Figure 5. Microarray analysis of one granddaughter cell in a sectored colony resulting from a recombination event on chromosome V.
By methods described in the text, we identified two granddaughter genotypes associated with the red and white sectors of the YYy310-9-5WR sectored colony. SNP-specific microarrays were done on genomic DNA isolated from all four granddaughter strains, and from spore derivatives of each of these granddaughters. (A) Microarray analysis of the W1 granddaughter strain. Genomic DNA was isolated, and hybridized to SNP-specific microarrays in competition with differentially-labeled genomic DNA from a heterozygous control strain (details in Materials and methods). The Y axis shows the hybridization ratio of the experimental samples to allele-specific SNPs normalized to the hybridization levels of the control heterozygous sample; blue and red circles indicate hybridization ratios to YJM789- and W303-1A-specific SNPs, respectively. Heterozygous samples have a ratio of about 1, samples in which the strain-specific allele is present in two copies have a ratio of about 1.7, and those in which the strain-specific allele is missing have a ratio of about 0.3. The X axis has SGD coordinates for chromosome V in the region of the recombination event. Between the left telomere (coordinate 1) and coordinate 51915, the W1 granddaughter is homozygous for the YJM789-derived SNPs, and heterozygous for SNPs between coordinates 60701 and the right telomere. In summary, chromosome V in this strain has a large terminal region that is homozygous for YJM789 SNPs, a short region of heterozygous SNPs, a short region that is homozygous for W303-1A SNPs, and a large heterozygous region that makes up the remainder of the chromosome. (B) Microarray analysis of a spore derived from the W1 granddaughter strain. The W1 diploid was sporulated, and dissected. We examined the genomic DNA of one spore by SNP microarrays. From the pattern of SNPs in the spore, we conclude that one homolog in W1 has blue SNPs for the heterozygous region located near coordinates 55000 and red SNPs for the heterozygous region located between coordinates 60000, and the right telomere. The other homolog has the reciprocal pattern. (C) Inferred arrangement of red and blue SNPs on the two homologs of W1 based on the microarray results shown in Figure 5A and B. This pattern is reproduced in the top part of Supplementary file 2 - S8.