Optimization of commercial SNP arrays and the generation of a high-efficiency GenoBaits Peanut 10K panel.

ABSTRACT: To create a more comprehensive genetic analysis panel for peanuts, three high-density SNP panels were exploited. The refined SNP panel, PHR0301_Ah10K, comprises 10,000 SNP sites and demonstrated outstanding performance in sequence data analysis. It recorded the highest proportions of 99.53%, 96.48%, and 59.72% for the SNPs with minor allele frequency thresholds of MAF > 5%, MAF > 10%, and MAF > 20%, respectively. Moderate polymorphic information content (PIC) values were observed, with an average of 0.26, suggesting that the optimized SNP panel is informative. However, the PIC value for the four panels were skewed due to the small population size and limited genetic diversity (GD), as evidenced by the Kinship, PCA, and LD decay analyses. However, PHR0301_Ah10K demonstrated superior perform

SUBMITTER: Zhao Y 

PROVIDER: S-EPMC11929915 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature