Genomic and Transcriptomic Approaches to Drought Tolerance in Pearl Millet

The rise of high-throughput genomic and transcriptomic technologies has revolutionised the exploration of drought tolerance in pearl millet (Pennisetum glaucum), a staple C4 cereal in arid regions. Genome sequencing and assembly have provided a reference for gene discovery, while transcriptome profiling under water deficit has mapped dynamic expression patterns across tissues and developmental stages. Studies have combined genome-wide association studies and quantitative trait loci mapping with RNA sequencing to pinpoint loci and networks that regulate osmotic adjustment, root system architecture and hormonal control. De novo transcriptome assembly has uncovered novel genes and alternative splice variants, and coexpression network analyses have identified hub regulators that coordinate stress-responsive pathways. Marker development, including single nucleotide polymorphisms and simple sequence repeats, enables marker-assisted selection for improved genotypes. Integrating these genomic and transcriptomic approaches accelerates breeding of drought-resilient cultivars, with global implications for food security and adaptation to climate change.

Research from Nature Portfolio

Field-mimicked drought experiments have yielded de novo assembled transcriptomes, revealing nearly 20 000 differentially expressed genes and over 7 500 transcription factors that underpin drought adaptation. A gene regulatory network analysis identified 45 hub genes governing drought response, highlighting pathways such as purine and tryptophan metabolism in abscisic acid accumulation and MAPK signalling as a central intracellular sensor. The study also generated a comprehensive set of putative markers—over 4 000 SSRs, 12 000 SNPs and 6 000 InDels—and launched an online genomic resource to facilitate candidate-gene discovery and trait association in pearl millet.

Genomic and Transcriptomic Approaches to Drought Tolerance in Pearl Millet publication trend

The graph below shows the total number of articles in genomic and transcriptomic approaches to drought tolerance in pearl millet across all publications each year (not limited to Nature Index journals).

Technical terms

De novo assembly: Reconstruction of genomic or transcript sequences from short reads without reference to a pre-existing genome.

Differentially expressed genes (DEGs): Genes whose transcript abundance significantly changes between conditions.

Transcription factor (TF): Protein that binds DNA to regulate gene expression.

Weighted gene coexpression network analysis (WGCNA): Method to group genes into modules based on expression similarity and relate them to traits.

Single nucleotide polymorphism (SNP): Variation at a single base position in the genome among individuals.

Simple sequence repeat (SSR): Repeated short DNA motifs used as genetic markers.

References

1. Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet. Plants (2023).
2. Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing. BMC Plant Biology (2020).
3. Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources. Scientific Reports (2018).