BAC-pool sequencing and analysis confirms growth-associated QTLs in the Asian seabass genome

Shen, Xueyan, Ngoh, Si Yan, Thevasagayam, Natascha May, Prakki, Sai Rama Sridatta, Bhandare, Pranjali, Tan, Andy Wee Kiat, Tan, Gui Quan, Singh, Siddharth, Phua, Norman Chun Han, Vij, Shubna, and Orbán, László (2016) BAC-pool sequencing and analysis confirms growth-associated QTLs in the Asian seabass genome. Scientific Reports, 6. 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.

Item ID: 58871
Item Type: Article (Research - C1)
ISSN: 2045-2322
Keywords: QTL, Asian seabass, growth, BAC Library
Copyright Information: © The Author(s) 2016. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
Funders: National Research Foundation, Singapore (NRFS)
Projects and Grants: NRFS Competitive Research Programme Award No: NRF-CRP7-2010-001
Date Deposited: 09 Jul 2019 04:44
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060412 Quantitative Genetics (incl Disease and Trait Mapping Genetics) @ 100%
SEO Codes: 83 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 8301 Fisheries - Aquaculture > 830102 Aquaculture Fin Fish (excl. Tuna) @ 100%
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