Comparative Transcriptomic Analysis Reveals Domestication and Improvement Patterns of Broomcorn Millet (Panicum miliaceum L.)

Broomcorn millet (<i>Panicum miliaceum</i> L.) is one of the earliest crops, domesticated nearly 8000 years ago in northern China. It gradually spread across the entire Eurasian continent, as well as to America and Africa, with recent improvement in various reproductive and vegetative traits. To identify the genes that were selected during the domestication and improvement processes, we performed a comparative transcriptome analysis based on wild types, landraces, and improved cultivars of broomcorn millet at both seeding and filling stages. The variations in gene expression patterns between wild types and landraces and between landraces and improved cultivars were further evaluated to explore the molecular mechanisms underlying the domestication and improvement of broomcorn millet. A total of 2155 and 3033 candidate genes involved in domestication and a total of 84 and 180 candidate genes related to improvement were identified at seedling and filling stages of broomcorn millet, respectively. The annotation results suggested that the genes related to metabolites, stress resistance, and plant hormones were widely selected during both domestication and improvement processes, while some genes were exclusively selected in either domestication or improvement stages, with higher selection pressure detected in the domestication process. Furthermore, some domestication- and improvement-related genes involved in stress resistance either lost their functions or reduced their expression levels due to the trade-offs between stress resistance and productivity. This study provided novel genetic materials for further molecular breeding of broomcorn millet varieties with improved agronomic traits.