Comparative transcriptome analyses and identification of candidate genes involved in vertebral abnormality of bighead carp Hypophthalmichthys nobilis

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...

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Bibliographic Details
Published in:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics
Main Authors: Luo, Weiwei, Wang, Junru, Yu, Xiaomu, Zhou, Ying, Tong, Jingou
Format: Report
Language:English
Published: ELSEVIER SCIENCE INC 2020
Subjects:
Bighead carp
Body deformity
Transcriptome
Muscles
Vertebrae
Differentially expressed genes (DEGs)
Biochemistry & Molecular Biology
Genetics & Heredity
SALMO-SALAR L
ATLANTIC SALMON
SEA BREAM
MORPHOLOGICAL DEFORMITIES
SKELETAL DEVELOPMENT
JAPANESE FLOUNDER
ANGUILLA-JAPONICA
CULTURED LARVAE
BONE
EXPRESSION
Atlantic salmon
Salmo salar
Online Access:http://ir.ihb.ac.cn/handle/342005/42874
https://doi.org/10.1016/j.cbd.2020.100752
Description
Summary: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 differen-tially 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.

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