Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet
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 in...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-06-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-38915-6 |
| _version_ | 1797795600709713920 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Katrien M. Devos |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-13T03:20:25Z |
| format | Article |
| id | doaj.art-ab78a9fd968d482eb132fa249a468bd2 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-13T03:20:25Z |
| publishDate | 2023-06-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-ab78a9fd968d482eb132fa249a468bd22023-06-25T11:21:24ZengNature PortfolioNature Communications2041-17232023-06-0114111510.1038/s41467-023-38915-6Genome analyses reveal population structure and a purple stigma color gene candidate in finger milletKatrien M. Devos0Peng Qi1Bochra A. Bahri2Davis M. Gimode3Katharine Jenike4Samuel J. Manthi5Dagnachew Lule6Thomas Lux7Liliam Martinez-Bello8Thomas H. Pendergast9Chris Plott10Dipnarayan Saha11Gurjot S. Sidhu12Avinash Sreedasyam13Xuewen Wang14Hao Wang15Hallie Wright16Jianxin Zhao17Santosh Deshpande18Santie de Villiers19Mathews M. Dida20Jane Grimwood21Jerry Jenkins22John Lovell23Klaus F. X. Mayer24Emmarold E. Mneney25Henry F. Ojulong26Michael C. Schatz27Jeremy Schmutz28Bo Song29Kassahun Tesfaye30Damaris A. Odeny31Institute of Plant Breeding, Genetics and Genomics, University of GeorgiaInstitute of Plant Breeding, Genetics and Genomics, University of GeorgiaInstitute of Plant Breeding, Genetics and Genomics, University of GeorgiaInstitute of Plant Breeding, Genetics and Genomics, University of GeorgiaDepartments of Computer Science, Biology and Genetic Medicine, Johns Hopkins UniversityInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT) – Eastern and Southern AfricaDepartment of Crop and Soil Sciences, University of GeorgiaPlant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum MünchenInstitute of Plant Breeding, Genetics and Genomics, University of GeorgiaInstitute of Plant Breeding, Genetics and Genomics, University of GeorgiaGenome Sequencing Center, HudsonAlpha Institute for BiotechnologyDepartment of Crop and Soil Sciences, University of GeorgiaInstitute of Plant Breeding, Genetics and Genomics, University of GeorgiaGenome Sequencing Center, HudsonAlpha Institute for BiotechnologyDepartment of Genetics, University of GeorgiaDepartment of Genetics, University of GeorgiaInstitute of Plant Breeding, Genetics and Genomics, University of GeorgiaInstitute of Plant Breeding, Genetics and Genomics, University of GeorgiaICRISATDepartment of Biochemistry and Biotechnology, Pwani UniversityDepartment of Crop and Soil Science, Maseno UniversityGenome Sequencing Center, HudsonAlpha Institute for BiotechnologyGenome Sequencing Center, HudsonAlpha Institute for BiotechnologyGenome Sequencing Center, HudsonAlpha Institute for BiotechnologyPlant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum MünchenMikocheni Agricultural Research InstituteICRISAT, Matopos Research StationDepartments of Computer Science, Biology and Genetic Medicine, Johns Hopkins UniversityGenome Sequencing Center, HudsonAlpha Institute for BiotechnologyBGI-Shenzhen, Beishan Industrial Zone, Yantian DistrictInstitute of Biotechnology, Addis Ababa UniversityInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT) – Eastern and Southern AfricaAbstract 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.https://doi.org/10.1038/s41467-023-38915-6 |
| spellingShingle | 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 Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet Nature Communications |
| title | Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet |
| title_full | Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet |
| title_fullStr | Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet |
| title_full_unstemmed | Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet |
| title_short | Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet |
| title_sort | genome analyses reveal population structure and a purple stigma color gene candidate in finger millet |
| url | https://doi.org/10.1038/s41467-023-38915-6 |
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