly of small-sized BAC pools by NGS technologies for detecting candidate genes underlying growth-related QTLs of this species; ii) provide potential validation/improvement for a complex segment of the Asian seabass de novo whole genome assembly; (iii) identify screened for nucleotide polymorphisms (SNPs) markers for candidate genes potentially associated with increased growth rate in Asian seabass; (iv) perform comparative analysis between LG2-derived sequences from Asian seabass and their homologs in several sequenced teleost genomes
The average number of BACs amplified per marker was four (Table 1)
Summary
Approaches that target subgenomic regions have been explored. These involve randomly chosen or MTP-based (minimum tiling path) BACs/FPC (Fingerprinted Contigs) and NGS sequencing. Using MTP as a guide, specific BAC clones representing a prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. The first such application was performed in Atlantic salmon: eight BACs belonging to a MTP covering ca. This study aims to: (i) test the strategy of sequencing and assembly of small-sized BAC pools by NGS technologies for detecting candidate genes underlying growth-related QTLs of this species; ii) provide potential validation/improvement for a complex segment of the Asian seabass de novo whole genome assembly; (iii) identify SNP markers for candidate genes potentially associated with increased growth rate in Asian seabass; (iv) perform comparative analysis between LG2-derived sequences from Asian seabass and their homologs in several sequenced teleost genomes
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