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

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 performance compared to the others in terms of variance explained in the PCA analysis while the outcomes of the genetic analyses confirmed its genotyping ability in peanut. The putative SNP sites associated with increased oleic acid levels have been integrated into this panel and validated, thus significantly enhancing its breeding potential. Moreover, the cost of genotyping by target sequencing (GBTS) using this panel is less than $9 per sample, making it more affordable. Due to its exceptional informativeness, cost-effectiveness, and breeding potential, we recommend this SNP panel for GBTS in peanut.