Research Note: Development and application of specific molecular identity cards for “Yufen 1” H line chickens

Abstract

The "Yufen 1" H line chicken (YF) has excellent characteristics including early sexual maturity and high egg production, and the conservation of its genetic diversity is the core of the breeding activity. To overcome misrepresented breeds and protect the integrity of the germplasm genetic resources, it is important to develop accurate and convenient methods to identify YF. In this study, whole genome resequencing was performed on the YF population, and bioinformatics analysis was conducted by combining the data from different breeds. Linkage disequilibrium (LD) analysis revealed that YF had the slowest LD-decay rate, suggesting strong natural and artificial selection in its history. Through selective sweep analysis, 1,126 selected regions in YF were identified, which contained 163,661 single nucleotide polymorphisms (SNPs). In particular, 5 specific SNPs (SNP1: Chr2:45509616, SNP2: Chr2:45510792, SNP3: Chr9:13788193, SNP4: Chr9:13795646, SNP5: Chr9:13798154) were found exclusively in the YF population. Subsequently, PCR amplification and Sanger sequencing confirmed the presence of these 5 SNPs in YF. Finally, 4 SNPs (SNP1, SNP2, SNP4, SNP5) were screened and verified using the Kompetitive Allele Specific PCR (KASP) typing technique. These SNPs can be used as specific molecular identity cards (IDs) for YF authentication. The present study is of great significance to ensure sustainable conservation and promotion of YF germplasm resources.