Recombination and gene expression
Changes in gene expression play a major role in the adaptive evolution that precedes and accompanies speciation and is a general phenomenon that contributes to the genetic diversity available for breeding and selection among crop species. The relative contributions and interplay of cis- and trans- acting regulatory factors to this evolutionary process in plants, however, remain poorly studied. We are describing and fine mapping the cis-acting genetic components involved in gene expression variation in the Bz1-Sh1 region of maize. The Bz1-Sh1 region was chosen because it is highly dynamic among maize inbred lines, consisting of multiple transposon insertions and deletions, rearrangements, and a high propensity toward recombination. This naturally occurring intergenic polymorphism provides a potential substrate for expression effects on neighboring genes.
To explore the relationship between genomic context and gene expression, we used 454 sequencing technology to quantify the cis-effects on variation in allelic gene expression for eight of the thirteen genes in the Bz1-Sh1 region in several maize inbred line crosses (Hawkins et al, 2014). Most of the genes in the Bz1-Sh1 region display striking variation in expression patterns among parental genotypes in the same genetic background and across different tissue types, despite high levels of sequence conservation at the nucleotide level among protein-coding sequences. Interestingly, the most significant expression variation is concentrated around a defined recombination hotspot.
To identify the precise cis-acting components responsible for this expression variation, we collected a large number of recombinants in the Bz1-Sh1 region for expression analysis. Because most recombination events will be in or near genes, recombinant promoter regions will be generated for most of the genes in the region. cDNA obtained from these recombinants, now containing chimeric promoter regions, will facilitate the fine-mapping of the precise cis-acting components effecting gene expression.
An ear from the selfing of a hybrid showing both types of recombinant kernels. Parental genotypes: (sh1, bz1) – bronze colored and excessively shrunken kernels. (Sh1, Bz1) – purple colored kernels with small indention. Recombinant genotypes: sh1, BZ1 – purple colored with excessively shrunken kernel as indicated by upper recombinant arrow. Sh1, bz1 – bronze colored kernel with small indention as indicated by lower recombinant arrow