Relationships of the wild peanut species, section Arachis: A resource for botanical classification, crop improvement, and germplasm management.

PREMISE: Wild species are strategic sources of valuable traits to be introduced into crops through hybridization. For peanut, the 33 currently described wild species in the section Arachis are particularly important because of their sexual compatibility with the domesticated species, Arachis hypogaea. Although numerous wild accessions are carefully preserved in seed banks, their morphological similarities pose challenges to routine classification. METHODS: Using a high-density array, we genotyped 272 accessions encompassing all diploid species in section Arachis. Detailed relationships between accessions and species were revealed through phylogenetic analyses and interpreted using the expertise of germplasm collectors and curators. RESULTS: Two main groups were identified: one with A genome species and the other with B, D, F, G, and K genomes. Species groupings generally showed clear boundaries. Structure within groups was informative, for instance, revealing the history of the proto-domesticate A. stenosperma. However, some groupings suggested multiple sibling species. Others were polyphyletic, indicating the need for taxonomic revision. Annual species were better defined than perennial ones, revealing limitations in applying classical and phylogenetic species concepts to the genus. We suggest new species assignments for several accessions. CONCLUSIONS: Curated by germplasm collectors and curators, this analysis of species relationships lays the foundation for future species descriptions, classification of unknown accessions, and germplasm use for peanut improvement. It supports the conservation and curation of current germplasm, both critical tasks considering the threats to the genus posed by habitat loss and the current restrictions on new collections and germplasm transfer.

Spontaneous generation of diversity in Arachis neopolyploids (Arachis ipaënsis × Arachis duranensis)4x replays the early stages of peanut evolution.

Polyploidy is considered a driving force in plant evolution and domestication. Although in the genus Arachis, several diploid species were traditionally cultivated for their seeds, only the allotetraploid peanut Arachis hypogaea became the successful, widely spread legume crop. This suggests that polyploidy has given selective advantage for domestication of peanut. Here, we study induced allotetraploid (neopolyploid) lineages obtained from crosses between the peanut's progenitor species, Arachis ipaënsis and Arachis duranensis, at earlier and later generations. We observed plant morphology, seed dimensions, and genome structure using cytogenetics (FISH and GISH) and SNP genotyping. The neopolyploid lineages show more variable fertility and seed morphology than their progenitors and cultivated peanut. They also showed sexual and somatic genome instability, evidenced by changes of number of detectable 45S rDNA sites, and extensive homoeologous recombination indicated by mosaic patterns of chromosomes and changes in dosage of SNP alleles derived from the diploid species. Genome instability was not randomly distributed across the genome: the more syntenic chromosomes, the higher homoeologous recombination. Instability levels are higher than observed on peanut lines, therefore it is likely that more unstable lines tend to perish. We conclude that early stages of the origin and domestication of the allotetraploid peanut involved two genetic bottlenecks: the first, common to most allotetraploids, is composed of the rare hybridization and polyploidization events, followed by sexual reproductive isolation from its wild diploid relatives. Here, we suggest a second bottleneck: the survival of the only very few lineages that had stronger mechanisms for limiting genomic instability.