(A) Mapping scheme for diploid crosses. Boxes represent F₂ progeny from an intercross of F₁ fish (not shown) heterozygous for the mutation and for many SNPs, two of which are shown. Numbers adjacent to the genotypes refer to the ratios at which they are present among F₂ progeny. SNPs from wild-type and mutant pools are differentially labeled as in Fig. 3. For recessive mutations, the SNP allele linked in cis to the mutation is present in both pools due to the presence of heterozygotes in the wild-type pool. Therefore, this allele is labeled with both colors, whereas its wild-type counterpart is labeled only with one color (green in this example). (B) Microarray data mapping thest11 mutation to LG2. A two-color image from the hybridized microarray and a graph of relative hybridization intensity for the four probes of two SNPs are shown. ZSNP163 on LG2 exhibited differential labeling characteristic of linked markers. Polymorphic markers at most other positions, including ZSNP1120 on LG13, showed labeling characteristic of unlinked markers. (C) Map of LG2 showing the positions of st11 and SNPs that showed differential labeling characteristic of linked markers. Analysis of ZSNP158, ZSNP163, ZSNP173, and SSLP marker Z11023 in individual embryos confirmed thatst11 resides in this region of LG2 (distances indicated). In another trial of this experiment (data not shown), we detected differential labeling indicative of linkage for markers ZSNP163, ZSNP165, ZSNP171, and ZSNP173 on LG2; no base calls were generated for ZSNP158, ZSNP159, and ZSNP167, or for ZSNP196, which was detected as a false positive in the other trial.