Figure 1

a, b: Theoretical outcomes of probe hybridization. A) Affymetrix short oligonucleotide arrays are fabricated with sets of eleven 25-mer probes to interrogate the expression level of a particular mRNA. Because of the short probe length, a SNP falling in the middle of the probe sequence will result in that probe's failure to hybridize. B) Three potential hybridization scenarios within a single probe set are depicted: 1) mRNA to target probes is not expressed in either breed, 2) mRNA to target probes is equivalent in both breeds or, 3) intensity of probes is expressed in one breed and negligible in the other breed. In this latter case, a probe-by-breed effect is seen with Meishan RNA hybridized to probe 2 of the probe set. The green hash represents the SFP located within a central nucleotide position within the probe.