Haploid transcriptome analysis reveals allelelic gene expression variants, co-expressed gene groups, and linkages between expression and copy number variation

Background Genetic variation can cause changes in gene expression (mRNA abundance) among individuals. This so-called heritable variation in gene expression is affected by genetic variants that are co-segregating with the gene locus (local/cis effects) and/or segregating independently from it (distant/trans effects). Genetic variation in gene expression can be measured to estimate the extant of variation in gene expression within a population, and to determine to what degree expression alleles of different genes are connected within regulatory networks. Furthermore, determining whether variation in the expression of a gene is linked to local or distant effects allows us to make inferences about how heritable variation may change depending on gene function, the number of interacting partners, genetic architecture and evolutionary history [1,2]. Detecting heritable variation in gene expression can be a challenging task in diploid organisms, mainly because of tissue-specificity and dominance effects of allelic expression. For example, up to 70% of gene expression alleles in Drosophila may be masked by dominance [3]. We developed an experimental system to overcome these obstacles by utilizing the conifer seed’s maternally derived haploid tissue, the megagametophyte. Analyzing a set of sibling megagametophytes allows us to first, measure separately the expression each of the two alleles in the maternal genome in the absence of dominance and second, identify genes whose expression levels are co-segregating. In addition, the megagametophyte allows us to categorize the underlying genetic variants into local or distant with a simple co-segregation assay.