Body deformity occurs both in wild and farmed fishes, which is one of the most challenging problems for aquaculture industry. In most cases, such body deformities are linked to skeletal deformities. Currently, very limited information is available on skeletal deformities of farmed fish species which may be caused by genetic factor. In this study, we performed muscle and vertebra transcriptome analyses in body deformity and normality of bighead carp Hypophthalmichthys nobilis (from one meiotic gynogenesis family) using RNA-Seq. A total of 43,923 and 44,416 unigenes were predicted in muscles and vertebrae, respectively. Based on these data, we further explored the gene expression profiles in gynogenetic normal and abnormal bighead carp. No differentially expressed gene (DEG) was found in transcriptome data of muscles. Totally, 20 key DEGs were identified in transcriptome data of vertebrae, such as low density lipoprotein-related protein 2 (lrp2), bone morphogenetic protein 2B (bmp2b) and collagen alpha-1(IV) (col4a1). 12 potential pathways were also identified in vertebra transcriptome data, which were mainly involved in development, growth, cytoskeleton and energy metabolism, such as MAPK signaling pathway, regulation of actin cytoskeleton and TGF-beta signaling pathway. Results of this study will be informative for the understanding of genetic mechanisms for body shape formation and also provide potential candidate genes for selection program involved in body shape and skeletal development in H. nobilis.

身体畸形既发生在野生鱼类中，也发生在养殖鱼类中，这是水产养殖业最具挑战性的问题之一。在大多数情况下，这种身体畸形与骨骼畸形有关。目前，关于养殖鱼类骨骼畸形的信息非常有限，这可能是遗传因素引起的。在这项研究中，我们进行了肌肉和脊椎转录身体畸形和鳙鱼常态分析鳙（来自一个减数分裂的雌激素发育家族）使用RNA-Seq。预计在肌肉和椎骨中分别有43,923和44,416个单基因。基于这些数据，我们进一步探讨了雌雄激素正常和异常abnormal鱼的基因表达谱。在肌肉的转录组数据中未发现差异表达基因（DEG）。总共在椎骨的转录组数据中鉴定出20个关键DEG，例如低密度脂蛋白相关蛋白2 （lrp2），骨形态发生蛋白2B （bmp2b）和胶原α-1（IV）（col4a1）。在椎骨转录组数据中还确定了12条潜在途径，这些途径主要涉及发育，生长，细胞骨架和能量代谢，例如MAPK信号通路，肌动蛋白细胞骨架的调节和TGF-β信号通路。这项研究的结果将为理解人体形状形成的遗传机制提供有益的信息，并为参与H. nobilis人体形状和骨骼发育的选择程序提供潜在的候选基因。