This study aims to investigate the phylogenetic relationships between Fengcheng duck (FCD) and Chinese indigenous duck breeds, analyze the genetic diversity and genetic structure of FCD and other duck breeds, so as to provide a theoretical foundation for the identification and conservation of Chinese indigenous duck resources.

Whole-genome resequencing at 12× coverage was performed on blood samples from 35 FCD individuals. Genome data from 420 individuals of 12 breeds from different regions in China were integrated, totaling 455 individuals across 13 breeds. Using a high-quality Ji'an Red duck genome as a reference, genome single nucleotide polymorphisms (SNPs) were detected using GATK software, and all variants were annotated using SnpEff software. Based on autosomal SNPs, a phylogenetic tree was constructed, and PCA clustering and Admixture analysis were performed to assess the population structure of indigenous ducks. Six parameters, were used to evaluate population genetic diversity, including common SNPs, expected heterozygosity, observed heterozygosity, inbreeding coefficient, population genetic distance, and runs of homozygosity, and the fixation index (Fst) was employed to quantify the degree of differentiation between populations.

A total of 8656794 SNPs were detected in the FCD population, with an average of one variant per 132 base pairs. Combined with the genomic data of other local duck breeds, a total of 8889170 SNPs were detected, which were mainly enriched in intergenic regions (45.50%), followed by intronic regions (32.82%), upstream regions (9.74%), downstream regions (9.27%), and exonic regions (1.67%). In protein-coding genes, 54150 missense mutations, 117021 synonymous mutations, 746673'UTR mutations, 73 start codon mutations, 1162 stop-loss mutations, 210 start-loss mutations, and 2346 stop-gain mutations were identified. The results of the phylogenetic tree, PCA, and Admixture analyses showed that each breed clustered independently, with significant differentiation among meat-type, dual-purpose, and egg-type duck groups. The relationships between different breeds were more based on economic use rather than geographical distance. FCD clustered with egg-type duck groups, particularly showing the closest relationship with Youxian duck. Genetic admixture was observed among some individuals of different duck breeds. Beijing duck and Jinding duck had higher inbreeding coefficients, fewer common SNPs, lower heterozygosity, and longer runs of homozygosity, indicating reduced genetic diversity due to strong artificial selection, whereas FCD exhibited the highest number of common SNPs and heterozygosity, indicating rich genetic diversity.

Using whole-genome SNP markers, this study systematically analyzed the genetic structure and diversity characteristics of Chinese indigenous ducks and Fengcheng ducks, providing important data support for the independent classification and conservation of Chinese indigenous duck resources.