A single hybrid origin of cultivated peanut

Abstract

This study, the first in a three-part series, lays the foundation for understanding the origin of the peanut crop (Arachis hypogaea). Its subsequent evolution is explored in the two papers that follow. The evidence that A. hypogaea originated from a single hybridization event between Arachis duranensis and Arachis ipaënsis less than 10 000 years ago was already very strong. Here, we extend this evidence using more than 1600 single-nucleotide polymorphisms to make an almost exhaustive comparison of wild Arachis section germplasm conserved ex situ with the A and B subgenomes of divergent, sequenced cultivated peanuts. The wild relatives of peanut are highly selfing and their geocarpy means they plant their own seeds, allowing them to persist as discrete populations for millennia. This unusual biology creates a rare opportunity for genetic archaeology: ancestral lineages can be identified with exceptional precision. Our results reaffirm a single origin for the cultigen, identifying A. duranensis from Río Seco and A. ipaënsis K 30076 as the closest known relatives of the A and B subgenomes of peanut. As a genomic resource, we generated a chromosome-scale assembly of the Río Seco A. duranensis K 30065 and confirmed that it is more closely related to the A subgenome of peanut than the current reference genome (V14167). Even if somewhat closer wild accessions were found through new field collections, they would still belong to the same ancestral lineage. With this level of evidence, the origin of peanut is now known in greater detail than that of any other ancient polyploid crop.

Keywords: Arachis duranensis; Arachis hypogaea; Arachis ipaënsis; Arachis monticola; crop evolution; domestication; groundnut; peanut; polyploid origin.