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

X. Shen; S.Y. Ngoh; N.M. Thevasagayam; S.R.S. Prakki; P. Bhandare; A.W.K. Tan; G.Q. Tan; S. Singh; N.C.H. Phua; S. Vij; L. Orbán

doi:10.1038/srep36647

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

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

X. Shen, S.Y. Ngoh, N.M. Thevasagayam, S.R.S. Prakki, P. Bhandare, A.W.K. Tan, G.Q. Tan, S. Singh, N.C.H. Phua, S. Vij, …

Scientific Reports, Vol.6

2016

DOI: https://doi.org/10.1038/srep36647

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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.

Details

Title: BAC-pool sequencing and analysis confirms growth-associated QTLs in the Asian seabass genome
Authors/Creators: X. Shen (Author/Creator) - Temasek Life Sciences Laboratory
S.Y. Ngoh (Author/Creator) - Nanyang Technological University
N.M. Thevasagayam (Author/Creator) - Temasek Life Sciences Laboratory
S.R.S. Prakki (Author/Creator) - Temasek Life Sciences Laboratory
P. Bhandare (Author/Creator) - Temasek Life Sciences Laboratory
A.W.K. Tan (Author/Creator) - Temasek Life Sciences Laboratory
G.Q. Tan (Author/Creator) - Temasek Life Sciences Laboratory
S. Singh (Author/Creator) - Pacific Biosciences (United States)
N.C.H. Phua (Author/Creator) - Temasek Life Sciences Laboratory
S. Vij (Author/Creator) - Temasek Life Sciences Laboratory
L. Orbán (Author/Creator) - Murdoch University
Publication Details: Scientific Reports, Vol.6
Publisher: Nature Publishing Group
Identifiers: 991005545275307891
Murdoch Affiliation: Centre for Comparative Genomics
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.64 Phylogenetics & Genomics; 3.64.71 Genetic Diversity
Web Of Science research areas: Genetics & Heredity
ESI research areas: Molecular Biology & Genetics