In silico analysis of the evolution of root phenotypes during maize domestication in Neolithic soils of Tehuacan

• Published in: bioRxiv
• Main Authors: Lopez-Valdivia, Ivan, Vallebueno-Estrada, Miguel, Rangarajan, Harini, Swarts, Kelly, Benz, Bruce, Blake, Michael, Jagdeep Singh Sidhu, Perez-Limon, Sergio, Sawers, Ruairidh Jh, Schneider, Hannah, Lynch, Jonathan
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 03.01.2025; Cold Spring Harbor Laboratory
• Edition: 3.2
• Subjects: Adaptation; Agricultural practices; Carbon dioxide; Corn; Domestication; Holocene; Phenotypes; Plant Biology; Soil degradation; Structure-function relationships; Zea luxurians; Tehuacan Valley
• ISSN: 2692-8205; 2692-8205
• DOI: 10.1101/2024.11.18.623787

Roots are essential for plant adaptation to changing environments, yet the role of roots in crop domestication remains unclear. This study examines the evolution of root phenotypes from teosinte to maize, a transition resulting in reduced nodal root number (NRN), multiseriate cortical sclerenchyma (MCS), and increased seminal root number (SRN). We reconstructed the root phenotypes of maize and teosinte, as well as the environments of the Tehuacan Valley over the last 18,000 years using a combination of ancient DNA, paleobotany, and functional-structural modeling. Our models reveal that increasing Holocene atmospheric CO2 concentrations favored the appearance of reduced NRN and MCS between 12000 to 8000 years before present (yBP), promoting deeper root systems. The advent of irrigation by 6000 yBP switched nitrogen distribution from topsoil to subsoil domains, a change which increased the utility of reduced NRN and MCS. Comparison of allelic frequencies among ancient samples ranging from 5500 to 500 yBP suggest that increased SRN may have appeared around 3500 yBP, coinciding with a period of increased human population, agricultural intensification, and soil degradation. Our results suggest that root phenotypes that enhance plant performance under nitrogen stress were important for maize adaptation to changing agricultural practices in the Tehuacan Valley.Competing Interest StatementThe authors have declared no competing interest.Footnotes* A supplementary video file has been added to this version.* https://github.com/ilovaldivia/Lopez-Valdivia_2023_RootEvolution.git