Zhao Ji, Wang Jiaying, Ke Qiaozhen, Zeng Junjia, Li Yin, Jiang Zhou, Pu Fei, Zhou Tao, Li Ning, Xu Peng
State Key Laboratory of Mariculture Breeding, College of the Environment and Ecology Xiamen University Xiamen China.
Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences Xiamen University Xiamen China.
Evol Appl. 2025 Jun 20;18(6):e70120. doi: 10.1111/eva.70120. eCollection 2025 Jun.
The large yellow croaker is one of the most important marine aquaculture species in China, yet its intensive farming industry faces challenges from various pathogens, particularly white spot disease caused by Cryptocaryon irritans. This study aimed to address the issue of white spot disease through genetic breeding. We implemented two consecutive generations of genomic selection (GS) of large yellow croaker against , resulting in three continuous generations for subsequent analyses. Challenge tests demonstrated significantly higher 96-h survival rates in the selected generations compared to corresponding controls, with increases of 18.5% and 79.7%, respectively. Survival analysis confirmed that the two selected generations exhibited significantly stronger resistance to . By merging the genotype files across generations, a comprehensive dataset containing 1844 individuals and 28,637 SNPs was created. Genomic Estimated Breeding Values (GEBVs) showed steady increases across the three consecutive generations, while genetic structure analysis revealed progressive population differentiation resulting from the two rounds of GS. Through genome-wide selection signature scanning, we identified five positive selection regions (PSRs) distributed across four chromosomes. These regions were enriched for multiple biological pathways related to energy metabolism, immune response, and cell death, including the HIF-1 signaling pathway, NOD-like receptor signaling pathway, and apoptosis. Within these pathways, we identified key candidate genes, including crebbp in the HIF-1 signaling pathway and traf2 involved in immune regulation, both significantly associated with resistance to . Our results validate the effectiveness of GS in selective breeding of large yellow croaker against and demonstrate that just two consecutive generations of GS can induce substantial differentiation in genetic structure. This approach facilitates the identification of candidate genes and biological pathways associated with disease resistance.
大黄鱼是中国最重要的海水养殖鱼类之一，但其集约化养殖产业面临着各种病原体的挑战，尤其是由刺激隐核虫引起的白点病。本研究旨在通过遗传育种解决白点病问题。我们对大黄鱼进行了连续两代针对[病原体名称缺失]的基因组选择（GS），从而产生了连续三代用于后续分析。攻毒试验表明，与相应对照组相比，选定世代的96小时存活率显著更高，分别提高了18.5%和79.7%。生存分析证实，选定的两代对[病原体名称缺失]表现出显著更强的抗性。通过合并各代的基因型文件，创建了一个包含1844个个体和28637个单核苷酸多态性（SNP）的综合数据集。基因组估计育种值（GEBV）在连续三代中呈稳步上升趋势，而遗传结构分析显示，两轮GS导致了种群的逐步分化。通过全基因组选择特征扫描，我们确定了分布在四条染色体上的五个正选择区域（PSR）。这些区域富集了与能量代谢、免疫反应和细胞死亡相关的多种生物学途径，包括缺氧诱导因子-1（HIF-1）信号通路、核苷酸结合寡聚化结构域样受体信号通路和细胞凋亡。在这些途径中，我们确定了关键候选基因，包括HIF-1信号通路中的crebbp和参与免疫调节的traf2，两者均与对[病原体名称缺失]的抗性显著相关。我们的结果验证了GS在大黄鱼抗[病原体名称缺失]选育中的有效性，并表明仅连续两代GS就能诱导遗传结构的显著分化。这种方法有助于识别与抗病性相关的候选基因和生物学途径。
