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 VilliersMathews 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

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

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.

Original languageEnglish
Article number3694
JournalNature Communications
Volume14
Issue number1
DOIs
StatePublished - Dec 2023

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