A First Generation BAC-Based Physical Map of the Asian Seabass (Lates calcarifer)

Abstract

BackgroundThe Asian seabass (Lates calcarifer) is an important marine foodfish species in Southeast Asia and Australia. Genetic improvement of this species has been achieved to some extent through selective breeding programs since 1990s. Several genomic tools such as DNA markers, a linkage map, cDNA and BAC libraries have been developed to assist selective breeding. A physical map is still lacking, although it is essential for positional cloning of genes located in quantitative trait loci (QTL) and assembly of whole genome sequences.Methodology/Principal FindingsA genome-wide physical map of the Asian seabass was constructed by restriction fingerprinting of 38,208 BAC clones with SNaPshot HICF FPC technique. A total of 30,454 were assembled into 2,865 contigs. The physical length of the assembled contigs summed up to 665 Mb. Analyses of some contigs using different methods demonstrated the reliability of the assembly.Conclusions/SignificanceThe present physical map is the first physical map for Asian seabass. This physical map will facilitate the fine mapping of QTL for economically important traits and the positional cloning of genes located in QTL. It will also be useful for the whole genome sequencing and assembly. Detailed information about BAC-contigs and BAC clones are available upon request.

A Preliminary Genetic Map in <b><i>Solea senegalensis</i></b> (Pleuronectiformes, Soleidae) Using BAC-FISH and Next-Generation Sequencing

“…BAC contig-based physical maps have been constructed in several aquaculture species, including Nile tilapia [Katagiri et al, 2005], Atlantic salmon [Ng et al, 2005], catfish [Quiniou et al, 2007;Xu et al, 2007], rainbow trout [Palti et al, 2009], Asian sea bass [Xia et al, 2010], oysters [Cunningham et al, 2006], Zhikong scallop [Zhang et al, 2008], red sea bream [Katagiri et al, 2002], and carp [Katagiri et al, 2001]. The physical maps have greatly enhanced genome research in these species.…”

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

“…A physical map of Asian seabass was previously published using SNaPshot HICF FPC technique which containing 38,208 clones from the above BAC library5. Out of 38,208 clones, 30,454 were assembled into 2,865 contigs, whereas 4,811 remained singletons.…”

“…The selected seabass individuals have shown a substantial increase in their growth rate in comparison to unselected controls. During this period, a number of advanced genomic tools, among them polymorphic DNA markers, expression microarrays, BAC libraries, BAC-based physical map and genetic linkage maps have been developed for the species3456.…”

“…This LG was predicted earlier to contain several QTLs associated with increased growth3. Based on the existing Asian seabass BAC-based physical map5, we performed the sequencing, assembly and annotation of BAC pools covering that portion of LG2 by using Illumina MiSeq technology. This study aims to: (i) test the strategy of sequencing and assembly of small-sized BAC pools by NGS technologies for detecting candidate genes underlying growth-related QTLs of this species; ii) provide potential validation/improvement for a complex segment of the Asian seabass de novo whole genome assembly; (iii) identify SNP markers for candidate genes potentially associated with increased growth rate in Asian seabass; (iv) perform comparative analysis between LG2-derived sequences from Asian seabass and their homologs in several sequenced teleost genomes.…”

Genomics and Genome Sequencing: Benefits for Finfish Aquaculture

“…An Atlantic salmon BAC library comprising approximately 300,000 clones and providing an 18-fold coverage of the genome is available , and it was used to generate a physical map (Ng et al, 2005). BAC libraries have been constructed for several aquaculture species including rainbow trout (Palti et al, 2009), catfish (Xu et al, 2007), common carp (Li et al, 2011b) and barramundi (Lates calcarifer) (Xia et al, 2010).…”