A genome-wide association study to identify growth-related SNPs and genes in blotched snakehead (Channa maculata)

• Published in: Aquaculture reports Vol. 35; p. 101932
• Main Authors: Liu, Haiyang, Xia, Weiwei, Ou, Mi, Luo, Qing, Zhang, Xincheng, Fei, Shuzhan, Huang, Sujing, Zhao, Xunjin, Zhang, Jin, Cui, Tongxin, Xiong, Bingyuan, Wu, Guohong, Chen, Kunci, Zhao, Jian
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01-04-2024; Elsevier
• Subjects: Candidate genes; Channa maculata; Genome resequencing; Growth trait; GWAS; SNP; Growth trait; GWAS; Genome resequencing; Channa maculata; SNP; Candidate genes
• ISSN: 2352-5134; 2352-5134
• DOI: 10.1016/j.aqrep.2024.101932

The blotched snakehead (Channa maculata) is a freshwater species of economic importance, widely distributed throughout Southeast Asia and Southern China. The comprehension of genetic regulatory mechanisms underlying growth traits, particularly body weight, is paramount for the advancement and economic viability of blotched snakehead aquaculture. Despite its importance, limited investigations have been undertaken regarding the growth properties of this species. To enhance our grasp of the genetic regulation mechanisms dictating growth traits and identify pertinent genetic loci, the inaugural genome-wide association study (GWAS) was executed. In this study, eight growth traits of 500 blotched snakeheads were measured and whole genome resequencing (WGS) were conducted. Genetic parameters were estimated for the eight traits, revealing moderate to high heritability (0.2245–0.5184) for seven traits, while one exhibited low heritability (0.1081). A comprehensive set of 2, 225, 993 high-quality SNPs were identified in the 500 blotched snakehead individuals, and the mixed linear model in GEMMA was applied for GWAS analysis. A total of 51 significant SNPs related to the seven growth traits were identified, and 112 genes were obtained by scanning 50 kb upstream and downstream regions. Thirteen genes harboring significant SNP sites were considered as important candidate genes, and these genes were associated with organelle formation, signal transduction, cell proliferation, and muscle growth. Notably, the HS6ST1 gene was significantly associated with body weight, body length and total length, designating it as a key candidate gene. This investigation makes a substantive contribution to our comprehension of the genetic architecture governing growth traits in the blotched snakehead, establishing a robust foundation for future initiatives in molecular marker-assisted selection and breeding strategies.
●The first GWAS analysis on eight growth traits of 500 spotted snakehead individuals by resequencing.●Seven growth traits exhibited significant correlations and moderate to high heritability.●A total of 51 chromosome-wide significantly SNPs and 112 candidate genes were identified related to seven growth traits.●Those results provide valuable information for molecular marker-assisted breeding of spotted snakehead.