China boasts an abundance of indigenous chicken genetic resources, where the exploitation of whole-genome single nucleotide polymorphism (SNP) information offers significant potential for their development. However, the current chicken SNP chips are primarily designed for commercial chickens or a few local breeds. To address this gap, we have developed “Shennong 1 chicken 40K” liquid chip utilizing the genotyping by targeted sequencing. This chip integrates SNPs and present/absent variants and is specifically crafted for Chinese indigenous chickens. It encompasses 44,849 target sites, selected through an integration of whole-genome resequencing data, pan-genome data, genome-wide association study data, and previously reported functional data for economic traits. Compared to published gene chips, this chip contains a higher number of polymorphic loci in Chinese indigenous chickens, demonstrating enhanced applicability. Our validation of the chip on 204 individuals from seven different breeds yielded a mean capture ratio of 99.474% for the target sites, with minor allele frequencies > 0.05 accounting for 98.557% of the total sites. This chip effectively classifies different breeds, aligning clustering results from population structure analysis with actual breed groupings, thereby demonstrating the chip's excellent applicability. Additionally, we identified genes associated with production and environmental adaptation in chickens through selection signal analysis (IGF1, SOX5, CACNA1G, and CXCR4). Importantly, the chip's functional sites allow for precise evaluation, aiding in understanding the economic traits of specific breeds for informed decision-making. Overall, the chip provides essential technical support for the conservation, breeding, identification, and evaluation of Chinese indigenous chicken genetic resources.
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2025 The Author(s). Animal Research and One Health published by John Wiley & Sons Australia, Ltd on behalf of Institute of Animal Science, Chinese Academy of Agricultural Sciences.
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