Patterns of stability and change in the maize genome: a case study of small RNA transcriptomes in two recombinant inbred lines and their progenitors

Small RNAs (sRNAs) are epigenetic regulators of eukaryotic genes and transposable elements (TEs). Diverse sRNA expression patterns exist within a species, but how this diversity arises is not well understood. To provide window into the dynamics maize patterning, mRNA transcriptomes were examined in two related Zea mays recombinant inbred lines (RILs) their parents. Analysis these RILs revealed that most clusters retained parental level. However, states differ from allele also observed, predominantly reflecting decreases expression. When RIL differed allele, new state was frequently similar between RILs, to found at other parent. Novel patterns, distinct those either parent, rare. Additionally, examination over TEs one TE family, Gyma, which showed consistent enrichment for differences compared alleles. These findings insights silencing might evolve generations suggest further investigation molecular nature trans warranted.