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Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet
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 21...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10284860/ https://www.ncbi.nlm.nih.gov/pubmed/37344528 http://dx.doi.org/10.1038/s41467-023-38915-6 |
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author | Devos, Katrien M. Qi, Peng Bahri, Bochra A. Gimode, Davis M. Jenike, Katharine Manthi, Samuel J. Lule, Dagnachew Lux, Thomas Martinez-Bello, Liliam Pendergast, Thomas H. Plott, Chris Saha, Dipnarayan Sidhu, Gurjot S. Sreedasyam, Avinash Wang, Xuewen Wang, Hao Wright, Hallie Zhao, Jianxin Deshpande, Santosh de Villiers, Santie Dida, Mathews M. Grimwood, Jane Jenkins, Jerry Lovell, John Mayer, Klaus F. X. Mneney, Emmarold E. Ojulong, Henry F. Schatz, Michael C. Schmutz, Jeremy Song, Bo Tesfaye, Kassahun Odeny, Damaris A. |
author_facet | Devos, Katrien M. Qi, Peng Bahri, Bochra A. Gimode, Davis M. Jenike, Katharine Manthi, Samuel J. Lule, Dagnachew Lux, Thomas Martinez-Bello, Liliam Pendergast, Thomas H. Plott, Chris Saha, Dipnarayan Sidhu, Gurjot S. Sreedasyam, Avinash Wang, Xuewen Wang, Hao Wright, Hallie Zhao, Jianxin Deshpande, Santosh de Villiers, Santie Dida, Mathews M. Grimwood, Jane Jenkins, Jerry Lovell, John Mayer, Klaus F. X. Mneney, Emmarold E. Ojulong, Henry F. Schatz, Michael C. Schmutz, Jeremy Song, Bo Tesfaye, Kassahun Odeny, Damaris A. |
author_sort | Devos, Katrien M. |
collection | PubMed |
description | 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 21(st) 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. |
format | Online Article Text |
id | pubmed-10284860 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-102848602023-06-23 Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet Devos, Katrien M. Qi, Peng Bahri, Bochra A. Gimode, Davis M. Jenike, Katharine Manthi, Samuel J. Lule, Dagnachew Lux, Thomas Martinez-Bello, Liliam Pendergast, Thomas H. Plott, Chris Saha, Dipnarayan Sidhu, Gurjot S. Sreedasyam, Avinash Wang, Xuewen Wang, Hao Wright, Hallie Zhao, Jianxin Deshpande, Santosh de Villiers, Santie Dida, Mathews M. Grimwood, Jane Jenkins, Jerry Lovell, John Mayer, Klaus F. X. Mneney, Emmarold E. Ojulong, Henry F. Schatz, Michael C. Schmutz, Jeremy Song, Bo Tesfaye, Kassahun Odeny, Damaris A. Nat Commun Article 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 21(st) 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. Nature Publishing Group UK 2023-06-21 /pmc/articles/PMC10284860/ /pubmed/37344528 http://dx.doi.org/10.1038/s41467-023-38915-6 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Devos, Katrien M. Qi, Peng Bahri, Bochra A. Gimode, Davis M. Jenike, Katharine Manthi, Samuel J. Lule, Dagnachew Lux, Thomas Martinez-Bello, Liliam Pendergast, Thomas H. Plott, Chris Saha, Dipnarayan Sidhu, Gurjot S. Sreedasyam, Avinash Wang, Xuewen Wang, Hao Wright, Hallie Zhao, Jianxin Deshpande, Santosh de Villiers, Santie Dida, Mathews M. Grimwood, Jane Jenkins, Jerry Lovell, John Mayer, Klaus F. X. Mneney, Emmarold E. Ojulong, Henry F. Schatz, Michael C. Schmutz, Jeremy Song, Bo Tesfaye, Kassahun Odeny, Damaris A. Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet |
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 |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10284860/ https://www.ncbi.nlm.nih.gov/pubmed/37344528 http://dx.doi.org/10.1038/s41467-023-38915-6 |
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