| dc.description.abstract | Peanut (Arachis hypogaea L.) is an important oilseed and food legume, but its improvement is constrained by narrow cultivated genetic diversity, allotetraploid genome complexity, foliar disease pressure, seed dormancy-related quality issues, and increasing drought risk. This dissertation integrates peanut genomics, association mapping, physiological phenotyping, transcriptomics, and gene co-expression network analysis to identify genetic and regulatory mechanisms underlying stress adaptation and agronomic trait variation. A genome-wide analysis of the mitogen-activated protein kinase (MAPK) gene family identified 30 MAPK genes in cultivated peanut and 16 and 15 MAPK genes in its diploid relatives A. duranensis and A. ipaensis, respectively. Comparative phylogenetic, structural, promoter, and synteny analyses showed conserved MAPK organization across peanut genomes. RNA-seq analysis under drought stress identified Ah_At_MAPK4 and Ah_Bt_MAPK4 as strongly drought-induced genes, with greater induction in drought-tolerant genotypes than in susceptible genotypes. Co-expression network analysis placed both genes in a drought-associated module enriched for calcium signaling and secondary metabolic pathways, supporting their roles as candidate regulators of drought-responsive signaling. To dissect genomic variation for disease resistance and seed traits, 87 accessions from the U.S. peanut mini-core collection were resequenced, generating 217 Gb of sequence data and 87,726 high-quality SNPs. Population structure analysis resolved three major genetic groups, and genome-wide association analysis identified significant loci for early leaf spot, late leaf spot, seed germination, and dormancy. Candidate-gene analysis highlighted Ah11g381400, homologous to ATE1, for early leaf spot resistance; Ah16g445600, homologous to ERF34, for late leaf spot resistance; and Ah19g214100, homologous to ICE1, as a candidate affecting germination and dormancy. Field-based physiological and transcriptomic analyses further examined drought adaptation in water-saver, water-spender, and drought-sensitive peanut genotypes. Progressive drought reduced photosynthesis, stomatal conductance, and electron transport rate while increasing intrinsic water-use efficiency. RNA-seq and WGCNA revealed a dominant drought-stage response, a secondary transcriptomic axis associated with water-use strategy, and partial recovery after rewatering. Together, these findings provide candidate genes, molecular markers, and regulatory frameworks for functional validation, marker development, and genomics-assisted breeding of peanut cultivars with improved drought resilience, foliar disease resistance, and seed quality under water-limited and disease-prone production environments. | en_US |
