Optimizing Breeding Strategies for Peking Ducks Using Genomic Selection: Genetic Parameter Evaluation and Selection Progress Analysis

Blood samples were drawn from the metatarsal vein using standard venipuncture and collected in vacuum tubes. Genomic DNA was extracted using the QIAampR DNA Blood Mini Kit (QIAGEN). Whole-genome resequencing was performed on the DNBSEQ-T7 platform with 150bp paired-end reads, achieving an average depth of over 2X per generation. For subsequent analysis, reads were aligned to the mallard duck reference genome ASM874695v1 [15] using BWA (v0.7.10) [16]. Following alignment, SNPs were identified using GATK HaplotypeCaller (v4.1) [17], with parameters set to default except for -stand_call_conf set to 30. Subsequently, the individual gvcf files were merged, and autosomal quality control was performed using VCFtools (v0.1.16) [18] with the parameters --remove-indels, --minQ 30, --min-alleles 2, and --max-alleles 2 to filter SNP sites for genotype imputation. After this, STITCH (v1.6.10) [19] was used for genotype imputation. Post-imputation, quality control was conducted using BCFtools (v1.8) [20] with INFO_SCORE > 0.4. Then, PLINK (v 1.90) [21] was used for further quality control based on --maf 0.01, --geno 0.05, and --mind 0.05. Following this, linkage disequilibrium pruning was performed with parameters 50 5 0.2 to extract independent SNP sites. Finally, 365,860 SNPs were retained for subsequent analysis (Figure S4).