Disease & heat resistance

Genomic Characterization and Selection Signatures of a Cryptocaryon irritans-Resistant Large Yellow Croaker (Larimichthys crocea)

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Abstract

The large yellow croaker (Larimichthys crocea) is one of the most economically important marine fish species in China, yet its intensive aquaculture is severely threatened by Cryptocaryon irritans, the pathogen responsible for white spot disease. To enhance disease resistance, we established a selectively bred strain (GS3) through one generation of population-based selection followed by four successive generations of genomic selection. Over four consecutive generations (F1à¢â‚¬â€œF4), indoor C. irritans challenge tests demonstrated that the GS3 strain exhibited significantly improved resistance, with 96-h post-infection survival rates increasing by 17.1% (F1) to 37.3% (F4) compared with the control population. To assess the genetic response to continuous selection, a total of 1800 individuals from the GS3 population (F1à¢â‚¬â€œF4) were genotyped using the à¢â‚¬Å“Ningxin No. 3à¢â‚¬Â 55K SNP breeding chip. Genomic estimated breeding values (GEBVs) for C. irritans resistance, as well as population genetic structure, genetic diversity, and selection signatures, were analyzed using genome-wide SNP data. The results showed that the GEBV for C. irritans resistance increased steadily across generations. Population structure analysis revealed progressive genetic differentiation under successive rounds of genomic selection, while heterozygosity and diversity indices remained largely stable, indicating only early signs of inbreeding accumulation. Genome-wide selection scans identified 22 positively selected regions (PSRs) across 13 chromosomes, enriched in immune regulation, developmental, and energy metabolism pathways. Notably, HSPA9 and ECI2 were located at the hub positions of the proteinà¢â‚¬â€œprotein interaction (PPI) network, indicating their potential roles in modulating immune and metabolic processes associated with disease resistance. These findings confirm the efficiency of genomic selection in improving C. irritans resistance in L. crocea, providing a robust framework for identifying candidate genes and biological pathways linked to disease resistance in marine aquaculture breeding programs.

Keywords: 2026

How to Cite:

Li, Y., Zhao, J., Wang, J., Zhou, T. & Xu, P., (2026) “Genomic Characterization and Selection Signatures of a Cryptocaryon irritans-Resistant Large Yellow Croaker (Larimichthys crocea)”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2284612. doi: https://doi.org/10.31274/wcgalp.23604

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