Two flavors of bulk segregant analysis in yeast

Genetic mapping methods typically rely upon genotyping many individuals in a mapping population. In contrast, bulk segregant analysis looks for biases in genotype in phenotyped pools of segregants. For relatively strong and genetically simple traits, it can be a fast, inexpensive approach. Although it is technically possible to use many genotyping platforms, microarray-based methods are convenient for their genome-wide coverage, ease of use, and quantitative output. Also, precise knowledge of polymorphic sites is not required. I present two methods for bulk segregant analysis using microarrays, one based on hybridization differences between polymorphisms, and the other using an enzymatic method for enriching identical by descent segments of the genome. The first method requires specialized array platforms, while the second, genomic mismatch scanning (GMS), is compatible with any microarray. Although the methods presented are with yeast, most steps are equivalent for other organisms.