Specific snp site primer combination for identifying taihe and wuji breeds and application thereof

Abstract

The application discloses a specific SNP site primer combination for identifying Taihe black-bone chicken varieties and application thereof. A chicken pan-genome containing a chicken reference genome GRCg7b and 2.49 Gb pan-sequence is taken as reference, WGS data of Taihe black-bone chicken and related chicken varieties is analyzed and screened to obtain two specific SNP sites, namely novel_th1 (G / T, dominant allele G) and novel_th2 (C / T, dominant allele C), wherein the T allele is medium to high frequency in most non-Taihe black-bone chicken varieties / strains. A FAM / VIC double-labeled TaqMan probe and a matching primer are designed based on the two sites to construct a real-time fluorescent quantitative PCR detection kit for joint typing of the two sites, and an amplification system and a Ct value judgment standard are established, so that 96 varieties / strains such as Taihe black-bone chicken, Zhushi chicken, other black-bone chicken, local chicken, white-feathered broiler and egg chicken can be quickly and accurately identified. The method has the advantages of high specificity, high sensitivity, simple operation and low cost, and is suitable for identification of authenticity of Taihe black-bone chicken and products thereof, purity monitoring and molecular-assisted breeding.

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