Pearl millet is a nutri-cereal that is mostly grown in harsh environments, making it an ideal crop to study heat tolerance mechanisms at the molecular level. Despite having a better-inbuilt tolerance to high temperatures than other crops, heat stress negatively affects the crop, posing a threat to productivity gain. Hence, to understand the heat-responsive genes, the leaf and root samples of two contrasting pearl millet inbreds, EGTB 1034 (heat tolerant) and EGTB 1091 (heat sensitive), were subjected to heat-treated conditions and generated genome-wide transcriptomes. We discovered 13,464 differentially expressed genes (DEGs), of which 6932 were down-regulated and 6532 up-regulated in leaf and root tissues. The pairwise analysis of the tissue-based transcriptome data of the two genotypes demonstrated distinctive genotype and tissue-specific expression of genes. The root exhibited a higher number of DEGs compared to the leaf, emphasizing different adaptive strategies of pearl millet. A large number of genes encoding ROS scavenging enzymes, WRKY, NAC, enzymes involved in nutrient uptake, protein kinases, photosynthetic enzymes, and heat shock proteins (HSPs) and several transcription factors (TFs) involved in cross-talking of temperature stress responsive mechanisms were activated in the stress conditions. Ribosomal proteins emerged as pivotal hub genes, highly interactive with key genes expressed and involved in heat stress response. The synthesis of secondary metabolites and metabolic pathways of pearl millet were significantly enriched under heat stress. Comparative synteny analysis of HSPs and TFs in the foxtail millet genome demonstrated greater collinearity with pearl millet compared to proso millet, rice, sorghum, and maize. In this study, 1906 unannotated DEGs were identified, providing insight into novel participants in the molecular response to heat stress. The identified genes hold promise for expediting varietal development for heat tolerance in pearl millet and similar crops, fostering resilience and enhancing grain yield in heat-prone environments.

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.