Zhou Zhaolong, Shao Guangming, Shen Yibo, He Fengjiao, Tu Xiaomei, Ji Jiawen, Ao Jingqun, Chen Xinhua
Fuzhou Institute of Oceanography, State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, China.
Animals (Basel). 2024 Oct 17;14(20):2995. doi: 10.3390/ani14202995.
Spotted sea bass () is an important marine economic fish in China, ranking third in annual production among marine fish. However, a declined growth rate caused by germplasm degradation has severely increased production costs and reduced economic benefits. There is an urgent need to develop the fast-growing varieties of and elucidate the genetic mechanisms underlying growth traits. Here, whole-genome resequencing technology combined with extreme phenotype genome-wide association analysis (XP-GWAS) was used to identify candidate markers and genes associated with growth traits in . Two groups of , consisting of 100 fast-growing and 100 slow-growing individuals with significant differences in body weight, body length, and carcass weight, underwent whole-genome resequencing. A total of 4,528,936 high-quality single nucleotide polymorphisms (SNPs) were used for XP-GWAS. These SNPs were evenly distributed across all chromosomes without large gaps, and the average distance between SNPs was only 175.8 bp. XP-GWAS based on the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (Blink) and Fixed and random model Circulating Probability Unification (FarmCPU) identified 50 growth-related markers, of which 17 were related to body length, 19 to body weight, and 23 to carcass weight. The highest phenotypic variance explained () reached 15.82%. Furthermore, significant differences were observed in body weight, body length, and carcass weight among individuals with different genotypes. For example, there were highly significant differences in body weight among individuals with different genotypes for four SNPs located on chromosome 16: chr16:13133726, chr16:13209537, chr16:14468078, and chr16:18537358. Additionally, 47 growth-associated genes were annotated. These genes are mainly related to the metabolism of energy, glucose, and lipids and the development of musculoskeletal and nervous systems, which may regulate the growth of . Our study identified growth-related markers and candidate genes, which will help to develop the fast-growing varieties of through marker-assisted breeding and elucidate the genetic mechanisms underlying the growth traits.
花鲈（）是中国重要的海洋经济鱼类，年产量在海水鱼类中排名第三。然而，种质退化导致的生长速度下降严重增加了生产成本，降低了经济效益。迫切需要培育花鲈的快速生长品种，并阐明生长性状的遗传机制。在此，利用全基因组重测序技术结合极端表型全基因组关联分析（XP-GWAS）来鉴定与花鲈生长性状相关的候选标记和基因。两组花鲈，每组由100尾生长快和100尾生长慢的个体组成，它们在体重、体长和胴体重方面存在显著差异，对其进行全基因组重测序。共4,528,936个高质量单核苷酸多态性（SNP）用于XP-GWAS。这些SNP均匀分布在所有染色体上，没有大的间隙，SNP之间的平均距离仅为175.8 bp。基于贝叶斯信息和连锁不平衡迭代嵌套关键路径法（Blink）以及固定和随机模型循环概率统一法（FarmCPU）的XP-GWAS鉴定出50个与生长相关的标记，其中17个与体长相关，19个与体重相关，23个与胴体重相关。最高的表型变异解释率（）达到15.82%。此外，不同基因型个体在体重、体长和胴体重方面存在显著差异。例如，位于16号染色体上的四个SNP（chr16:13133726、chr16:13209537、chr16:14468078和chr16:18537358）的不同基因型个体在体重上存在极显著差异。此外，注释了47个与生长相关基因。这些基因主要与能量、葡萄糖和脂质代谢以及肌肉骨骼和神经系统发育有关，可能调控花鲈的生长。我们的研究鉴定出与生长相关的标记和候选基因，这将有助于通过标记辅助育种培育花鲈的快速生长品种，并阐明生长性状的遗传机制。
