Reshuffling of Genic Variation via Intragenic Meiotic Recombination Generates Novel Gene Expression Patterns

The shuffling of sequences among different haplotypes by meiotic recombination creates new genetic variation. In particular, intragenic recombination has the potential to combine portions of different alleles to create protein variants not previously found within a species. We hypothesize that intragenic recombination could also create novel expression patterns. We performed RNA-Sequencing on 105 maize recombined inbred lines derived from two maize inbred lines to understand how the genome-wide pattern of meiotic recombination and intragenic recombination affects gene expression. In total, 7,574 crossover recombinants and 922 non-crossovers were observed. Seven-hundred-and-ninety-three recombinant alleles of 591 distinct genes were created via intragenic crossover. Thirty-nine percent of all these intragenic crossovers occurred within 107 hotspot genes which experienced at least two independent intragenic crossovers. Characterization of these hotspot genes indicates that they exhibit low levels of heterochromatin-related epigenetic marks. Importantly, we validate the hypothesis that meiotic recombination creates functional variation by identifying recombinant alleles exhibiting non-parental expression patterns. Furthermore, hotspot genes are more likely to be syntenic with sorghum, and recombination is more prevalent in syntenic regions. Meiotic recombination provides a source of novel alleles for evolution and breeding that may primarily affect syntenic genomic regions.