Small RNAs (sRNAs) are hypothesized to contribute to hybrid vigor because they maintain genome integrity, contribute to genetic diversity, and control gene expression. We used Illumina sequencing to assess how sRNA populations vary between two maize inbred lines (B73 and Mo17) and their hybrid. We sampled sRNAs from the seedling shoot apex and the developing ear, two rapidly growing tissues that program the greater growth of maize hybrids. We found that parental differences in siRNAs primarily originate from repeat regions. Although the maize genome contains greater number and complexity of repeats compared with Arabidopsis or rice, we confirmed that, like these simpler plant genomes, 24-nt siRNAs whose abundance differs between maize parents also show a trend of down-regulation following hybridization. Surprisingly, hybrid vigor is fully maintained when 24-nt siRNAs are globally reduced by mutation of the RNA-dependent RNA polymerase 2 encoded by modifier of paramutation1 (mop1). We also discovered that 21-22-nt siRNAs derived from a number of distinct retrotransposon families differentially accumulate between B73 and Mo17 as well as their hybrid. Thus, maize possesses a unique source of genetic variation for regulating transposons and genes at a genomic scale, which may contribute to its high degree of observed heterosis.transposon regulation | 22-nucleotide RNAs

Plant breeding programs primarily focus on improving a crop's environmental adaptability and biotic stress tolerance in order to increase yield. Crop improvements made since the 1950s – coupled with inexpensive agronomic inputs, such as fertilizers, pesticides, and water – have allowed agricultural production to keep pace with human population growth. Plant breeders, particularly those at public institutions, have an interest in reducing agriculture's negative impacts and improving the natural environment to provide or maintain ecosystem services (eg clean soil, water, and air; carbon sequestration), and in creating new agricultural paradigms (eg perennial polycultures). Here, we discuss recent developments in, as well as the goals of, plant breeding, and explain how these may be connected to the specific interests of ecologists and naturalists. Plant breeding can be a powerful tool to bring “harmony” between agriculture and the environment, but partnerships between plant breeders, ecologists, urban planners, and policy makers are needed to make this a reality.

Background:Promoters of active genes in eukaryotes are typically depleted of histone proteins. Results: Histone eviction from the induced CHA1 promoter is compromised by mutations in transcription factors, and higher histone occupancy is also seen at constitutively active promoters in such mutants. Conclusion: Preinitiation complex formation promotes reduced histone occupancy at active gene promoters. Significance: Preinitiation complex components participate in chromatin remodeling.

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