Nature Communications (Jun 2023)
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,
- Damaris A. Odeny
Affiliations
- Katrien M. Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia
- Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia
- Bochra A. Bahri
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia
- Davis M. Gimode
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia
- Katharine Jenike
- Departments of Computer Science, Biology and Genetic Medicine, Johns Hopkins University
- Samuel J. Manthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) – Eastern and Southern Africa
- Dagnachew Lule
- Department of Crop and Soil Sciences, University of Georgia
- Thomas Lux
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München
- Liliam Martinez-Bello
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia
- Thomas H. Pendergast
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia
- Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology
- Dipnarayan Saha
- Department of Crop and Soil Sciences, University of Georgia
- Gurjot S. Sidhu
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia
- Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology
- Xuewen Wang
- Department of Genetics, University of Georgia
- Hao Wang
- Department of Genetics, University of Georgia
- Hallie Wright
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia
- Jianxin Zhao
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia
- Santosh Deshpande
- ICRISAT
- Santie de Villiers
- Department of Biochemistry and Biotechnology, Pwani University
- Mathews M. Dida
- Department of Crop and Soil Science, Maseno University
- Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology
- Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology
- John Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology
- Klaus F. X. Mayer
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München
- Emmarold E. Mneney
- Mikocheni Agricultural Research Institute
- Henry F. Ojulong
- ICRISAT, Matopos Research Station
- Michael C. Schatz
- Departments of Computer Science, Biology and Genetic Medicine, Johns Hopkins University
- Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology
- Bo Song
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District
- Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University
- Damaris A. Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) – Eastern and Southern Africa
- DOI
- https://doi.org/10.1038/s41467-023-38915-6
- Journal volume & issue
-
Vol. 14,
no. 1
pp. 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.
