Little millet genome reveals evolutionary insights into tetraploid structure and genetic basis of micronutrient density

Abstract

Abstract Little millet is a hardy and nutrient-rich cereal which improves food and nutritional security in marginal environments. Despite its importance, genomic resources for this orphan crop have been limited. Here, we report a high quality, chromosome-scale genome assembly of little millet comprising 18 chromosomes and 59,045 genes. Eleven chromosomes are assembled from telomere to telomere, revealing an 850 Mb tetraploid genome that closely resembles broomcorn millet. Comparative analyses indicate early stages of diploidization, characterized by gene loss and subgenome-specific expression biases that vary across genes and tissues. Resequencing of 300 accessions uncovers extensive genetic diversity, including single-nucleotide polymorphism and structural variants. Genome-wide association studies identify genetic loci linked to grain micronutrient traits, including several associated with high iron content. These genomic and phenotypic resources provide a foundation for molecular breeding and marker-assisted selection, enabling the improvement of little millet as a climate-resilient crop to support global food and nutritional security.