Hatchery stock replenishment efforts for flatfish populations often result in high rates of malpigmentation. Efforts to identify the molecular processes leading to malpigmentation in flatfish have implicated some pathways, but the exact mechanisms leading to malpigmentation in hatcheries remain poorly understood. Furthermore, identification of predictive gene expression profiles that could indicate future high levels of malpigmentation may allow hatcheries to test tanks early and not spend resources on predicted high-malpigmentation batches.
To investigate the molecular pathways leading to malpigmentation and determine early gene expression predictors of malpigmentation, we collected southern flounder larvae at 27, 34, and 41 days post-hatching from larvae in our Fisheries and Mariculture Laboratory (FAML) and a Texas Parks and Wildlife Department (TPWD) hatchery, where malpigmentation rates average 30%.
We determined the rate of malpigmentation for each tank at day 55 and conducted 3’ tag-sequencing on the collected larvae to profile gene expression. Principal component analysis demonstrated mRNA expression signatures clustering by age (Fig 1A), rearing site (Fig 1B), and tank malpigmentation rate (Fig 1C).
On Days 27 and 34, PC2 separated out 9 samples from tanks with a high malpigmentation rate (Fig 1C), indicating expression profiles that may predict future malpigmentation. Genes previously implicated in pigmentation pathways and that had strong PC2 loadings included, prostaglandin E receptor 2b (ptger2b) and retinol binding protein 4 (Rbp4) which contributed to negative PC2 eigenvalues and therefore may be predictive of future malpigmentation at 27 days post-hatching or earlier. Genes for melanin production and thyroid hormone signaling strongly contributed to positive PC2 values. Taken together, our results provide novel insights into the molecular underpinnings of malpigmentation and identify potential marker genes for facilitating early diagnosis of malpigmentation.