Genetic variation mining of the blackened turbot (Scophthalmus maximus) based on transcriptome data

Malpigmentation on the blind-side skin of Scophthalmus maximus represents a significant concern in flatfish aquaculture. To explore the underlying mechanism, transcriptome sequencing was conducted on blind-side skin from both hypermelanotic and normal turbot. Specifically, samples were collected from the blind side of normal fish, and from both pigmented and non-pigmented blind-side skin of hypermelanotic fish. Sixteen SNP loci within the coding regions of 12 genes were identified as candidates involved in pigment synthesis-related KEGG pathways, and three SNPs —tyrp1b-709-G/A (in tyrosinase-related protein 1b , tyrp1b ), notum2–277-T/C (in notum pectinacetylesterase 2 , notum2 ), and kitb-1154-A/G (in KIT proto-oncogene receptor tyrosine kinase b , kitb )—may be associated with hypermelanosis on the blind side. This study is the first to identify SNPs associated with malpigmentation in S. maximus . At the tyrp1b-709-G/A locus, the predominant genotype in normal turbot was GG homozygote (41.67 %), followed by GA heterozygote (33.33 %) and AA homozygote (25 %). In hypermelanotic turbot, GG homozygote was predominant (74 %), followed by GA (22 %) and AA (4 %). At the notum2–277-T/C locus, TC heterozygote represented 60.00 % of all genotypes in normal turbot, whereas CC homozygote predominated in hypermelanotic turbot (86.00 %), followed by TC (12.00 %) and TT (2.00 %). At the kitb-1154-A/G locus, AG genotype predominated in normal turbot (96.00 %). In hypermelanotic turbot, GG homozygote accounted for 48.00 %, followed by AA (32.00 %) and AG (20.00 %). The qRT-PCR results revealed higher expression of the tyrp1b gene in the pigmented blind-side skin of hypermelanotic turbot compared to the non-pigmented blind-side skin of both hypermelanotic and normal individuals, which was consistent with transcriptome data. Although notum2 and kitb were identified as differentially expressed in the RNA-seq analysis, their relative expression levels showed no significant differences among skin types. These three SNPs may serve as molecular markers to screen and exclude abnormal broodstock, thereby aiding in the selective breeding of high-quality S. maximus strains. ● Three SNPs in tyrp1b , kitb , notum2 genes are associated with hypermelanosis in Scophthalmus maximus . ● This is the first report of SNPs related to malpigmentation in S. maximus . ● The SNPs may be used for screening out hypermelanosis brood stock for S. maximus breeding.