The genomic origin of early maize in eastern North America

Jazmín Ramos-Madrigal; Gayle J. Fritz; Bryon Schroeder; Bruce Smith; Fátima Sánchez-Barreiro; Christian Carøe; Anne Kathrine Wiborg Runge; Sarah Boer; Krista McGrath; Filipe G. Vieira; Shanlin Liu; Rute R. da Fonseca; Chunxue Guo; Guojie Zhang; Bent Petersen; Thomas Sicheritz-Pontén; Shyam Gopalakrishnan; M. Thomas P. Gilbert; Nathan Wales

doi:10.1016/j.cell.2024.11.003

The genomic origin of early maize in eastern North America

Jazmín Ramos-Madrigal^*, Gayle J. Fritz, Bryon Schroeder, Bruce Smith, Fátima Sánchez-Barreiro, Christian Carøe, Anne Kathrine Wiborg Runge, Sarah Boer, Krista McGrath, Filipe G. Vieira, Shanlin Liu, Rute R. da Fonseca, Chunxue Guo, Guojie Zhang, Bent Petersen, Thomas Sicheritz-Pontén, Shyam Gopalakrishnan, M. Thomas P. Gilbert, Nathan Wales

^*Corresponding author for this work

Research output: Contribution to journal › Journal article › Research › peer-review

Abstract

Indigenous maize varieties from eastern North America have played an outsized role in breeding programs, yet their early origins are not fully understood. We generated paleogenomic data to reconstruct how maize first reached this region and how it was selected during the process. Genomic ancestry analyses reveal recurrent movements northward from different parts of Mexico, likely culminating in at least two dispersals from the US Southwest across the Great Plains to the Ozarks and beyond. We find that 1,000-year-old Ozark specimens carry a highly differentiated wx1 gene, which is involved in the synthesis of amylose, highlighting repeated selective pressures on the starch metabolic pathway throughout maize's domestication. This population shows a close affinity with the lineage that ultimately became the Northern Flints, a major contributor to modern commercial maize.

Original language	English
Journal	Cell
Volume	188
Issue number	1
Pages (from-to)	33-43.e16
ISSN	0092-8674
DOIs	https://doi.org/10.1016/j.cell.2024.11.003
Publication status	Published - 9 Jan 2025

Bibliographical note

Funding Information:
Permission for destructive sampling of archaeological material was kindly granted by the Botanical Museum at Harvard University, the Center for Archaeological Investigations at Southern Illinois University Carbondale, the Center for Big Bend Studies, the University of Arkansas Collection Facility, the Osage Nation, and the University of Michigan Museum of Archaeological Anthropology. In particular, we acknowledge the invaluable assistance of Andrea A. Hunter, Tribal Historic Preservation Officer, Osage Nation; Mary Suter, Curator of Collections, University Museum, University of Arkansas; and Heather Lapham, Curator at the Center for Archaeological Investigations. We thank the Danish National High-throughput Sequencing Centre, Sarah Mak, and BGI Shenzhen for assistance in generating the sequencing data, as well as to the Computerome2 and University of York High Performance Computing service that were used to analyze the data. We would like to thank J. V\u00EDctor Moreno-Mayar, Aldo Carmona Baez, and Logan Kistler for their helpful discussion. We thank Kelly Swarts and R.G. Matson for further details on the dating of Turkey Pen Shelter. Thanks to Chris Troll, Josh Kapp, and Beth Shapiro for suggestions on the SCR library preparation method. We acknowledge DFF grants DFF-10-081390 and DFF-1325-00136, Danish National Research Foundation grant DNRF143, and Marie Sk\u0142odowska-Curie Actions grant 272927\u2014\u201CMaizeKey\u201D for funding this research. R.R.d.F. is funded by the VILLUM FONDEN grant no. 25925.

Publisher Copyright:
© 2024 Elsevier Inc.

Keywords

ancient DNA
domestication
evolution
maize
maize genomics
paleogenomics
starch pathway
wx1

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10.1016/j.cell.2024.11.003

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Ramos-Madrigal, J., Fritz, G. J., Schroeder, B., Smith, B., Sánchez-Barreiro, F., Carøe, C., Runge, A. K. W., Boer, S., McGrath, K., Vieira, F. G., Liu, S., da Fonseca, R. R., Guo, C., Zhang, G., Petersen, B., Sicheritz-Pontén, T., Gopalakrishnan, S., Gilbert, M. T. P., & Wales, N. (2025). The genomic origin of early maize in eastern North America. Cell, 188(1), 33-43.e16. https://doi.org/10.1016/j.cell.2024.11.003

The genomic origin of early maize in eastern North America. / Ramos-Madrigal, Jazmín; Fritz, Gayle J.; Schroeder, Bryon; Smith, Bruce; Sánchez-Barreiro, Fátima; Carøe, Christian; Runge, Anne Kathrine Wiborg; Boer, Sarah; McGrath, Krista; Vieira, Filipe G.; Liu, Shanlin; da Fonseca, Rute R.; Guo, Chunxue; Zhang, Guojie ; Petersen, Bent ; Sicheritz-Pontén, Thomas ; Gopalakrishnan, Shyam ; Gilbert, M. Thomas P.; Wales, Nathan.

In: Cell, Vol. 188, No. 1, 09.01.2025, p. 33-43.e16.

Research output: Contribution to journal › Journal article › Research › peer-review

Ramos-Madrigal, J, Fritz, GJ, Schroeder, B, Smith, B, Sánchez-Barreiro, F, Carøe, C, Runge, AKW, Boer, S, McGrath, K, Vieira, FG , Liu, S, da Fonseca, RR, Guo, C, Zhang, G , Petersen, B , Sicheritz-Pontén, T , Gopalakrishnan, S , Gilbert, MTP & Wales, N 2025, 'The genomic origin of early maize in eastern North America', Cell, vol. 188, no. 1, pp. 33-43.e16. https://doi.org/10.1016/j.cell.2024.11.003

Ramos-Madrigal, Jazmín ; Fritz, Gayle J. ; Schroeder, Bryon ; Smith, Bruce ; Sánchez-Barreiro, Fátima ; Carøe, Christian ; Runge, Anne Kathrine Wiborg ; Boer, Sarah ; McGrath, Krista ; Vieira, Filipe G. ; Liu, Shanlin ; da Fonseca, Rute R. ; Guo, Chunxue ; Zhang, Guojie ; Petersen, Bent ; Sicheritz-Pontén, Thomas ; Gopalakrishnan, Shyam ; Gilbert, M. Thomas P. ; Wales, Nathan. / The genomic origin of early maize in eastern North America. In: Cell. 2025 ; Vol. 188, No. 1. pp. 33-43.e16.

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abstract = "Indigenous maize varieties from eastern North America have played an outsized role in breeding programs, yet their early origins are not fully understood. We generated paleogenomic data to reconstruct how maize first reached this region and how it was selected during the process. Genomic ancestry analyses reveal recurrent movements northward from different parts of Mexico, likely culminating in at least two dispersals from the US Southwest across the Great Plains to the Ozarks and beyond. We find that 1,000-year-old Ozark specimens carry a highly differentiated wx1 gene, which is involved in the synthesis of amylose, highlighting repeated selective pressures on the starch metabolic pathway throughout maize's domestication. This population shows a close affinity with the lineage that ultimately became the Northern Flints, a major contributor to modern commercial maize.",

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author = "Jazm{\'i}n Ramos-Madrigal and Fritz, {Gayle J.} and Bryon Schroeder and Bruce Smith and F{\'a}tima S{\'a}nchez-Barreiro and Christian Car{\o}e and Runge, {Anne Kathrine Wiborg} and Sarah Boer and Krista McGrath and Vieira, {Filipe G.} and Shanlin Liu and {da Fonseca}, {Rute R.} and Chunxue Guo and Guojie Zhang and Bent Petersen and Thomas Sicheritz-Pont{\'e}n and Shyam Gopalakrishnan and Gilbert, {M. Thomas P.} and Nathan Wales",

note = "Funding Information: Permission for destructive sampling of archaeological material was kindly granted by the Botanical Museum at Harvard University, the Center for Archaeological Investigations at Southern Illinois University Carbondale, the Center for Big Bend Studies, the University of Arkansas Collection Facility, the Osage Nation, and the University of Michigan Museum of Archaeological Anthropology. In particular, we acknowledge the invaluable assistance of Andrea A. Hunter, Tribal Historic Preservation Officer, Osage Nation; Mary Suter, Curator of Collections, University Museum, University of Arkansas; and Heather Lapham, Curator at the Center for Archaeological Investigations. We thank the Danish National High-throughput Sequencing Centre, Sarah Mak, and BGI Shenzhen for assistance in generating the sequencing data, as well as to the Computerome2 and University of York High Performance Computing service that were used to analyze the data. We would like to thank J. V\u00EDctor Moreno-Mayar, Aldo Carmona Baez, and Logan Kistler for their helpful discussion. We thank Kelly Swarts and R.G. Matson for further details on the dating of Turkey Pen Shelter. Thanks to Chris Troll, Josh Kapp, and Beth Shapiro for suggestions on the SCR library preparation method. We acknowledge DFF grants DFF-10-081390 and DFF-1325-00136, Danish National Research Foundation grant DNRF143, and Marie Sk\u0142odowska-Curie Actions grant 272927\u2014\u201CMaizeKey\u201D for funding this research. R.R.d.F. is funded by the VILLUM FONDEN grant no. 25925. Publisher Copyright: {\textcopyright} 2024 Elsevier Inc.",

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AU - Gilbert, M. Thomas P.

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N1 - Funding Information: Permission for destructive sampling of archaeological material was kindly granted by the Botanical Museum at Harvard University, the Center for Archaeological Investigations at Southern Illinois University Carbondale, the Center for Big Bend Studies, the University of Arkansas Collection Facility, the Osage Nation, and the University of Michigan Museum of Archaeological Anthropology. In particular, we acknowledge the invaluable assistance of Andrea A. Hunter, Tribal Historic Preservation Officer, Osage Nation; Mary Suter, Curator of Collections, University Museum, University of Arkansas; and Heather Lapham, Curator at the Center for Archaeological Investigations. We thank the Danish National High-throughput Sequencing Centre, Sarah Mak, and BGI Shenzhen for assistance in generating the sequencing data, as well as to the Computerome2 and University of York High Performance Computing service that were used to analyze the data. We would like to thank J. V\u00EDctor Moreno-Mayar, Aldo Carmona Baez, and Logan Kistler for their helpful discussion. We thank Kelly Swarts and R.G. Matson for further details on the dating of Turkey Pen Shelter. Thanks to Chris Troll, Josh Kapp, and Beth Shapiro for suggestions on the SCR library preparation method. We acknowledge DFF grants DFF-10-081390 and DFF-1325-00136, Danish National Research Foundation grant DNRF143, and Marie Sk\u0142odowska-Curie Actions grant 272927\u2014\u201CMaizeKey\u201D for funding this research. R.R.d.F. is funded by the VILLUM FONDEN grant no. 25925. Publisher Copyright: © 2024 Elsevier Inc.

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The genomic origin of early maize in eastern North America

Abstract

Bibliographical note

Keywords

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