A High Density Genetic Linkage Map for Yellowtail (Seriola quinqueradiata) Containing EST-Based SNPs

The marine products industry has developed as majority of the fishery, which are captured and directly using of aquatic resources. Only recently the breeding are considered as important research because available of aquatic resources are restricted gradually. The expectation of aquaculture research is getting higher in response to the prediction of aquatic resources depletion. Also the genetic improvement of economic traits are needed, it hopes apply to superior fish breeding, because artificial juvenile have a possibility to improve the phenotype for suited to aquaculture condition in every generation. We are researching practical application about selection of economic important traits from natural genetic resources using yellow tail (Seriola quinqueradiata) as target species.

High density SNP arrays have become the tool of choice for QTL mapping, Genome-wide association studies, marker-assisted selection (MAS) and genomic selection (GS). More recently, high-density linkage maps generated by SNP array data have proven to be crucial for the accurate assembly of scaffolds and contigs in whole-genome sequencing efforts. Earlier mapping studies have identified QTL for important commercial traits including parasite disease resistance, and combining the resources of a high density genetic map with genome sequence data will facilitate the fine mapping of these loci and the identification of candidate genes. In this study, Affymetrix SNP array was used to genotype 460 samples collected across five families from wild population in coastal waters of Goto Fukue-island.

To establish EST (expressed sequence tag) -based SNP array, a cDNA library was generated from pooled RNA samples extracted from 11 tissues from a single individual. Sequencing on Roche/454 GS FLX platform generated 1,353,405reads. The sequencing of SNP identification produced 570,846 raw reads derived from the full-length library and 456,482 raw reads derived from the 3’-anchored library derived from 5 hundred juveniles. Quality –based variant calling using CLC Genomics Workbench detected 9,356 biallelic putative SNPs in 6,025 contigs, with a minor allele frequency (MAF) >25%.

A Linkage analysis was performed using application package of LINKMFEX version 2.3. This application can separate originated alleles from male or female. In order to avoid the error of genotyping, the accuracy of genotypes in their progenies was checked from parental male and female alleles. Genotype data were converted to a backcross format as though the grandparent genotype was unknown. Pairwise analysis was performed, and markers were sorted in linkage group at a minimum LOD threshold of 5.0. Linkage phases were determined retrospectively by examining the assortment of alleles among linked markers. A total of 6,275 EST-based SNPs were mapped to 24 linkage groups.

This map is currently being used to map QTL for a number of commercially important traits, and will be used to improve the assembly of the yellowtail genome. It is possible to rapidly develop domesticated strains having commercially important traits in yellowtail aquaculture.