Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet

Katrien M. Devos (), Peng Qi, Bochra A. Bahri, Davis M. Gimode, Katharine Jenike, Samuel J. Manthi, Dagnachew Lule, Thomas Lux, Liliam Martinez-Bello, Thomas H. Pendergast, Chris Plott, Dipnarayan Saha, Gurjot S. Sidhu, Avinash Sreedasyam, Xuewen Wang, Hao Wang, Hallie Wright, Jianxin Zhao, Santosh Deshpande, Santie de Villiers, Mathews M. Dida, Jane Grimwood, Jerry Jenkins, John Lovell, Klaus F. X. Mayer, Emmarold E. Mneney, Henry F. Ojulong, Michael C. Schatz, Jeremy Schmutz, Bo Song, Kassahun Tesfaye and Damaris A. Odeny
Additional contact information
Katrien M. Devos: University of Georgia
Peng Qi: University of Georgia
Bochra A. Bahri: University of Georgia
Davis M. Gimode: University of Georgia
Katharine Jenike: Johns Hopkins University
Samuel J. Manthi: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) – Eastern and Southern Africa
Dagnachew Lule: University of Georgia
Thomas Lux: Helmholtz Zentrum München
Liliam Martinez-Bello: University of Georgia
Thomas H. Pendergast: University of Georgia
Chris Plott: HudsonAlpha Institute for Biotechnology
Dipnarayan Saha: University of Georgia
Gurjot S. Sidhu: University of Georgia
Avinash Sreedasyam: HudsonAlpha Institute for Biotechnology
Xuewen Wang: University of Georgia
Hao Wang: University of Georgia
Hallie Wright: University of Georgia
Jianxin Zhao: University of Georgia
Santosh Deshpande: ICRISAT
Santie de Villiers: Pwani University
Mathews M. Dida: Maseno University
Jane Grimwood: HudsonAlpha Institute for Biotechnology
Jerry Jenkins: HudsonAlpha Institute for Biotechnology
John Lovell: HudsonAlpha Institute for Biotechnology
Klaus F. X. Mayer: Helmholtz Zentrum München
Emmarold E. Mneney: Mikocheni Agricultural Research Institute
Henry F. Ojulong: ICRISAT, Matopos Research Station
Michael C. Schatz: Johns Hopkins University
Jeremy Schmutz: HudsonAlpha Institute for Biotechnology
Bo Song: Beishan Industrial Zone, Yantian District
Kassahun Tesfaye: Addis Ababa University
Damaris A. Odeny: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) – Eastern and Southern Africa

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: Abstract Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a ‘poor man’s crop’, finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.

Date: 2023
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DOI: 10.1038/s41467-023-38915-6

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