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

• DOI: 10.1038/srep36647
• Publication Date: 2016-11-08T09:53:42Z
• Authors: Xueyan Shen; Si Yan Ngoh; Natascha May Thev...; Sai Rama Sridatta...; Pranjali Bhandare; Andy Wee Kiat Tan; Gui Quan Tan; Siddharth Singh; Norman Chun Han Phua; Shubha Vij; László Orbán
• Keywords: Sequence assembly; SNP array; SNP

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 hampered efforts to improve its selective breeding. A 3D BAC pool set generated this study was screened using 22 SSR markers located on linkage group 2 which contains growth-related QTL region. Seventy-two clones corresponding FPC contigs were sequenced by Illumina MiSeq technology. We co-assembled MiSeq-derived scaffolds from each contig with error-corrected PacBio reads, resulting 187 sequences covering 9.7 Mb. Eleven genes annotated within region found be potentially associated growth and their tissue-specific expression investigated. Correlation analysis demonstrated SNPs ctsb, skp1 ppp2ca can used as selecting fast-growing fingerlings. Conserved syntenies between LG2 five other teleosts identified. This i) provided 10 Mb targeted assembly; ii) NGS pools potential approach mining candidates underlying QTLs species; iii) detected eleven responsible region; iv) identified useful SNP breeding programs seabass.