Identification of the causative gene of a transparent phenotype of juvenile red sea bream Pagrus major.

Deformities in cultured fish species may be genetic, and identifying causative genes is essential to expand production and maintain farmed animal welfare. We previously reported a genetic deformity in juvenile red sea bream, designated a transparent phenotype. To identify its causative gene, we conducted genome-wide linkage analysis and identified two single nucleotide polymorphisms (SNP) located on LG23 directly linked to the transparent phenotype.

Identification, Characterization, and Mapping of a Novel SNP Associated with Body Color Transparency in Juvenile Red Sea Bream (Pagrus major).

We previously reported a body color deformity in juvenile red sea bream, which shows transparency in the juvenile stage because of delayed chromatophore development compared with normal individuals, and this finding suggested a genetic cause based on parentage assessments. To conduct marker-assisted selection to eliminate broodstock inheriting the causative gene, developing DNA markers associated with the phenotype was needed. We first conducted SNP mining based on AFLP analysis using bulked-DNA from normal and transparent individuals.

Identification of Quantitative Trait Loci for Resistance to RSIVD in Red Sea Bream (Pagrus major).

Red sea bream iridoviral disease (RSIVD) is a major viral disease in red sea bream farming in Japan. Previously, we identified one candidate male individual of red sea bream that was significantly associated with convalescent individuals after RSIVD. The purpose of this study is to identify the quantitative trait loci (QTL) linked to the RSIVD-resistant trait for future marker-assisted selection (MAS).

DNA barcoding and morphological analyses revealed validity of Diadema clarki Ikeda, 1939 (Echinodermata, Echinoidea, Diadematidae).

A long-spined sea urchin Diadema-sp reported from Japanese waters was genetically distinct from all known Diadema species, but it remained undescribed. Extensive field surveys in Japan with molecular identification performed in the present study determined five phenotypes (I to V) in Diadema-sp according to the presence and/or shape of a white streak and blue iridophore lines in the naked space of the interambulacral area. All phenotypes were distinct from Diadema setosum (Leske, 1778) and Diadema savignyi (Audouin, 1829), of which a major type (I) corresponded to Diadema clarki Ikeda, 1939 that was questioned and synonymized with Diadema setosum by Mortensen (1940).

Population genetic structure of the messmate pipefish Corythoichthys haematopterus in the northwest pacific: evidence for a cryptic species.

The population genetic structure of the messmate pipefish, Corythoichthys haematopterus, in the northwest Pacific was investigated based on the partial mitochondrial DNA cytochrome b (589 bp) and 16S rRNA (528 bp) region sequences of 108 individuals collected from six sites along the coast of the Japanese archipelago and one site on Mactan Island, the Philippines. A total of 60 and 28 haplotypes were obtained from the cytochrome b and 16S rRNA regions, respectively. Two genetically distinct lineages were detected: lineage A and B, which are separated by mean pairwise genetic distances of 23.

Isolation and characterization of 13 microsatellite markers for the viviparous surfperch Ditrema temmincki (Embiotocidae) and cross-species amplification.

Thirteen microsatellite loci were isolated from a size-selected genomic library of the surfperch (Ditrema temmincki Bleeker). All loci displayed a high degree of length polymorphism, as observed in the total number of alleles per locus (two to 23) and a high degree of estimated heterozygosity, ranging from 0.080 to 0.

DNA markers indicate low genetic diversity and high genetic divergence in the landlocked freshwater goby, Rhinogobius sp. YB, in the Ryukyu Archipelago, Japan.

Genetic diversity and genetic divergence were investigated in the landlocked goby Rhinogobius sp. YB by analysis of seven microsatellite DNA loci and the mtDNA control region sequence, and were compared with those of the closely related amphidromous species Rhinogobius sp. DA.