Transcriptome Characterization and Construction of a First Generation Genetic Linkage Map for Asian Arowana (Scleropages formosus)

Asian arowana or dragonfish (Scleropages formosus) is an important fish species due to its unusual breeding biology and extreme high price in the ornamental fish markets. However, the genomic resources and genetic tools available for Asian arowana are current surprisingly scarce. In the present study, we aimed to (i) investigate the Asian arowana brain and gonad transcriptome by the use of Roche 454 pyrosequencing; (ii) identify differentially expressed genes between the two sexes and develop microsatellite (SSR) markers; and (iii) construct a first generation SSR-based genetic linkage map.

A total of 1,313,474 raw reads were obtained from male brain, female brain, testis and ovary of adult Asian arowana individuals through pyrosequencing. These reads were assembled into 16,242 contigs which were further grouped into 13,639 isogroups. BLASTX annotation identified a total of 8,316 unique proteins from all these isogroups. Gene ontology (GO) and KEGG pathway analyses also recovered diverse biological functions and regulation pathways. Sexual differentially expressed genes and some important candidate genes putatively involved in sex development were identified. Among them, further analysis of putative sex associated gene sox9 showed no gene duplication and sex dimorphism expression in Asian arowana and its phylogenetic analysis revealed that Asian arowana sox9 was closely related to sox9b of other fish species.

A total of 8,541 SSR containing ESTs were identified through the analysis of the current transcriptome dataset, of which 316 EST-SSRs were developed. In addition, 356 new genomic-SSRs were obtained by screening through SSR-enriched genomic libraries. Accordingly, a first generation genetic linkage map of Asian arowana were constructed based on these EST-SSR and genomic-SSR markers in a mapping panel containing two F1 families, including a total of 96 progenies. Linkage analysis allowed for mapping of 308 markers (196 EST-SSRs and 112 genomic-SSRs) to 28 linkage groups (LGs), ranging in size from 14.9 to 160.6 cM. Each LG contained 3-43 markers. The linkage map covered a genetic distance of 2,218.3 cM with an average marker interval of 8.2 cM. Potential sex associated gene sox9 was mapped to LG4 on the consensus linkage map. Pairwise putative conserved syntenies between the Asian arowana, zebrafish and three-spined stickleback were established.

This study represents the first transcriptome resources and also the first genetic linkage map based on SSR markers of Asian arowana, which will provide benefits for the future genetic and breeding studies on the species. Furthermore, it will be also suitable for future identification of QTLs associated with important traits in the species and comparative genome analysis among the members of the Osteoglossidae family.