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).

采用标准静脉穿刺术从跖静脉采集血液样本，收集于真空采血管中。使用QIAamp® DNA血液微量试剂盒（QIAGEN）提取基因组DNA。在DNBSEQ-T7测序平台上开展全基因组重测序，采用150bp双端reads，平均测序深度达2X以上。为进行后续分析，使用BWA（v0.7.10）[16]将reads比对至绿头鸭参考基因组ASM874695v1[15]。比对完成后，使用GATK HaplotypeCaller（v4.1）[17]识别单核苷酸多态性（Single Nucleotide Polymorphism，SNP）位点，除将-stand_call_conf参数设置为30外，其余参数均采用默认设置。随后合并个体gvcf文件，使用VCFtools（v0.1.16）[18]进行常染色体质量控制，设置参数--remove-indels、--minQ 30、--min-alleles 2及--max-alleles 2以过滤SNP位点，用于基因型填充。此后使用STITCH（v1.6.10）[19]完成基因型填充。填充完成后，使用BCFtools（v1.8）[20]开展质量控制，筛选INFO_SCORE＞0.4的位点。随后使用PLINK（v1.90）[21]基于参数--maf 0.01、--geno 0.05及--mind 0.05进行进一步质量控制。此后采用参数50 5 0.2进行连锁不平衡修剪，以提取独立SNP位点。最终保留365860个SNP位点用于后续分析（图S4）。