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BAC-pool sequencing and analysis confirms growth-associated QTLs in the Asian seabass genome
Shen, X.; Ngoh, S.Y.; Thevasagayam, N.M.; Prakki, S.R.S.; Bhandare, P.; Tan, A.W.K.; Tan, G.Q.; Singh, S.; Phua, N.C.H.; Vij, S.; Orbán, L. (2016). BAC-pool sequencing and analysis confirms growth-associated QTLs in the Asian seabass genome. NPG Scientific Reports 6(36647): 13 pp. http://dx.doi.org/10.1038/srep36647
In: Scientific Reports (Nature Publishing Group). Nature Publishing Group: London. ISSN 2045-2322; e-ISSN 2045-2322
Peer reviewed article  
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  • Shen, X.
  • Ngoh, S.Y.
  • Thevasagayam, N.M.
  • Prakki, S.R.S.
  • Bhandare, P.
  • Tan, A.W.K.
  • Tan, G.Q.
  • Singh, S.
  • Phua, N.C.H.
  • Vij, S.
  • Orbán, L.
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.
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