The giant grouper, Epinephelus lanceolatus, is the largest coral reef-dwelling bony fish species. However, despite extremely fast growth performance and the considerable economic importance in this species, its genetic regulation of growth remains unknown. Here, we performed the first genome-wide association study (GWAS) for five growth traits in 289 giant groupers using 42,323 single nucleotide polymorphisms (SNPs) obtained by genotyping-by-sequencing (GBS). We identified a total of 36 growth-related SNPs, of which 11 SNPs reached a genome-wide significance level. The phenotypic variance explained by these SNPs varied from 7.09% for body height to 18.42% for body length. Moreover, 22 quantitative trait loci (QTLs) for growth traits, including nine significant QTLs and 13 suggestive QTLs, were found on multiple chromosomes. Interestingly, the QTL (LG17: 6934451) was shared between body weight and body height, while two significant QTLs (LG7: 22596399 and LG15: 11877836) for body length were consistent with the associated regions of total length at the genome-wide suggestive level. Eight potential candidate genes close to the associated SNPs were selected for expression analysis, of which four genes (phosphatidylinositol transfer protein cytoplasmic 1, protein tyrosine phosphatase receptor type E, alpha/beta hydrolase domain-containing protein 17C, and vascular endothelial growth factor A-A) were differentially expressed and involved in metabolism, development, response stress, etc. This study improves our understanding of the complex genetic architecture of growth in the giant grouper. The results contribute to the selective breeding of grouper species and the conservation of coral reef fishes.

中文翻译：

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第一个全基因组关联分析，针对最大的居住在珊瑚礁的骨鱼（巨型石斑鱼）（Epinephelus lanceolatus）。

巨型石斑鱼，Epinephelus lanceolatus，是居住在珊瑚礁中的最大的骨鱼类。然而，尽管该物种具有极高的生长性能和相当重要的经济意义，但其生长的遗传调控仍然未知。在这里，我们进行了第一个全基因组关联研究（GWAS），研究了289个大石斑鱼中的五个生长性状，使用通过基因分型（GBS）获得的42,323个单核苷酸多态性（SNP）。我们鉴定出总共36个与生长相关的SNP，其中11个SNP达到了全基因组意义。这些SNP解释的表型差异从体高的7.09％到体长的18.42％不等。此外，在多个染色体上发现了22个生长性状的数量性状基因座（QTL），包括9个重要QTL和13个暗示性QTL。有趣的是，QTL（LG17：在体重和身高之间共享了6934451），而两个重要的体长QTL（LG7：22596399和LG15：11877836）与全基因组暗示水平的总长度相关区域一致。选择了八个接近相关SNP的潜在候选基因进行表达分析，其中四个基因（磷脂酰肌醇转移蛋白胞质1，蛋白酪氨酸磷酸酶受体E型，含α/β水解酶结构域的蛋白17C和血管内皮生长因子AA）差异表达，并参与新陈代谢，发育，反应应激等。这项研究提高了我们对巨型石斑鱼生长的复杂遗传结构的理解。结果有助于石斑鱼物种的选择性繁殖和珊瑚礁鱼类的保护。