Our second approach to identify promising candidate genes relied on the generation of genomewide eye mRNA expression data for 26 strains of the AXB/BXA RI strain set. This massive data set was uploaded to GeneNetwork and made publicly available for use with various tools of the Web site. Specifically, we used the trait correlations tool to identify genes within the high-density SNP portion of
Cpnc10 whose mRNA expression covaried with cone photoreceptor number across the RI strain set. The mRNA expression of nine genes from this interval covaried with cone photoreceptor number (minimum Pearson's product moment correlation,
r = |0.4|). Seven of these genes can be dismissed because of poor microarray probes that aligned to multiple transcripts, targeted sequences in the array that had SNPs between the parental strains, or aligned to the intronic region of a gene. For the remaining two genes,
Bclaf1 and
Enpp1, we sought to determine whether their variation in expression across the strains might be attributed to a regulatory SNP, potentially the variant driving
Cpnc10. This was assessed by interval mapping of the expression data across the AXB/BXA RI strain set for both genes. The localization of a significant eQTL of a gene to its chromosomal position indicated the possibility of a
cis-acting variant regulating the expression of the gene (
cis-eQTL). This exercise eliminated
Bclaf1, which mapped an eQTL at a locus disparate from the chromosomal position from the gene (
trans-eQTL). However,
Enpp1 did map a
cis-eQTL (
Fig. 5), its expression covarying with
Cpnc10 (
r = 0.49;
P = 0.007); furthermore, there was a 1.26-fold increase in expression from A/J to B6/J. All three attributes of
Enpp1 expression, elucidated through use of the eye mRNA expression data set for the AXB/BXA RI strain set, suggested
Enpp1 as a promising candidate gene for
Cpnc10.