Genetic selection response and genomic basis of resistance to Cryptocaryon irritans in large yellow croaker (Larimichthys crocea)

Abstract

Artificial domestication imposes sustained directional selection on cultured populations, driving genomic differentiation and the accumulation of traits favored under anthropogenic breeding regimes. Yet, how genomes respond to long-term selection and how genetic gain accumulates across successive generations remain poorly resolved. Here, we systematically characterized phenotypic improvement, selection response, population genetic structure, genetic diversity, and genomic signatures of selection across multiple generations of artificial domestication in Larimichthys crocea. The results showed that survival after Cryptocaryon irritans challenge increased from G0 to G4, with the selected population showing higher survival than the control. Genomic estimated breeding value based on survival time increased from 70.6 in G0 to 98.0 in G4, corresponding to a cumulative relative gain of 38.8%, indicating sustained genetic improvement under continuous selection. Population genomic analyses revealed progressive divergence of the selected population from the founder population and the gradual formation of relatively independent genetic clusters. Although the genomic inbreeding coefficient reached 0.080 in G4, nucleotide diversity and heterozygosity remained generally stable. Furthermore, selection signal analysis identified 22 putative selected regions, and integrated analyses highlighted VEPH1, JAK2, PIK3R6, and CSPG4 as key candidate genes. Among them, VEPH1 emerged as a promising candidate potentially involved in immune activation, cell survival, and tissue repair. These results provide a theoretical basis for molecular breeding and sustainable utilization of resistant germplasm in L. crocea.

Keywords

Larimichthys crocea / Cryptocaryon irritans / Genomic selection / Selection signatures / Disease resistance

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