The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

TLDR

Tetraploid peanut is a leading oil and food legume due to its high oil and protein content. The study aims to characterize gene functional groups involved in seed size evolution, seed oil content, disease resistance, and symbiotic nitrogen fixation. The high‑quality 2.54‑Gb peanut genome, comprising 20 pseudomolecules and 83,709 genes, reveals B‑subgenome dominance, LTR expansion in the A subgenome, independent domestication events, and provides a resource for mapping traits such as seed size, color, and disease resistance.

Abstract

High oil and protein content make tetraploid peanut a leading oil and food legume. Here we report a high-quality peanut genome sequence, comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models. We characterize gene functional groups implicated in seed size evolution, seed oil content, disease resistance and symbiotic nitrogen fixation. The peanut B subgenome has more genes and general expression dominance, temporally associated with long-terminal-repeat expansion in the A subgenome that also raises questions about the A-genome progenitor. The polyploid genome provided insights into the evolution of Arachis hypogaea and other legume chromosomes. Resequencing of 52 accessions suggests that independent domestications formed peanut ecotypes. Whereas 0.42–0.47 million years ago (Ma) polyploidy constrained genetic variation, the peanut genome sequence aids mapping and candidate-gene discovery for traits such as seed size and color, foliar disease resistance and others, also providing a cornerstone for functional genomics and peanut improvement. High-quality genome sequence of cultivated peanut comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models provides insights into genome evolution and the genetic mechanisms underlying seed size and leaf resistance in peanut.