Pearl millet is an important crop of the arid and semi-arid ecologies to sustain food and fodder production. The greater tolerance to drought stress attracts us to examine its cellular and molecular mechanisms via functional genomics approaches to augment the grain yield. Here, we studied the drought response of 48 inbreds representing four different maturity groups at the flowering stage. A set of 74 drought-responsive genes were separated into five major phylogenic groups belonging to eight functional groups, namely ABA signaling, hormone signaling, ion and osmotic homeostasis, TF-mediated regulation, molecular adaptation, signal transduction, physiological adaptation, detoxification, which were comprehensively studied. Among the conserved motifs of the drought-responsive genes, the protein kinases and MYB domain proteins were the most conserved ones. Comparative in-silico analysis of the drought genes across millet crops showed foxtail millet had most orthologs with pearl millet. Of 698 haplotypes identified across millet crops, MyC2 and Myb4 had maximum haplotypes. The protein–protein interaction network identified ABI2, P5CS, CDPK, DREB, MYB, and CYP707A3 as major hub genes. The expression assay showed the presence of common as well as unique drought-responsive genes across maturity groups. Drought tolerant genotypes in respective maturity groups were identified from the expression pattern of genes. Among several gene families, ABA signaling, TFs, and signaling proteins were the prospective contributors to drought tolerance across maturity groups. The functionally validated genes could be used as promising candidates in backcross breeding, genomic selection, and gene-editing schemes in pearl millet and other millet crops to increase the yield in drought-prone arid and semi-arid ecologies.

Foliar blast, caused by Pyricularia grisea, poses a major challenge to pearl millet (Pennisetum glaucum (L.) R. Br) production, leading to severe yield losses, particularly in rainfed ecologies. This study aimed to elucidate the genetic basis of blast resistance through a genome-wide association study (GWAS) involving 281 diverse pearl millet inbreds. GWAS panel was phenotyped for blast resistance against three distinct isolates of P. grisea collected from Delhi, Gujarat, and Rajasthan locations, revealing a significant variability with 16.7% of the inbreds showing high resistance. Bayesian information and linkage disequilibrium iteratively nested keyway (BLINK) and Multi-Locus Mixed Model (MLMM) models using transformed means identified 68 significant SNPs linked to resistance, with hotspots for resistance-related genes on chromosomes 1, 2, and 6. These regions harbor genes involved in defense mechanisms, including immune response, stress tolerance, signal transduction, transcription regulation, and pathogen defense. Genes, namely 14-3-3-like proteins RGA2, RGA4, hypersensitive-induced response proteins, NHL3, NBS-LRR, LRR-RLK, LRRNT_2, and various transcription factors such as AP2/ERF and WRKY, played a crucial role in the stress-responsive pathways. Analyses of transporter proteins, redox processes, and structural proteins revealed additional mechanisms contributing to blast resistance. This study offers valuable insights into the complex genetic architecture of blast resistance in pearl millet, offering a solid foundation for marker-assisted breeding programs and gene-editing experiments.