Wang Hao-Jie, Huang Shu-Pei, Amenyogbe Eric, Liu Yue, Jin Jing-Hui, Lu Yi, Boateng Charles Narteh, Wang Zhong-Liang, Huang Jian-Sheng
Fishery College, Guangdong Ocean University, Zhanjiang 524025, China.
Department of Water Resources and Aquaculture Management, University of Environment and Sustainable Development, PMB, Somanya, Eastern Region, Ghana.
Animals (Basel). 2025 Aug 25;15(17):2498. doi: 10.3390/ani15172498.
The Naozhou stock of large yellow croakers () exhibits unique phenotypic traits and high genetic diversity, making it a valuable resource for selective breeding and genetic conservation in aquaculture. Despite its importance, simple sequence repeat (SSR) markers have not been developed for this stock, which limits efforts in genetic evaluation, breeding optimization, and sustainable utilization of this commercially important species. In this study, 195,263 SSRs were identified from the genome of the Naozhou stock of large yellow croaker, covering a total length of 16,578,990 bp with a density of 288 bp/Mb. Dinucleotide repeats were the most common, with the AC motif being the most prevalent. The frequency of SSR markers ranged from 245.63 to 346.60 per Mb. A total of 30 primer pairs were synthesized, of which 28 pairs (93.3%) successfully amplified clear and reproducible bands in PCR assays. Among these, 28 SSR markers exhibited distinct and reproducible bands following gel electrophoresis. For eight SSR loci, the number of alleles (Na) ranged from 4 to 22 (mean = 11.375), while the effective number of alleles (Ne) ranged from 1.5401 to 10.4727 (mean = 5.6475). The assembled mitochondrial genome (mtDNA) was 16,467 bp in length and comprised 37 genes, including 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The total sequence length of the PCGs was 11,431 bp, accounting for 69.4% of the mtDNA. A large portion of the PCGs (5) used incomplete stop codons (e.g., , , ), while others used TAA stop codons (e.g., , , ). The mtDNA encoded a total of 3808 codons, with UAA showing the highest relative synonymous codon usage value. The SSR markers and mtDNA data generated in this study provide valuable tools for future genetic breeding and genomic research on the Naozhou stock of large yellow croakers.
硇洲大黄鱼（）种群表现出独特的表型特征和高遗传多样性，使其成为水产养殖中选择性育种和遗传保护的宝贵资源。尽管其具有重要性，但尚未针对该种群开发简单序列重复（SSR）标记，这限制了对这种商业上重要物种的遗传评估、育种优化和可持续利用的努力。在本研究中，从硇洲大黄鱼基因组中鉴定出195,263个SSR，总长度为16,578,990 bp，密度为288 bp/Mb。二核苷酸重复最为常见，其中AC基序最为普遍。SSR标记的频率范围为每Mb 245.63至346.60个。总共合成了30对引物，其中28对（93.3%）在PCR检测中成功扩增出清晰且可重复的条带。其中，28个SSR标记在凝胶电泳后表现出明显且可重复的条带。对于8个SSR位点，等位基因数（Na）范围为4至22（平均值 = 11.375），而有效等位基因数（Ne）范围为1.5401至10.4727（平均值 = 5.6475）。组装的线粒体基因组（mtDNA）长度为16,467 bp，包含37个基因，包括13个蛋白质编码基因（PCG）、22个tRNA基因和2个rRNA基因。PCG的总序列长度为11,431 bp，占mtDNA的69.4%。大部分PCG（5个）使用不完全终止密码子（例如，，，），而其他的使用TAA终止密码子（例如，，，）。mtDNA总共编码3808个密码子，其中UAA显示出最高的相对同义密码子使用值。本研究中产生的SSR标记和mtDNA数据为未来硇洲大黄鱼种群的遗传育种和基因组研究提供了有价值的工具。
