Integrative multi-omics and biotechnology for climate resilience and micronutrient biofortification in millets: from trait discovery to precision crop improvement

Abstract

Millets are small-seeded cereals of the family Poaceae that tolerate drought, heat and poor soils. Their grains are rich in iron, zinc, calcium and phenolic antioxidants. Finger millet is exceptionally rich in calcium, and pearl millet is a good source of iron and zinc. These properties make millet crops useful for tackling climate change and micronutrient malnutrition. This review brings together recent progress in genomics, transcriptomics, proteomics, metabolomics, ionomics, epigenomics, phenomics and genome editing in these crops. Foxtail millet, pearl millet and finger millet now have chromosome-scale reference genomes and multi-omics databases, and pan-genome assemblies are available for foxtail millet, pearl millet and proso millet. In these three species, the stress-signaling network is built around abscisic acid (ABA) signaling, several transcription factor families, reactive oxygen species (ROS) scavenging and osmolyte metabolism. Genetic transformation was long the main bottleneck, but this is now changing. Foxtail millet supports a set of validated genome edits, including base editing and edits that improve grain amino acid quality. High-throughput and simplified protocols are extending transformation to pearl millet and finger millet and genome editing to pearl millet. Research on proso millet, little millet, kodo millet and barnyard millet lags behind. One major gap remains. The molecular machinery that controls micronutrient loading, including metal transporters, chelators and storage proteins, is still poorly understood. We suggest three priorities: biofortification based on mechanism; a transformation and editing platform that works across millet species; and precision breeding that links genomic prediction with digital phenomics and artificial intelligence.