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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. and Orbán, L. (2016) BAC-pool sequencing and analysis confirms growth-associated QTLs in the Asian seabass genome. Scientific Reports, 6 . p. 36647.

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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.

Publication Type: Journal Article
Murdoch Affiliation: Centre for Comparative Genomics
Publisher: Nature Publishing Group
Copyright: © 2016 Macmillan Publishers Limited
URI: http://researchrepository.murdoch.edu.au/id/eprint/34540
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