Advances in Pearl Millet Genomics for Nutritional Traits Improvement

Pearl millet (Pennisetum glaucum (L.) R. Br.) is a highly climate-resilient cereal extensively cultivated in arid and semi-arid agroecological zones. It plays a vital role in the diets of nutritionally vulnerable populations, particularly those suffering from iron and zinc deficiencies, key contributors to hidden hunger and widespread malnutrition. Over the past two decades, significant progress in genomic research has revolutionized pearl millet improvement by providing deep insights into its genome structure, organization, and functional complexity. Initially limited to traditional molecular markers like RFLPs, RAPDs, SSRs, and AFLPs, pearl millet genomics has now advanced to include high-density SNP arrays, genotyping-by-sequencing (GBS), and the development of platinum-grade reference genomes and pangenome resources. These advancements have facilitated the construction of dense genetic linkage maps and enabled the identification of quantitative trait loci (QTLs) and marker-trait associations through genome-wide association studies (GWAS), significantly accelerating the dissection of complex traits. Such progress has led to the discovery of candidate genes controlling important agronomic and nutritional traits. For instance, genes like PgZIP (zinc transporter), PgNAS3 (nicotianamine synthase), PgFER (ferritin), and lipid-degrading enzymes such as PgTAG lipase, PgLOX, and PgPLA2 have been linked to iron/zinc accumulation, protein quality, and flour rancidity. Modern approaches such as genomic selection (GS), pangenome analysis, and integrated multi-omics are reshaping predictive breeding strategies. However, challenges persist due to the genome’s complexity, including high repetitive DNA, structural variation, and heterogeneity. Future directions involving long-read sequencing, haplotype-resolved assemblies, CRISPR/Cas genome editing, and AI-driven breeding will be crucial for unlocking pearl millet’s full genetic potential to support climate resilience and nutritional security.