Family-Aware Genome-Wide Association Mapping of Growth and Body-Shape Traits in Bighead Carp (Hypophthalmichthys nobilis)

Reliable marker–trait associations can support genetic improvement of growth and body conformation in bighead carp (Hypophthalmichthys nobilis). We investigated eight traits in 569 fish assigned to 34 inferred consensus full-sib groups. Genotypes at 89,684 reference-consistent SNP positions were recalled from sequencing alignments and filtered by read depth, genotype quality, and heterozygote-allele balance. Common-mask validation of 274,566 genotype cells supported a 60% pre-imputation call-rate threshold, achieving 94.17% overall, 90.26% non-reference, and 89.04% heterozygote concordance, with hard-dosage r2 = 0.859. The final imputed matrix contained 32,304 SNPs; 9086 LD-pruned SNPs were used to estimate population structure and genomic covariance. Primary mixed-model scans used recalled genotype inputs before Beagle imputation and identified 18 suggestive trait–marker combinations. Candidate analyses using actual observed genotypes supported 17 combinations at within-group permutation FDR < 0.05, representing 16 markers. Grouping, model, and group-omission sensitivity analyses characterized their robustness. Prioritized regions contained developmentally relevant genes, including sulf1, dmrt2, cyp24a1, chst12, efcab7, and anapc7. These family-supported candidates provide targets for replication and functional investigation and may inform genetic improvement and new-variety development in bighead carp.