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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. One SNP was identified from a transparent-specific AFLP fragment, which significantly associated with transparent individuals. Two alleles (A/G) were observed in this locus, and the genotype G/G was dominantly observed in the transparent groups (97.1%) collected from several production lots produced from different broodstock populations. A few normal individuals inherited the G/G genotype (5.0%), but the A/A and A/G genotypes were dominantly observed in the normal groups. The homologs region of the SNP was searched using a medaka genome database, and intron 12 of the Nell2a gene (located on chromosome 6 of the medaka genome) was highly matched. We also mapped the red sea bream Nell2a gene on the previously developed linkage maps, and this gene was mapped on a male linkage group, LG4-M. The newly found SNP was useful in eliminating broodstock possessing the causative gene of the body color transparency observed in juvenile stage of red sea bream.

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We thank Dennis Murphy for editing this manuscript.


This work was supported by JSPS KAKENHI grant numbers JP15H00471 and JP16H00480.

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Corresponding author

Correspondence to Eitaro Sawayama.

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The authors declare that they have no conflict of interest.

Ethical Statement

All experiments described in this manuscript were carried out in accordance with the Guide for the Care and Use of Laboratory Animals from Ehime University.

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Sawayama, E., Noguchi, D., Nakayama, K. et al. Identification, Characterization, and Mapping of a Novel SNP Associated with Body Color Transparency in Juvenile Red Sea Bream (Pagrus major). Mar Biotechnol 20, 481–489 (2018).

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  • Red sea bream
  • Pagrus major
  • Body color
  • Transparency
  • AFLP
  • SNP