Drought is a significant abiotic stressor that has widespread implications for crop growth, productivity, and the long-term viability of agriculture. Poaceae, the grass family, is a vital group of plants that boasts roughly 600 genera and 10,000 species, and plays a critical role in global food demand (Lee et al., 2020). Among these, finger millet stands out as an orphan crop with exceptional drought tolerance, making it a valuable model for studying drought adaptation mechanisms in cereals. While staple crops like wheat and rice are highly vulnerable to water stress, suffering substantial yield losses under drought conditions (Landi et al., 2017), finger millet thrives in arid and semi-arid regions with minimal irrigation. This crop not only sustains millions in drought-prone regions but also harbors genetic traits that could inform breeding programs for climate-resilient cereals. By focusing on finger millet, this study aims to unravel its unique drought resistance strategies, which are critical for addressing food security challenges in water-limited environments and advancing our understanding of stress adaptation in Poaceae crops.

Finger millet (Eleusine coracana [L.] Gaertn.) is a significant C4 cereal crop that boasts excellent storage properties and high nutritional value (Wambi et al., 2020). Finger millet is an allotetraploid (2n = 4x = 36, AABB) annual species that is typically self-fertilized (Sood et al., 2019). It is generally agreed that the A genome was inherited from the wild diploid species E. indica or a close relative, such as E. tristachya, while the B genome progenitor is either unknown or most likely extinct (Hatakeyama et al., 2018). Compared with major cereals, the grains of finger millet are gluten-free and are abundant in protein, carbohydrates, dietary fibre, ash, calcium, amino acids, micronutrients, polyphenols, and vitamins (Kumar et al., 2016; Puranik et al., 2017; Puranik et al., 2020; Krishna et al., 2021). It is the fourth most valuable millet after sorghum, pearl millet, and foxtail millet (Hittalmani et al., 2017). Its global presence is noteworthy, accounting for 12% of the millet area worldwide and cultivated across 4.0–4.5 million hectares, resulting in a production of approximately 4.5 million tonnes (Krishnamurthy et al., 2016; Talwar et al., 2020). It can produce reasonable grain and fodder yields in hot, arid regions with low soil fertility. This capacity is partly due to the C4 pathway, an efficient carbon concentrating process (Hittalmani et al., 2017; Puranik et al., 2020). These characteristics make finger millet a crucial crop for food and nutritional security as well as a valuable resource for cereal crop improvement (Mbinda and Mukami, 2021). Many researchers have evaluated finger millet germplasm resources or varieties and discovered varying levels of drought tolerance among them (Mude et al., 2020). However, studies on the regulatory mechanisms responsible for its drought resistance are limited.

Despite the significance of finger millet, limited efforts have been made to produce genomic information for this crop, in contrast to sorghum, foxtail millet, and pearl millet (Paterson et al., 2009; Zhang et al., 2012; Varshney et al., 2017; Jin et al., 2025). As a polyploid species, genome assembly of finger millet has been a major challenge because homeologous genes are by definition highly similar, which tends to split the assembly into shorter contigs, or collapse homeologous loci (Sood et al., 2019). Although there have been some recent developments in finger millet whole-genome studies (Hittalmani et al., 2017; Hatakeyama et al., 2018), the quality of assembly for these genomes was suboptimal until the very recent assembly of variety 796 from Kenya (Devos et al., 2023). In recent years, genome-wide association studies (GWAS) have been widely applied in drought research of important crops, such as maize (Wang et al., 2025), rice (Nyasulu et al., 2024), and wheat (Yang et al., 2024). To better understand the genetic and molecular basis of finger millet traits and to further promote genomic and breeding studies in finger millet, here we present a chromosome-scale reference genome for the finger millet variety C142, featuring two fully represented subgenome. This particular cultivar exhibits broad adaptability, generates a sizable yield, and possesses robust resistance to drought. We integrated GWAS and differential gene expression under drought stress to accurately identify key genes associated with drought resistance in finger millet. Our findings reveal the evolutionary history of the finger millet genome and important features of water stress response.