Integrated mRNA and miRNA expression profile analyses reveal the potential roles of miRNA–mRNA pairs in skin color variation between wild-type and yellow mutant rainbow trout

As an important cold-water economic fish species, rainbow trout (Oncorhynchus mykiss) exhibits several intra-specific variation in skin pigmentation that can give rise to distinctive phenotypes, and wild-type rainbow trout with black skin (WR) and yellow mutant rainbow trout with yellow skin (YR) are the major two types in the farms, whose distinct skin colors make them suitable model for elucidating the skin pigmentation process. Skin color as a key indicator for selection in rainbow trout farming as well as has a strong visual impact on the consumer when rainbow trout are marketed. Previously, extensive studies have been conducted on skin color in rainbow trout, including the observation of skin spots and the expression analysis of some important pigment genes. However, up to date, no studies have systematically examined the molecular regulation mechanism of skin color difference between WR and YR through a high throughput method. Therefore, the aim of this study was to reveal the molecular regulation mechanism of skin color difference between these two strains at the mRNA and miRNA transcriptome level, and candidate genes, miRNAs and miRNA-mRNA pairs that may be responsible for rainbow trout albinism were obtained. This study simultaneously analysis mRNA and miRNA expression profiles and construct miRNA-mRNA regulatory networks to identify key miRNA-mRNA pairs that may participate in skin color formation of WR and YR.

虹鳟（Oncorhynchus mykiss）作为重要的冷水经济鱼类，其皮肤色素存在多种种内变异，可产生各具特色的表型；养殖生产中主要存在两类主流品系：野生型黑皮肤虹鳟（WR）与黄色突变型黄皮肤虹鳟（YR），二者鲜明的皮肤色泽差异使其成为阐明皮肤色素沉着过程的理想模型。皮肤颜色既是虹鳟养殖选育的关键指标，在产品上市时也对消费者具有极强的视觉影响。此前已有大量针对虹鳟皮肤颜色的研究，包括皮肤斑点观察以及部分重要色素基因的表达分析，但截至目前，尚无研究通过高通量技术系统解析WR与YR之间皮肤颜色差异的分子调控机制。为此，本研究旨在从mRNA与miRNA（microRNA）转录组层面，揭示这两个品系皮肤颜色差异的分子调控机制，并筛选出可能参与虹鳟皮肤白化相关过程的候选基因、miRNA及miRNA-mRNA调控对。本研究同时分析mRNA与miRNA的表达谱，构建miRNA-mRNA调控网络，以鉴定可能参与WR与YR皮肤颜色形成的关键miRNA-mRNA调控对。