Chromosomal ploidy manipulation is one of the means to create excellent germplasm. Triploid fish could provide an ideal sterile model for searching of a underlying mechanism of abnormality in meiosis. The complete understanding of the coding and noncoding RNAs regulating sterility caused by meiosis abnormality is still not well understood. By high-throughput sequencing, we compared the expression profiles of gonadal mRNA, long non-coding RNA (lncRNA), and microRNA (miRNA) at three different developmental stages between the diploid (XX) and triploid (XXX) female rainbow trout. These stages were gonads before differentiation (65 days post fertilisation, dpf), at the beginning of morphological differences (180 dpf) and showing clear difference between diploids and triploids (600 dpf), respectively. A majority of differentially expressed (DE) RNAs were identified, and 22 DE mRNAs related to oocyte meiosis and homologous recombination were characterized. The predicted miRNA-mRNA/lncRNA networks of 3 developmental stages were constructed based on the target pairs of DE lncRNA-miRNA and DE mRNA-miRNA. According to the networks, meiosis-related gene of ccne1 was targeted by dre-miR-15a-5p_R + 1, and 6 targeted DE lncRNAs were identified. Also, qRT-PCR was performed to validate the credibility of the network. Overall, this study explored the potential interplay between coding and noncoding RNAs during the gonadal development of polyploid fish. The mRNA, lncRNA and miRNA screened in this study may be helpful to identify the functional elements regulating fertility of rainbow trout, which may provide reference for character improvement in aquaculture.

染色体倍性操作是创造优良种质的手段之一。三倍体鱼可以为寻找减数分裂异常的潜在机制提供理想的无菌模型。对由减数分裂异常引起的调节不育的编码和非编码 RNA 的完整理解仍然没有得到很好的理解。通过高通量测序，我们比较了二倍体 (XX) 和三倍体 (XXX) 雌性虹鳟在三个不同发育阶段的性腺 mRNA、长链非编码 RNA (lncRNA) 和 microRNA (miRNA) 的表达谱. 这些阶段是分化前的性腺（受精后 65 天，dpf），形态差异开始时（180 dpf），并分别显示二倍体和三倍体之间的明显差异（600 dpf）。鉴定了大多数差异表达（DE）RNA，并表征了与卵母细胞减数分裂和同源重组相关的22个DE mRNA。基于DE lncRNA-miRNA和DE mRNA-miRNA的靶对构建预测的3个发育阶段的miRNA-mRNA/lncRNA网络。根据网络， ccne1的减数分裂相关基因被dre-miR-15a-5p_R + 1靶向，鉴定出6个靶向DE lncRNA。此外，还进行了 qRT-PCR 以验证网络的可信度。总体而言，本研究探讨了多倍体鱼性腺发育过程中编码和非编码 RNA 之间的潜在相互作用。本研究筛选的mRNA、lncRNA和miRNA可能有助于鉴定调节虹鳟繁殖力的功能元件，为水产养殖的性状改良提供参考。