Genetic Variation for Retrotransposon Derived Si RNAs in Maize.

Transposons regulate the growth and development of eukaryotes through their generation of small interfering RNAs (siRNAs).  In maize, long terminal repeat (LTR)-retrotransposons produce a large and diverse source of 21-24-nt siRNAs in proliferating cells.  Using sRNA sequencing data from the shoot apex of 36 diverse maize inbred lines, we demonstrate that the regulation of LTR-retrotransposons dramatically varies in the species and contributes to its genetic diversity.  The generation of siRNAs from LTR-retrotransposons largely depends on the total amount of DNA of a LTR-retrotransposon family and its insertion date, but varies due to genetic background.  The largest families that expanded the maize genome 0.5-1.5 million years ago are responsible for the majority of retrotransposon derived siRNAs and produce siRNAs in all of the lines.  However, lines differ in their total abundance of 21-22-nt and 23-24-nt siRNAs for these families.  Other families only produced siRNAs in one line.  This variation among lines is not due to differences in family copy number and may not result from all genomic regions containing homologous DNA because the potential to generate siRNAs from a retrotransposon does not follow the family’s distribution in the genome.  We discovered that the variation in retrotransposon siRNA abundance can distinguish lines representing populations artificially isolated by breeders to exploit hybrid vigor in maize.  Thus, the generation of siRNAs provides another way for LTR-retrotransposons to contribute to genetic diversity and is a tractable source of regulatory variation that can be used to enhance our understanding of genetic variation for species with complex genomes.