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ARS Home » Pacific West Area » Maricopa, Arizona » U.S. Arid Land Agricultural Research Center » Water Management and Conservation Research » Research » Publications at this Location » Publication #430587
Research Project: Developing Sustainable Turfgrass Systems in the U.S. Southwest

Location: Water Management and Conservation Research

Title: Unravelling the genetic basis of water deficit stress tolerance in pearl millet (Pennisetum glaucum (L.) R. Br.) using genome-wide association study and haplotype analysis

Author
item PARRAY, SABREENA - Kansas State University
item RAMALINGAM, AJAY - Kansas State University
item Serba, Desalegn
item VARA PRASAD, P.V. - Kansas State University
item PERUMAL, RAMASAMY - Kansas State University

Submitted to: Plant Stress
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/29/2026
Publication Date: 4/30/2029
Citation: Parray, S.A., Ramalingam, A.P., Serba, D.D., Vara Prasad, P., Perumal, R. 2029. Unravelling the genetic basis of water deficit stress tolerance in pearl millet (Pennisetum glaucum (L.) R. Br.) using genome-wide association study and haplotype analysis. Plant Stress. 21. Article 101401. https://doi.org/10.1016/j.stress.2026.101401.
DOI: https://doi.org/10.1016/j.stress.2026.101401

Interpretive Summary: Drought and heat stress are major challenges to crop productivity, especially in semi-arid regions with limited water and erratic rainfall. Pearl millet is a climate resilient cereal crop widely cultivated for food, forage, and feed in these desolute semi-arid regions. To further improve pearl millet for environmental stress tolerance, the conventional breeding approach needs to be enhanced with marker-assisted selection. However, there are limited genomic resources that can be utilized for genomic assisted breeding. This study was conducted to identify genomic regions or molecular markers and candidate gene haplotypes associated with drought tolerance traits in pearl millet. Ninety-five quantitative trait nucleotides (QTNs) were mapped across all seven chromosomes of pearl millet using four different genome-wide association analysis (GWAS) models and 23 superior haplotypes associated with higher drought tolerance traits. These findings serve as valuable genomic resources for improving pearl millet for climate resilience and advance dryland agriculture.

Technical Abstract: Drought and heat stress are major challenges to crop productivity, especially in semi-arid regions with limited water and erratic rainfall. Pearl millet, the sixth most widely cultivated cereal for food, forage, and feed, has emerged as a promising climate-resilient crop to address these challenges. However, the genomic regions associated with its drought-tolerance remain largely unknown. This study utilizes genome-wide association analysis (GWAS) to identify drought related quantitative trait nucleotides (QTNs) in 187 pearl millet germplasms, genotyped using genotyping-by-sequencing (GBS), yielding 35,071 high-quality single nucleotide polymorphic (SNP) markers. Phenotypic variation was observed between irrigated and rainfed treatments, and the stress tolerance index (STI) derived from these data was used as the GWAS phenotype. Ninety-five QTNs were mapped across all seven chromosomes using four GWAS models (MLMM, FarmCPU, Blink, and 3VmrMLM). These QTNs co-localized with 86 candidate genes, including PMF1G04719 and PMF2G07960 (Rubisco binding protein), PMF1G07862 (Actin-7) were involved in drought response mechanisms, such as reactive oxygen species (ROS) scavenging, and abscisic acid pathway. Candidate gene haplotype analysis identified 23 superior haplotypes with higher drought tolerance traits, offering promising targets for further investigation and breeding efforts. These findings serve as valuable genetic and genomic resources for improving pearl millet for climate resilience and advance dryland agriculture.