Integrative genomics and genetics from evolutionary insights to precision breeding in peanuts (Arachis Hypogaea L.)

Peanut (Arachis hypogaea L.), a globally important oilseed crop, increasingly challenged by rising edible oil demands as well as biotic and abiotic stresses. This review synthesizes recent advances in peanut genomics, evolutionary biology, and breeding technologies to address these challenges aimed at improving yield, oil quality, and resilience. Cultivated peanut is an allotetraploid (AABB), derived from hybridization of the diploid ancestors, A. duranensis and A. ipaensis followed by polyploidization. However, competing evolutionary models highlight unresolved aspects of its domestication history. Advances in sequencing have enabled the high-quality genome assembly of cultivated peanuts, facilitating the development of markers (SSRs, SNPs), trait dissection, and cross omics integration. Genomic studies reveal asymmetric subgenome evolution, chromosomal rearrangements, and structural variations associated with key traits like oil biosynthesis and stress adaptation. Markers assisted selection (MAS) and genomic selection (GS) now accelerate breeding by enabling accurate prediction of complex traits, including yield, disease resistance, and oil quality. Genome editing via CRISPR-Cas9 has transformed trait improvement by enabling accurate modifications in fatty acid desaturases (FAD2), allergen genes, and stress regulators. Multi-omics strategies like transcriptomics, proteomics, metabolomics, lipidomics, and single-cell atlases uncover cell-type specific networks governing pod development and drought responses. Despite progress, polyploid complexity, low transformation efficiency, and genotype-environment interactions remain bottlenecks. Future efforts must leverage pangenomes, machine learning, and high throughput phenotyping to bridge these gaps. This review highlights the potential of integrated genomics and precision breeding to develop high oleic, climate resilient peanut varieties, critical for global food and nutritional security.