Development and Validation of a 40K Liquid SNP Array for Meat-Type Duck Breeding and Germplasm Identification

High-density SNP chips have been demonstrated to be effective instruments for simultaneously genotyping large numbers of loci, thereby facilitating genome-scale analyses and advancing genomic selection (GS) in poultry and livestock. The meat-type duck, an economically valuable poultry species in China, has so far lacked precise and high-throughput genotyping systems, which has constrained the broader implementation of GS and genome-wide association analyses (GWASs) and consequently slowed genetic progress. In this study, we developed and validated a novel SNP array based on Genotyping-by-Targeted-Sequencing (GBTS) technology. The array comprises 40,875 SNP markers evenly distributed across 32 duck chromosomes. Using data generated from this array, genomic heritability estimates were obtained for six economic traits in a cultured duck population (n = 400), with values of 0.61 ± 0.09, 0.69 ± 0.08, 0.80 ± 0.08, 0.11 ± 0.09, 0.14 ± 0.08, 0.31 ± 0.09 for age at first egg (AFE), egg production number at 38 weeks (EN38w), egg weight at 38 weeks (EW38w), body weight at 35 days (BW35d), shank length at 35 days (SL35d) and thickness of breast muscle at 40 days (TB40d). A total of 163 significant SNPs associated with economic traits were identified through GWAS, and annotation revealed 28 candidate genes related to five of these traits. Moreover, the prediction accuracy of ssGBLUP for AFE, EN38w, EW38w, BW35d, SL35d, and TB40d reached 0.55 ± 0.16, 0.56 ± 0.12, 0.57 ± 0.08, 0.25 ± 0.19, 0.31 ± 0.19, and 0.47 ± 0.17, respectively—values that exceeded those obtained using BLUP. Population genomic analyses of 400 ducks demonstrated that this SNP array provides improved genomic prediction accuracy over pedigree-based BLUP for most analyzed traits. Overall, the developed SNP array provides a robust, high-efficiency, and cost-effective genotyping platform that will accelerate genetic progress and promote the sustainable development of the meat-type duck industry.