An EST/RNAseq Library and First-Generation Linkage Map for Sablefish (Anoplopoma fimbria)

A number of genetic resources have been developed for use with the Sablefish (Anoplopoma fimbria), an economically important wild, and more recently, cultured species in the Pacific Northwest. Combined data from EST library sequencing and Illumina RNAseq has resulted in the addition of 35973 transcripts to the NCBI database. PCR primers were developed to target DNA polymorphisms; 463 primer pairs were developed to target simple-sequence repeats, and 406 primer pairs were developed to detect single-nucleotide polymorphisms (SNPs). Along with 13 previously published microsatellite primer pairs (Aggarwal et al., 2011), these primers were used with DNA from two Sablefish families (progeny = 83, 96) to construct a first-generation linkage map using LINKMFEX (V2.3); 227 microsatellite and 133 SNP loci were mapped across 25 linkage groups, with a total coverage of 1334 cM in the merged map. BLATing the marker sequences against the Stickleback (Gasterosteus aculeatus) genome (Assembly Feb.2006; UCSC web-server http://genome.ucsc.edu/ ) shows a strong syntenic relationship between the two species; 17 linkage groups show a 1:1 relationship with single Stickleback chromosomes, while the remaining 8 linkage groups show a 2:1 relationship with the remaining 4 Stickleback chromosomes. The sex phenotype is found to be mapped to linkage group 14 in the male-specific Sablefish map. The construction of a second-generation linkage map is currently underway using the Genotyping-by-Sequencing approach (Elshire et al., 2011).This work greatly expands the available genetic data for Sablefish and should prove to be a useful resource for aquaculture development as well as genetic monitoring of wild populations.