Disentangling genetic variation for endurance and resistance to visceral white-nodules disease in large yellow croaker (Larimichthys crocea) using genome information

Abstract

Visceral white-nodules disease (VWND) caused by Pseudomonas plecoglossicida is a major threat for large yellow croaker (Larimichthys crocea) farming, resulting in considerable economic loss. Selection breeding for enhancing host resistance to infectious disease is an alternative strategy for disease control. The present work is aimed at using genome-wide association studies (GWAS) to identify quantitative trait loci (QTLs) and potential genes associated with VWND endurance and resistance in large yellow croaker. A total of 1408 fish from different populations were exposed to P. plecoglossicida. The first dead fish were labelled as susceptible group, whereas the last dead fish were assigned to endurant group, and the survivals were jugged to resistant group. Genotyping was conducted using whole genome resequencing and 10,586,121 high quality single nucleotide polymorphisms (SNPs) were discovered. Both binary survival (BS) and time to death (DT) traits were used in GWAS for endurant (421) and resistant (479) fish. A total of 6 SNPs were associated with disease endurance, and 7 SNPs were associated with disease resistance, where a major QTL associated with disease endurance was discovered on chromosome 5. Within these QTL regions, 41 candidate genes were mapped with immune response and defense mechanisms, and 4 SNPs were found in intron region of trim21, gtse1, pot1 and cald1. In addition, moderate to high heritability values (0.51–0.72) were estimated using a restricted maximum likelihood (REML) analysis. Finally, the correlation between Estimated Breeding Value (EBV) and the phenotype was calculated in different groups with the values of 0.39–0.55. Based on our investigations, VWND endurance and resistance are two perfectly distinct traits, and they can evolve independently in population. These results will be useful for the future breeding programs for improving the natural resistance of large yellow croaker against VWND. To our knowledge, this is the first study in large yellow croaker disentangling the genetic basis of endurance and resistance to VWND.