Hegedűs Bettina, Bagi Zoltán, Kusza Szilvia
Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Egyetem tér 1., 4032 Debrecen, Hungary.
Doctoral School of Animal Science, University of Debrecen, Böszörményi út 138., 4032 Debrecen, Hungary.
Genes (Basel). 2025 Jun 18;16(6):717. doi: 10.3390/genes16060717.
Aquaculture has become a crucial component of global food production, yet catfish (10.8% of global finfish production) breeding programs often lack sufficient genetic data to fully utilize their production potential. In the last 15 years, there have been improvements in this field as two high-density (HD) single nucleotide polymorphism (SNP) arrays (250K and 690K) and low-density panels have been developed for North American channel catfish () and blue catfish (). This lack of genomic tools hinders genetic improvement efforts in other commercially relevant catfish species besides them. Therefore, this review investigated the reason behind the lack of SNP chip usage in genetic-based selections in most catfish breeding programs and the cross-species applicability of the already existing high-density SNP arrays for genotyping members of the , African catfish (), and , European catfish (), families. This paper systematically reviews the literature of more than 16 SNP arrays, with 66 non-target species, and assesses the possibility of adapting catfish SNP arrays to the catfish families of interest. With lowered filtering (e.g., MAF > 0) thresholds, the Affymetrix Axiom 250K and Axiom Catfish 690K Genotyping Array could potentially be used on important market species like African and European catfishes. In the long term, chip development would be the solution for these species, but, until then, cross-application is a viable alternative. Despite low polymorphic SNPs (1%) and call rates (0%), this SNP array could aid researchers and breeders, improving catfish aquaculture and management.
水产养殖已成为全球粮食生产的关键组成部分，但鲶鱼（占全球硬骨鱼产量的10.8%）育种计划往往缺乏足够的遗传数据来充分发挥其生产潜力。在过去15年中，该领域取得了一些进展，为北美鲶鱼和蓝鲶开发了两种高密度（HD）单核苷酸多态性（SNP）芯片（250K和690K）以及低密度分型板。除了它们之外，这种基因组工具的缺乏阻碍了其他具有商业相关性的鲶鱼品种的遗传改良工作。因此，本综述调查了大多数鲶鱼育种计划在基于遗传的选择中缺乏使用SNP芯片的原因，以及现有高密度SNP芯片对胡子鲶科、非洲鲶鱼和鲇科、欧洲鲶鱼的基因分型的跨物种适用性。本文系统回顾了16种以上SNP芯片、66个非目标物种的文献，并评估了将鲶鱼SNP芯片应用于目标鲶鱼科的可能性。降低筛选（例如，最小等位基因频率>0）阈值后，Affymetrix Axiom 250K和Axiom鲶鱼690K基因分型芯片有可能用于非洲和欧洲鲶鱼等重要市场品种。从长远来看，芯片开发将是这些物种的解决方案，但在此之前，交叉应用是一个可行的选择。尽管单核苷酸多态性较低（约1%）且检出率较低（约0%），但这种SNP芯片可以帮助研究人员和育种者，改善鲶鱼养殖和管理。
