Ancient DNA of millets shed new lights for its spread in northern China and Tibetian plautue

Ancient DNA (aDNA) analysis offers valuable insights into the domestication and spread of foxtail millet (Setaria italica) across northern China and the Tibetan Plateau. This study leverages advanced genomic techniques to reconstruct the evolutionary history and adaptation of this crucial crop.
To overcome the limitations of ancient environmental DNA (aeDNA) in paleoecology and evolutionary studies, we developed eProbe, a flexible toolkit for designing, assessing, and validating hybridization capture probes. Benchmarking a foxtail millet probe set generated by eProbe demonstrated a 455-fold increase in target DNA recovery and high genome coverage, enabling detailed population and evolutionary genetic analyses.
Using these custom-designed probes, we enriched foxtail millet aDNA from archaeological and lake sediment samples across the Tibetan Plateau and northern China. This approach provides unprecedented insights into the spread and adaptation of foxtail millet as it ascended the plateau and underwent domestication. Combined with data from ancient seed enrichment, this dual analysis offers a comprehensive understanding of foxtail millet's evolutionary history and its role in high-altitude agricultural adaptation.
By integrating data from both ancient seed enrichment and environmental samples, this study offers critical insights into the complex processes of foxtail millet domestication and its impact on ancient agricultural systems in East Asia. Furthermore, these findings provide valuable context for understanding how ancient trade networks, such as the Silk Road, may have facilitated the exchange and adaptation of staple crops, influencing agricultural development and cultural interactions across Eurasia.