Genome-wide association study identifies loci for traits related to swim bladder in yellow drum (Nibea albiflora)

• Published in: Aquaculture 2020-09, Vol.526, p.735327, Article 735327
• Main Authors: Liu, Guijia, Han, Zhaofang, Jiang, Dan, Li, Wanbo, Zhang, Wenjing, Ye, Kun, Gu, Linlin, Dong, Linsong, Fang, Ming, Wang, Zhiyong
• Format: Article
• Language: English
• Subjects: Breeding; Candidate genes; GWAS; Nibea albiflora; Swim bladder
• ISSN: 0044-8486; 1873-5622
• DOI: 10.1016/j.aquaculture.2020.735327

The yellow drum (Nibea albiflora) is a kind of marine fish in China and East-Asia. The swim bladder is an important economic trait, which has medicinal and edible value. However, genetic studies of the yellow drum are relatively lacking. We performed two genome-wide association study (GWAS) methods on 371 samples (183 males and 188 females) to identify the genes associated with the swim bladder weight (SBW) and the swim bladder index (SBI). The assembled genome has been deposited into European Nucleotide Archive (accession no. PRJEB24302). Our sequencing technology is based on second-generation sequencing technology, and the longest piece currently assembled is scaffold level. Therefore, totally ten significantly SNPs, located on scaffold18, scaffold75, scaffold120, scaffold148, scaffold238, scaffold328, scaffold670, scaffold1334 and scaffold6097, were identified, respectively. Combining the biological function of the genes around the GWAS signals, ten candidate genes (wnt5a, sstr5, bcl2l11, lum, s1pr1, sec24b, ppp3ca, akap2, dagl and fgf12) were found to be most related to SBW and SBI. It has been fully recognized that the lung and the swim bladder are homologous based on morphological and embryological evidence. Most of these candidate genes are involved in lung development and lung diseases, suggesting they are possibly related to swim bladder. •We performed GWAS using mixed linear model and BayesCπ methods for traits related to swim bladder in the yellow drum.•We also compare the advantages and disadvantages of mixed linear model and BayesCπ methods in searching for significant SNPs.•The 10 most important candidate genes were revealed to be associated with the swim weight and swim bladder index.