Genetic architecture for drought tolerance in pearl millet (Pennisetum glaucum (L.) Br.) germplasms

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, its potential remains underexplored due to limited breeding efforts. This thesis focuses on identifying drought-tolerant pearl millet germplasms and uncovering genomic regions associated with drought resilience to support the development of improved forage hybrids, particularly for drought-prone areas like western Kansas. Two experiments were conducted to achieve these objectives. The first experiment evaluated 188 diverse pearl millet accessions under irrigated and rainfed conditions at Kansas State University’s Agricultural Research Center in Hays in summer 2023 and 2024. Agronomic traits such as days to 50% flowering, chlorophyll index, plant height, number of productive tillers, staygreen, and biomass were measured. Accessions were grouped into early, medium, and late maturity classes based on flowering time. Principal component analysis using genotyping-by-sequencing single nucleotide polymorphism (SNPs) data revealed broad genetic diversity within maturity groups. Drought-tolerant accessions were identified using multiple selection indices including Rank Summation Index, BLUP-based GGE biplot, MTSI, MGIDI, and FAI-BLUP. Nine stable and widely adapted drought-tolerant accessions were selected, with chlorophyll content, staygreen, and biomass proving to be reliable drought resilience indicators due to their moderate to high heritability. The second experiment involved genome-wide association studies (GWAS) on 187 accessions genotyped using GBS, yielding 35,071 high-quality SNP markers. Phenotypic data on ten traits and calculated stress tolerance indices were used to identify quantitative trait nucleotides (QTNs) linked to drought tolerance. Sixty-two QTNs were mapped across all seven chromosomes using four GWAS models (MLMM, FarmCPU, Blink, and 3vRMLM). These QTNs co-localized with 77 candidate genes, including PMF1G04719, PMF2G07960, and PMF1G07862, many of which are involved in drought response mechanisms, such as reactive oxygen species (ROS) scavenging, abscisic acid pathway and so on. After validation, together, these findings will serve as valuable genetic and genomic resources for improving pearl millet breeding programs and to advance climate resilience in dryland agriculture.