Two separate hybridizations were performed for each of the DNA pools using the Affymetrix 50K Hind 240 and the 50K Xba 240 arrays (Affymetrix, Santa Clara, CA). Five hundred ng DNA (in 120 μl) from each pool was ethanol precipitated, resuspended in 10 μl TE, and processed according to manufacturer’s protocol (Affymetrix). Processed arrays were scanned using an Affymetrix GeneChip Scanner 3000. Data was acquired using the GeneChip Operating System (GCOS) and analyzed using the GTYPE genotype Analysis Software (Affymetrix). Variant annotations are available from the NetAffx Analysis Center (http://www.affymetrix.com/analysis/index.affx).
