50k liquid-phase chip for pigs based on multiple single nucleotide polymorphisms

Abstract

The present disclosure relates to the field of genetic molecular breeding, specifically to a 50K liquid-phase chip for pigs based on multiple single nucleotide-polymorphism (mSNP) and its application. The DNA probe design of the chip in the present disclosure takes into account the distribution of captured SNP loci across the genome, the polymorphism of the loci, the quality of mSNP markers, and other issues, effectively avoiding problems such as uneven marker density and poor polymorphism. It also considers the quality of mSNP markers and the issue of linkage disequilibrium among mSNP markers. While adhering to the basic principles of liquid-phase chip design, genomic regions with moderate linkage disequilibrium between markers were selected, generating more SNP markers with high genotyping quality and moderate linkage disequilibrium within the probe region with the target loci. The mSNP liquid-phase chip of the present disclosure expands the detectable number of SNPs to 1.5-2 times that of the target loci, addressing the issue of the relatively small number of high-quality mSNP markers in traditional liquid-phase chips without increasing costs.

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