Identification of candidate genes associated with body weight in swimming crab (Portunus trituberculatus) according to conjunctive analyses of BSA-seq and RNA-seq

• Published in: Aquaculture reports Vol. 32; p. 101732
• Main Authors: Duan, Baohua, Kang, Tongxu, Zhang, Chen, Wan, Haifu, Mu, Shumei, Guan, Yueqiang, Liu, Weibiao, Li, Zejian, Tian, Yang, Ren, Yuqin, Kang, Xianjiang
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01-10-2023; Elsevier
• Subjects: Body weight; BSA-seq; Portunus trituberculatus; RNA-seq; Portunus trituberculatus; RNA-seq; BSA-seq; Body weight
• ISSN: 2352-5134; 2352-5134
• DOI: 10.1016/j.aqrep.2023.101732

The swimming crab (Portunus trituberculatus) is a valuable crustacean species extensively cultivated in China, owing to its fast development, palatability, and rich nutrition. However, the genetic factors regulating its growth remain elusive, impeding the progress of breeding initiatives for this economically important species. In this study, we combined bulk segregation analysis sequencing (BSA-seq) and transcriptome sequencing (RNA-seq) to identify potential candidate genes related to the body weight of P. trituberculatus using a full-sib family. BSA-seq successfully identified five candidate intervals on chromosomes 31, 38, and 47, spanning a total length of 9.76 Mb, which encompassed 137 annotated genes. By conducting RNA-seq analysis on swimming crab individuals in two extreme weight groups, 1581 genes were mined as differentially expressed genes (DEGs), involving 357 up-regulated and 1224 down-regulated genes. GO enrichment analysis demonstrated that DEGs were significantly enriched in proteolysis, obsolete oxidation-reduction process, nucleus, cytoplasm, molecular function, and metal ion binding. KEGG enrichment analysis showed that the proteasome signaling pathway could play a prominent role in the growth difference of P. trituberculatus. The conjunctive analyses of BSA-seq and RNA-seq led to the identification of eight critical DEGs, including peripheral plasma membrane protein CASK (CASK), cytoplasmic dynein 2 heavy chain 1 (Dyh1b), RNA-binding protein 5 (Rbm5), structural maintenance of chromosomes protein 3 (Smc3), hemicentin-2 (Hmcn1), A-kinase anchor protein 13 (Akap13), zinc finger MYM-type protein 2 (Zmym3), and extracellular matrix protein FRAS1 (Fras1), which exert influence over the growth of P. trituberculatus. This study not only enhances our understanding of the molecular mechanism governing the growth of P. trituberculatus but also provides valuable insights for future aquaculture programs aimed at selective breeding of this species.
•BSA-seq analysis identified weight genes in P. trituberculatus.•A 9.76 Mb region was located in groups of weight extremes.•The conjunctive analysis of BSA-seq and RNA-seq revealed growth-related genes.•This study provides new insights into P. trituberculatus growth mechanisms.