Heritable variation in gene expression has been largely studied in model organisms by taking advantage of pure and inbred lines. Comparative studies on organisms with contrasting evolutionary history, population size and genome architecture have been hindered by practical considerations, as many of these species are poorly suited for breeding. We have developed a method for determining expression variation in an undomesticated tree species by directly measuring the segregation of gene expression in the haploid meiotic products of a single diploid individual. We show the utility of our approach by identifying expression variation that segregates consistent with one causal variant and identify an unexpectedly large number of these Mendelian expression traits. The megagametophyte approach opens the doors for the application of genetical genomics approaches in a large number of undomesticated plant species.
Transcriptomics data from 18 megagametophytes of two unrelated mother trees. In tree 80112, all of the 18 megagametophytes were analyzed on to different microarrays with two different dyes. In tree 77111, 16 megagametophytes were replicated as above.