Peanut (Arachis hypogaea L.) is a significant oilseed and food legume crop, with seed size/weight being a critical trait for domestication and breeding. However, genomic variations like structural variations (SVs) underlying seed size/weight remain unclear. Here, we present a comprehensive pangenome analysis utilizing eight high-quality genomes (two diploid wild, two tetraploid wild, and four tetraploid cultivated peanuts) and resequencing data of 269 accessions with diverse seed sizes. We identified 22,222 core/softcore, 22,232 distributed and 5,643 private gene families. The frequency of SVs in sub-genome A is higher than in sub-genome B. We identified 1,335 domestication-related SVs and 190 SVs associated with seed size/weight. Notably, a 275-bp deletion in gene AhARF2-2 results in the loss of AUX/IAA domain, which reduces its interaction with AhIAA13 and TPL, reducing the inhibitory effect on AhGRF5 and promoting seed expansion. This high-quality pangenome serves as a fundamental resource for the genetic enhancement of peanuts and other legume crops.

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