Whole-genome resequencing of grass carp (Ctenopharyngodon idella) for genome-wide association study on GCRV resistance

Grass carp (Ctenopharyngodon idella) is a highly productive freshwater fish species that annually contributes significant economic value to the aquaculture industry. However, its production is frequently affected by grass carp haemorrhagic disease (GCHD), which is caused by grass carp reovirus (GCRV). To elucidate the molecular mechanism of GCRV resistance in C. idella, whole-genome resequencing of both susceptible and resistant C. idella was conducted, yielding a total of 3,941,776 high quality single nucleotide polymorphisms (SNPs). A genome-wide association study (GWAS) then identified five significant SNPs, located on chromosomes 2, 3, 5, 6 and 10, associated with the trait of GCRV resistance. An integrative analysis of the GWAS and a previous transcriptome study was performed, and five common genes were identified, including b4galt2 (β-1,4-galactosyltransferase 2), kif2c (Kinesin family member 2C), jmjd8 (JmjC domain containing 8), selenom (Selenoprotein M), and znfx1 (Zinc finger NFX1-type containing 1). This study serves as a valuable basis for implementing marker-assisted selection (MAS) to improve GCRV resistance in C. idella breeding programs, and provides insight into developing methods to control the spread of GCHD.