BAC-pool sequencing and analysis confirms growth-associated QTLs in the Asian seabass genome.
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.
Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore.
Xueyan
X
Shen
Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore.|Nanyang Technological University, 639798 Singapore.
Si Yan
SY
Ngoh
Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore.
Natascha May
NM
Thevasagayam
Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore.
Sai Rama Sridatta
SR
Prakki
Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore.
Pranjali
P
Bhandare
Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore.
Andy Wee Kiat
AW
Tan
Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore.
Gui Quan
GQ
Tan
Pacific Biosciences, Menlo Park, CA 94025, USA.
Siddharth
S
Singh
Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore.
Norman Chun Han
NC
Phua
Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore.
Shubha
S
Vij
Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore.|Department of Animal Sciences and Animal Husbandry, Georgikon Faculty, University of Pannonia, 8360 Keszthely, Hungary.|Centre for Comparative Genomics, Murdoch University, Murdoch 6150, Australia.
László
L
Orbán
D000818:Animals; D001492:Bass / Q000235:genetics* / Q000254:growth & development; D022202:Chromosomes, Artificial, Bacterial; D016678:Genome; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable