Chromosome-level genome assembly of finger millet (<i>Eleusine coracana</i>) provides insights into drought resistance

Jiguang Li; Chaonan Guan; Xiaobo Li; Yanlan Wang; Jiayue He; Liqin Hu; Yaliang Shi; Yuqi He; Kaixuan Zhang; Rui Tang; Meiliang Zhou

doi:10.1016/j.jgg.2025.07.012

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Chromosome-level genome assembly of finger millet (Eleusine coracana) provides insights into drought resistance

doi: 10.1016/j.jgg.2025.07.012

a. Hunan Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China;
b. Yuelushan Lab, Changsha, Hunan 410128, China;
c. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
d. National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572024, China;
e. Annoroad Gene Technology (Beijing) Co. Ltd, Beijing 100176, China

Funds:

This work was supported by the National Crop Germplasm Repository (NCGR-2024-056) and the National Natural Science Foundation of China (32301813).

Received Date: 2025-01-20
Accepted Date: 2025-07-28
Rev Recd Date: 2025-07-23

Available Online: 2025-08-06

Abstract

Abstract

Finger millet (Eleusine coracana Gaertn.), a nutritionally rich and drought-resilient C4 cereal, possesses exceptional grain storage longevity (up to 50 years). Here, we report a high-quality genome assembly of the allotetraploid cultivar C142, revealing extensive structural rearrangements between its two subgenomes (subA and subB), which are associated with asymmetric gene expression and subgenome dominance favoring subA. SubB diverged from its presumed progenitor E. indica approximately 6.8 million years ago, and two whole-genome duplication events shaped the current genome architecture, contributing to gene redundancy and adaptive potential. Notably, expansion of stress-related gene families, such as aldo-keto reductases, suggests a role in oxidative stress response and drought adaptation. Using genome-wide association studies (GWAS), we identify several candidate genes associated with key agronomic traits. Among them, EcMDHAR, encoding monodehydroascorbate reductase, plays a critical role in enhancing drought tolerance. Different EcMDHAR haplotypes exhibit distinct expression profiles, supporting their functional relevance in drought adaptation. This genomic resource not only advances our understanding of polyploid genome evolution in millets but also provides a foundation for genome-assisted improvement of drought resistance and nutritional quality in finger millet.
- Eleusine coracana,
- Comparative genomics,
- Structural variation,
- GWAS,
- Drought resistance

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Ahmad, R., Waraich, E.A., Nawaz, F., Ashraf, M.Y., Khalid, M., 2016. Selenium (Se) improves drought tolerance in crop plants--a myth or fact? J. Sci. Food Agric. 96, 372-380.

Bottani, S., Zabet, N.R., Wendel, J.F., Veitia, R.A., 2018. Gene expression dominance in allopolyploids: hypotheses and models. Trends Plant Sci. 23, 393-402.

Chauhan, R., Awasthi, S., Srivastava, S., Dwivedi, S., Pilon-Smits, E.A.H., Dhankher, O.P., Tripathi, R.D., 2019. Understanding selenium metabolism in plants and its role as a beneficial element. Crit. Rev. Environ. Sci. Technol. 49, 1937-1958.

Chang, S., Huang, G., Wang, D., Zhu, W., Shi, J., Yang, L., Liang, W., Xie, Q., Zhang, D., 2022. Rice SIAH E3 ligases interact with RMD formin and affect plant morphology. Rice 15, 6.

Chao, M., Zhang, Q., Huang, L., Wang, L., Dong, J., Kou, S., Wang, T., 2024. ADP-glucose pyrophosphorylase gene family in soybean and implications in drought stress tolerance. Genes Genom. 46, 1183-1199.

Chen, Z.J., Ni, Z., 2006. Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. Bioessays 28, 240-252.

Concia, L., Veluchamy, A., Ramirez-Prado, J. S., Martin-Ramirez, A., Huang, Y., Perez, M., Huang, Y., Perez, M., Domenichini, S., Granados, R., et al., 2020. Wheat chromatin architecture is organized in genome territories and transcription factories. Genome Biol. 21, 1-20.

Devarumath, R.M., Hiremath, S.C., Rao, S.R., Kumar, A., Bewal, S., 2005. Genome analysis of finger millet E. coracana by interspecific hybridization among diploid wild species of Eleusine (Poaceae). Cytologia 70, 427-434.

Den Herder, G., De Keyser, A., De Rycke, R., Rombauts, S., Van de Velde, W., Clemente, M.R., Verplancke, C., Mergaert, P., Kondorosi, E., Holsters, M., et al., 2008. Seven in absentia proteins affect plant growth and nodulation in Medicago truncatula. Plant Physiol. 148, 369-382.

Devos, K.M., Qi, P., Bahri, B.A., Gimode, D.M., Jenike, K., Manthi, S.J., Lule, D., Lux, T., Martinez-Bello, L., Pendergast, T.H.t., et al., 2023. Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet. Nat. Commun. 14, 3694.

Ding, Z., Weissmann, S., Wang, M., Du, B., Huang, L., Wang, L., Tu, X., Zhong, S., Myers, C., Brutnell, T.P., et al., 2015. Identification of photosynthesis-associated C4 candidate genes through comparative leaf gradient transcriptome in multiple lineages of C3 and C4 species. PLoS ONE 10, e0140629.

Fang, J., Chai, Z., Huang, R., Huang, C., Ming, Z., Chen, B., Zhang, M., 2023. Receptor-like cytoplasmic kinase ScRIPK in sugarcane regulates disease resistance and drought tolerance in Arabidopsis. Front. Plant Sci. 14, 1191449.

Ferrer, J.L., Austin, M.B., Stewart, C., Jr., Noel, J.P., 2008. Structure and function of enzymes involved in the biosynthesis of phenylpropanoids. Plant Physiol. Biochem. 46, 356-370.

Hall, N.D., Patel, J.D., McElroy, J.S., Goertzen, L.R., 2021. Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet). BMC Genomics 22, 175.

Han, X., Zhang, J., Han, S., Chong, S.L., Meng, G., Song, M., Wang, Y., Zhou, S., Liu, C., Lou, L., et al., 2022. The chromosome-scale genome of Phoebe bournei reveals contrasting fates of terpene synthase (TPS)-a and TPS-b subfamilies. Plant Commun. 3, 100410.

Hatakeyama, M., Aluri, S., Balachadran, M.T., Sivarajan, S.R., Patrignani, A., Gruter, S., Poveda, L., Shimizu-Inatsugi, R., Baeten, J., Francoijs, K.J., Nataraja, K.N., et al., 2018. Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop. DNA Res. 25, 39-47.

He, J., Hao, Y., He, Y., Li, W., Shi, Y., Khurshid, M., Zhou, M., 2024. Genome-wide associated study identifies FtPMEI13 gene conferring drought resistance in tartary buckwheat. Plant J. 120(6), 2398-2419.

Hilu, K.W., de Wet, J.M.J., 1976. Domestication of Eleusine coracana. Econ. Bot. 30, 199-208.

Hittalmani, S., Mahesh, H.B., Shirke, M.D., Biradar, H., Uday, G., Aruna, Y.R., Lohithaswa, H.C., Mohanrao, A., 2017. Genome and transcriptome sequence of Finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties. BMC Genomics 18, 465.

Hirsch, C., Springer, N., 2017. Transposable element influences on gene expression in plants. BBA-Gene Regul. Mech. 1, 157-165.

Hollister, J.D., Gaut, B.S., 2009. Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res. 19, 1419-1428.

Jorgensen, M.E., Nour-Eldin, H.H., Halkier, B.A., 2015. Transport of defense compounds from source to sink: lessons learned from glucosinolates. Trends Plant Sci. 20, 508-514.

Jaime, C., Dezar, C., Pagan, I., Dunger, G., 2024 Expression of the alfalfa gene MsMDHAR in Arabidopsis thaliana increases water stress tolerance. Physiol. Plantarum 176(4), e14448.

Jin, Y.R, Yan, H.D., Zhu, X., Yang, Y.C., Jia, J.Y., Sun, M., Najeeb, A., Luo, J.C., Wang, X.S., He, M., et al., 2025. Single-cell transcriptomes reveal spatiotemporal heat stress response in pearl millet leaves. New Phytol. 2, 637-650.

Krishna, S.S., Reddy, Y.A.N., Kumar, R.L.R., 2021. Assessment of traits for grain yield under drought in finger millet. Plant Physiol. Rep. 26, 84-94.

Krishnamurthy, L., Upadhyaya, H.D., Kashiwagi, J., Purushothaman, R., Dwivedi, S.L., Vadez, V., 2016. Variation in drought-tolerance components and their interrelationships in the minicore collection of finger millet germplasm. Crop Sci. 56, 1914-1926.

Kumar, A., Metwal, M., Kaur, S., Gupta, A.K., Puranik, S., Singh, S., Singh, M., Gupta, S., Babu, B.K., Sood, S., et al., 2016. Nutraceutical value of finger millet [Eleusine coracana (L.) Gaertn.], and their improvement using omics approaches. Front. Plant Sci. 7, 934.

Landi, S., Hausman, J.F., Guerriero, G., Esposito, S., 2017. Poaceae vs. abiotic stress: focus on drought and salt stress, recent insights and perspectives. Front. Plant Sci. 8, 1214.

Lee, S., Choi, S., Jeon, D., Kang, Y., Kim, C., 2020. Evolutionary impact of whole genome duplication in Poaceae family. J. Crop Sci. Biotechnol. 23, 413-425.

Li, C., Fu, K., Guo, W., Zhang, X., Li, C., Li, C., 2023. Starch and sugar metabolism response to post-anthesis drought stress during critical periods of elite wheat (Triticum aestivum L.) endosperm development. J. Plant Growth Regul. 42, 5476-5494.

Lisch, D., 2013. How important are transposons for plant evolution? Nat. Rev. Genet. 14, 49-61.

Liu, Q., Jiang, B., Wen, J., Peterson, P.M., 2014. Low-copy nuclear gene and McGISH resolves polyploid history of Eleusine coracana and morphological character evolution in Eleusine. Turk J. Bot. 38, 1-12.

Mbinda, W., Mukami, A., 2021. A review of recent advances and future directions in the management of salinity stress in finger millet. Front. Plant Sci. 12, 734798.

Mude, L.N., Mondam, M., Gujjula, V., Jinka, S., Pinjari, O.B., Yellodu Adi Reddy, N., Patan, S., 2020. Morpho-physiological and biochemical changes in finger millet [Eleusine coracana (L.) Gaertn.] under drought stress. Physiol. Mol. Biol. Plants. 26, 2151-2171.

Niemeyer, H.M., 2009. Hydroxamic acids derived from 2-hydroxy-2H-1,4-benzoxazin-3(4H)-one: key defense chemicals of cereals. J. Agric. Food Chem. 57, 1677-1696.

Paterson, A.H., Bowers, J.E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Hellsten, U., Mitros, T., Poliakov, A., et al., 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457, 551-556.

Pepper, I.J., Van Sciver, R.E., Tang, A.H., 2017. Phylogenetic analysis of the SINA/SIAH ubiquitin E3 ligase family in Metazoa. BMC Evol. Biol. 17, 182.

Pitsili, E., Rodriguez-Trevino, R., Ruiz-Solani, N., Demir, F., Kastanaki, E., Dambire, C., Coll, N.S., 2023. A phloem-localized Arabidopsis metacaspase (AtMC3) improves drought tolerance. New Phytol. 239, 1281-1299.

Puranik, S., Kam, J., Sahu, P.P., Yadav, R., Srivastava, R.K., Ojulong, H., Yadav, R., 2017. Harnessing finger millet to combat calcium deficiency in humans: challenges and prospects. Front. Plant Sci. 8, 1311.

Puranik, S., Sahu, P.P., Beynon, S., Srivastava, R.K., Sehgal, D., Ojulong, H., Yadav, R., 2020. Genome-wide association mapping and comparative genomics identifies genomic regions governing grain nutritional traits in finger millet (Eleusine coracana L. Gaertn.). Plants People Planet 2, 649-662.

Qi, J., Kim, H., Scortegagna, M., Ronai, Z.A., 2013. Regulators and effectors of Siah ubiquitin ligases. Cell Biochem. Biophys. 67, 15-24.

Sengupta, D., Naik, D., Reddy, A.R., 2015. Plant aldo-keto reductases (AKRs) as multi-tasking soldiers involved in diverse plant metabolic processes and stress defense: a structure-function update. J. Plant Physiol. 179, 40-55.

Shen, Y., Li, W., Zeng, Y., Li, Z., Chen, Y., Zhang, J., Zhao, H., Feng, L., Ma, D., Mo, X., et al., 2022. Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli. Nat. Commun. 13, 3511.

Sood, S., Joshi, D.C., Chandra, A.K., Kumar, A., 2019. Phenomics and genomics of finger millet: current status and future prospects. Planta 250, 731-751.

Talwar, H.S., Kumar, S., Madhusudhana, R., Nanaiah, G.K., Ronanki, S., Tonapi, V.A., 2020. Variations in drought tolerance components and their association with yield components in finger millet (Eleusine coracana). Funct. Plant Biol. 47, 659-674.

Thomsen, H. C., Eriksson, D., Moeller, I. S., Schjoerring, J. K., 2014. Cytosolic glutamine synthetase: a target for improvement of crop nitrogen use efficiency?. Trends Plant Sci. 19, 656-663.

VanBuren, R., Man Wai, C., Wang, X., Pardo, J., Yocca, A.E., Wang, H., Chaluvadi, S.R., Han, G., Bryant, D., Edger, P.P., et al., 2020. Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff. Nat. Commun. 11, 884.

Varshney, R.K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., et al., 2017. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nat Biotechnol. 35, 969-976.

Wambi, W., Otienno, G., Tumwesigye, W., Mulumba, J., 2020. Genetic and genomic resources for finger millet improvement: opportunities for advancing climate-smart agriculture. J. Crop Improv. 35, 204-233.

Wang, L., Sun, X., Peng, Y., Chen, K., Wu, S., Guo, Y., Zhang, J., Yang, H., Jin, T., Wu, L., et al., 2022. Genomic insights into the origin, adaptive evolution, and herbicide resistance of Leptochloa chinensis, a devastating tetraploid weedy grass in rice fields. Mol. Plant 15, 1045-1058.

Wei, Y., Xiong, S., Zhang, Z., Meng, X., Wang, L., Zhang, X., Ma, X., 2021. Localization, gene expression, and functions of glutamine synthetase isozymes in wheat grain (Triticum aestivum L.). Front. Plant Sci. 12, 580405.

Yan, C., Song, S., Wang, W., Wang, C., Sun, X., 2020. Screening diverse soybean genotypes for drought tolerance by membership function value based on multiple traits and drought-tolerant coefficient of yield. BMC Plant Biol. 20, 321.

Yang, Z., Ge, X., Yang, Z., Qin, W., Sun, G., Wang, Z., Li, Z., Liu, J., Wu, J., Wang, Y., et al., 2019. Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. Nat. Commun. 10, 2989.

Zahoor, R., Dong, H., Abid, M., Zhao, W., Wang, Y., Zhou, Z., 2017. Potassium fertilizer improves drought stress alleviation potential in cotton by enhancing photosynthesis and carbohydrate metabolism. Environ. Exp. Bot. 137, 73-83.

Zhang, A., Yang, X., Lu, J., Song, F., Sun, J., Wang, C., Lian, J., Zhao, L., Zhao, B., 2021. OsIAA20, an Aux/IAA protein, mediates abiotic stress tolerance in rice through an ABA pathway. Plant Sci. 308, 110903.

Zhang, C., Hao, Z., Ning, Y., Wang, G.L., 2019a. SINA E3 ubiquitin ligases: versatile moderators of plant growth and stress response. Mol. Plant 12, 610-612.

Zhang, H., Hall, N., Goertzen, L.R., Bi, B., Chen, C.Y., Peatman, E., Lowe, E.K., Patel, J., McElroy, J.S., 2019b. Development of a goosegrass (Eleusine indica) draft genome and application to weed science research. Pest Manag. Sci. 75, 2776-2784.

Zhang, G., Liu, X., Quan, Z., Cheng, S., Xu, X., Pan, S., Xie, M., Zeng, P., Yue, Z., Wang, W., et al., 2012. Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat. Biotechnol. 30, 549-554.

Zhang, J., Zhang, X., Tang, H., Zhang, Q., Hua, X., Ma, X., Zhu, F., Jones, T., Zhu, X., Bowers, J., et al., 2018. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nat. Genet. 50, 1565-1573.

Zhang, X., Chen, S., Shi, L., Gong, D., Zhang, S., Zhao, Q., Zhan, D., Vasseur, L., Wang, Y., Yu, J., et al., 2021. Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis. Nat. Genet. 53, 1250-1259.

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