Whole-Genome Resequencing Identifies Loci Associated with Body Weight and Body-Size-Related Head Height in Bighead Carp (Hypophthalmichthys nobilis)

Growth traits are economically important in bighead carp (Hypophthalmichthys nobilis), but their genetic basis remains unclear. We conducted whole-genome association analyses in 298 fish using 2,891,492 single-nucleotide polymorphisms and linear mixed models controlling for population structure and genomic relatedness. Five variants reached the per-trait genome-wide threshold. The strongest body-weight association occurred at 13:40990738:C:T on linkage group 13 (LG13) (p = 5.09 × 10−10; effect = 5.50 ± 0.87 g). Two LG04 variants were associated with body weight, while two adjacent LG14 variants were associated with head height (lead p = 8.34 × 10−9; effect = 2.59 ± 0.44 mm). However, associations with head dimensions were substantially attenuated after body-length adjustment, indicating that head-specific genetic effects were not established. Regional linkage disequilibrium and conditional analyses distinguished compact LG13 and LG14 signals from a complex LG04 pattern, and complementary sensitivity analyses supported their robustness. Sanger sequencing confirmed all 118 tested LG13 genotypes. The LG13 body-weight association was reproduced in an independent population of 268 fish and remained significant after body-length adjustment. Genotype-stratified reverse-transcription quantitative polymerase chain reaction assays detected higher expression of mchr2-like gene13.20, syngr1-like gene32.45, and cacng2-like gene32.46 in effect-allele carriers after multiple-test correction. These findings provide independent support for the LG13 body-weight association, while LG14 and LG04 remain discovery-stage candidate regions requiring independent replication and functional investigation before potential breeding applications can be considered.