Insertions of Mutator-Like Transposable Elements and Their Impact on Gene Expression in the Illinois Long-Term Selection Experiment Maize Strains

Mutator-like elements (MULEs) are highly mutagenic and have the propensity to insert into low copy genic regions, which may influence the expression of adjacent genes as well as the relevant developmental processes. The Illinois Long-Term Selection Experiment (ILTSE) maize strains are elite experimental materials for a variety of studies, especially studies on the effects of selection on the kernel chemical composition (oil or protein). However, little is known about the molecular mechanism underlying the selection. Particularly, it is not clear whether transposons have played any role in the artificial selection. To this end, MULE insertions that are co-segregating with either high or low protein maize strains (IHP and ILP) were studied. Out of 200 co-segregating insertions detected, 191 produced significant alignments with the B73 maize genomic sequence. Consistent with previous findings, ~79% of the 191 insertions were located in low-copy genomic regions. Interestingly, similar numbers of co-segregating insertions were located at the 5′ and 3′ regions of protein-coding genes, which is in contrast to the 5′ region preference of MULEs reported in previous studies. Compared with that in the B73 genome, the fraction of co-segregating MULE insertions in exons is over one fold higher, suggesting exonic insertions may be involved in the selection. Additionally, ten out of 55 genes (~18%) associated with MULE insertions showed reduced expression levels and five (~9%) showed enhanced expression levels compared to the alleles without MULE insertions in immature kernels. Eight of the differentially expressed genes were further tested in young leave, where half exhibited similar expression pattern as that in immature kernels but the alteration associated with MULE insertions was not observed with the other half of the genes, suggesting they might be involved in the selected trait.