Construction of High-Density Genetic Linkage Maps and Mapping of Growth-Related Quantitative Trail Loci in the Japanese Flounder (Paralichthys olivaceus)

Abstract

High-density genetic linkage maps were constructed for the Japanese flounder (Paralichthys olivaceus). A total of 1624 microsatellite markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 resulted in the mapping of 1487 markers to 24 linkage groups, a result which was consistent with the 24 chromosomes seen in chromosome spreads. The female map was composed of 1257 markers, covering a total of 1663.8 cM with an average interval 1.35 cM between markers. The male map consisted of 1224 markers, spanning 1726.5 cM, with an average interval of 1.44 cM. The genome length in the Japanese flounder was estimated to be 1730.3 cM for the females and 1798.0 cM for the males, a coverage of 96.2% for the female and 96.0% for the male map. The mean recombination at common intervals throughout the genome revealed a slight difference between sexes, i.e. 1.07 times higher in the male than female. High-density genetic linkage maps are very useful for marker-assisted selection (MAS) programs for economically valuable traits in this species and for further evolutionary studies in flatfish and vertebrate species. Furthermore, four quantiative trait loci (QTL) associated with growth traits were mapped on the genetic map. One QTL was identified for body weight on LG 14 f, which explained 14.85% of the total variation of the body weight. Three QTL were identified for body width on LG14f and LG14m, accounting for 16.75%, 13.62% and 13.65% of the total variation in body width, respectively. The additive effects were evident as negative values. There were four QTL for growth traits clustered on LG14, which should prove to be very useful for improving growth traits using molecular MAS.

The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry

“…We constructed high-resolution genetic maps for Japanese flounder using simple-sequence repeats and singlenucleotide polymorphisms, respectively 6,7 . The scaffolds, with markers located on different chromosomes, were filtered.…”

Comparative mapping for bighead carp (Aristichthys nobilis) against model and non-model fishes provides insights into the genomic evolution of cyprinids

“…(http://www.ensembl.org/index.html). Welldefined or high-density genetic linkage maps have been constructed for several food fishes, e.g., rainbow trout Oncorhynchus mykiss (Guyomard et al 2012;Rexroad et al 2008), Atlantic salmon Salmo salar (Lien et al 2011;Brenna-Hansen et al 2012), gilthead seabream Sparus aurata (Sarropoulou et al 2007), half-smooth tongue sole Cynoglossus semilaevis (Song et al 2012a) and Japanese flounder Paralichthys olivaceus (Song et al 2012b). Physical maps have also been reported in a few commercial fishes, such as channel catfish Ictalurus punctatus (Quiniou et al 2007), Nile tilapia Oreochromis niloticus (Katagiri et al 2005) and European seabass Dicentrarchus labrax (Kuhl et al 2010).…”

Genetic and genomic analyses for economically important traits and their applications in molecular breeding of cultured fish

“…Cnaani et al [28,29] identified a QTL for tilapia growth on LG23, which is the linkage group with the genetic sex-determining region. Song et al [12] used 1487 SSRs to produce a high-density genetic linkage map and successfully identified a QTL affecting body weight in LG14 of Japanese flounder.…”