Development and use of SNP-based markers for eventual development of a peanut DNA chip for marker-assisted breeding

In summary, the validation work so far has generally been successful. However, we have found that the greatest success rate comes from having a DNA-based genomic sequence, to identify when there are multiple copies of a gene, or to identify when the presence of introns results in a product that perhaps cannot be sequenced as efficiently (from both ends) as expected. 
For this reason, we are (1) taking our initial 300 gene picks, and comparing to the genomic sequence of A. duranensis and A. ipaensis, to select genes that have only two copies ( one each from the A and B genomes) and that are not expected to contain introns, or at least to select SNPs that are far from introns and will result in assays not affected by the presence of introns. We will also (2) expand our number of gene, after comparison to the genomic DNA sequence, to 500. 
After this has been done, we plan to perform the SNP analysis on 94 individuals of the A genome mapping population, using up to 500 SNP markers.