Genome-Wide Association Analysis and Candidate Gene Identification for Resistance to "Milky Disease" in the Chinese Mitten Crab (<i>Eriocheir sinensis</i>).

Abstract

"Milky disease" of the Chinese mitten crab (<i>Eriocheir sinensis</i>), caused by <i>Metschnikowia bicuspidata</i>, leads to substantial economic losses. Despite extensive research on its pathogenesis, the genetic basis of host resistance and underlying regulatory mechanisms remain unclear, limiting the development of disease-resistant varieties. This study aimed to (1) evaluate resistance differences among 10 <i>E. sinensis</i> families (five highly resistant and five sensitive) via artificial challenge; (2) identify disease-resistance-associated genetic loci using genome-wide association analysis (GWAS). Our findings revealed that the F05 family exhibited the strongest resistance, with a mortality rate of only 3% and a molting rate of 73%, accompanied by superior growth performance. Whole-genome resequencing identified 10,161,545 high-quality SNPs, and GWAS detected 767 loci significantly associated with disease-resistance traits, among which two pleiotropic SNPs (Chr46:18395778 and Chr1:20680490) were simultaneously associated with both "dead or not" and "qPCR fixed amount of fungi", reflecting their functional relevance in regulating survival and pathogen load. Notably, we propose for the first time that <i>E. sinensis</i> achieves resistance by inducing <i>M. bicuspidata</i> into a viable but nonculturable (VBNC) state, in which the fungal cells remain metabolically active but cannot form colonies on conventional culture media. This study establishes a multidimensional resistance evaluation system, clarifies the genetic basis and novel mechanism of resistance, and provides valuable molecular markers for marker-assisted breeding. The findings contribute to reducing disease-related losses and promoting sustainable development of the <i>E. sinensis</i> aquaculture industry.