Development and identification of KASP-SNP markers correlated with Aeromonas hydrophila resistance traits in blunt snout bream (Megalobrama amblycephala).

Abstract

The blunt snout bream (Megalobrama amblycephala) is an economically important freshwater fish species. However, it is highly susceptible to Aeromonas hydrophila infection, especially in intensive pond aquaculture in China. Molecular marker-assisted selection provides an efficient approach for breeding disease-resistant varieties; however, the key genes or molecular markers linked to A. hydrophila resistance remain scarce in this species. A 436 differential SNP sites with disease-resistant were screened on basis of whole-genome resequencing. Then, a high-throughput genomic KASP genotyping technique was utilized to discover favorable genes and SNP sites associated with A. hydrophila resistance. A total of 46 KASP markers were successfully developed with an accuracy of 92&#xa0;%. These markers were used to genotyping 120 blunt snout bream individuals. Through trait correlation analysis and general linear models (GLM), five SNPs significantly (P&#xa0;<&#xa0;0.05) associated with resistance to A. hydrophila were identified and mapped to five candidate genes (btnl2, cfhr2, slc47a1, neu3, nlrp1). Survival rate of individuals carrying the dominant genotype demonstrated an average survival rate of 81.39&#xa0;%, which represents a 69.35&#xa0;% increase in comparison with that of 48&#xa0;% in total population. This effect was validated in an external population of 100 fish. These findings identify key genetic markers associated with A. hydrophila resistance and provide a direction for elucidating the underlying molecular immune mechanisms, thus establishing a genetic foundation for future breeding strategies.