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

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

基金项目:

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

详细信息

通讯作者:
Chaonan Guan,E-mail:guanchaonan2014@163.com

Rui Tang,E-mail:19542439@qq.com

Meiliang Zhou,E-mail:zhoumeiliang@caas.cn

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出版历程
- 收稿日期: 2025-01-20
- 录用日期: 2025-07-28
- 修回日期: 2025-07-23
- 网络出版日期: 2025-08-06

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

Jiguang Li^a,b,
Chaonan Guan^{c,d
, ,},
Xiaobo Li^e,
Yanlan Wang^a,
Jiayue He^c,
Liqin Hu^a,b,
Yaliang Shi^c,
Yuqi He^c,
Kaixuan Zhang^c,
Rui Tang^{a
, ,},
Meiliang Zhou^{b,c,d
, ,}

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).

摘要

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

doi: 10.1016/j.jgg.2025.07.012

通讯作者:
Chaonan Guan,E-mail:guanchaonan2014@163.com

Rui Tang,E-mail:19542439@qq.com

Meiliang Zhou,E-mail:zhoumeiliang@caas.cn

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

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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

通讯作者: Chaonan Guan,E-mail:guanchaonan2014@163.com Rui Tang,E-mail:19542439@qq.com Meiliang Zhou,E-mail:zhoumeiliang@caas.cn

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出版历程

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

计量

出版历程

目录

通讯作者:
Chaonan Guan,E-mail:guanchaonan2014@163.com

Rui Tang,E-mail:19542439@qq.com

Meiliang Zhou,E-mail:zhoumeiliang@caas.cn