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

Devos, K M and Qi, P and Bahri, B A and Gimode, D M and Jenike, K and Manthi, S J and Lule, D and Lux, T and Martinez-Bello, L and Pendergast IV, T H and Plott, C and Saha, D and Sidhu, G S and Sreedasyam, A and Wang, X and Wang, H and Wright, H and Zhao, J and Deshpande, S P and Villiers, S de and Dida, M M and Grimwood, J and Jenkins, J and Lovell, J and Mayer, K F X and Mneney, E E and Ojulong, H F and Schatz, M C and Schmutz, J and Song, B and Tesfaye, K and Odeny, D A (2023) Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet. Nature Communications (TSI), 14. pp. 1-15. ISSN 2041-1723

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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.

Item Type:	Article
Divisions:	Research Program : East & Southern Africa
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Agricultural genetics, Genetic variation, Natural variation in plants, Plant evolution, finger millet
Subjects:	Others > Agriculture Mandate crops > Millets > Finger Millet Others > Genetics and Genomics
Depositing User:	Mr Nagaraju T
Date Deposited:	04 Jan 2024 10:52
Last Modified:	04 Jan 2024 10:52
URI:	http://oar.icrisat.org/id/eprint/12339
Official URL:	https://www.nature.com/articles/s41467-023-38915-6
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	This research was supported by awards from the National Science Foundation – Basic Research to Enable Agricultural Development (NSF-BREAD) (award #1543901 to K.M.D., M.C.S., D.O., M.M.D., K.T. and S.d.V.), BioInnovate Africa (award to K.T., E.E.M., S.d.V., K.M.D. and M.M.D.) and Consortium of International Agricultural Research Centers (CGIAR) – Dryland Cereals partnership funds. D.S. was supported by a United States-India Educational Foundation (USIEF) Fulbright Nehru Senior Research Fellowship (2013-14). The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. We thank J.L. Bennetzen for critically reading the manuscript.
Links:	Google Scholar

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