Double Reduction in Allotetraploid Peanut and the Role of Chromosomal Imbalance in Unexpected Linkage Map Artifacts

Abstract Polyploidization in peanut (Arachis hypogaea L.) fixed heterosis but also caused a genetic bottleneck isolating cultivated peanut from its wild diploid relatives. Mechanisms such as homoeologous exchange can partially restore genetic diversity by generating new allelic combinations. Double reduction is a rare polyploid-specific segregation pattern in which a single-dosage locus yields duplex gametes. It requires multivalent formation—associated with homoeologous exchange in allopolyploids—and crossing over between non-sister chromatids. Although peanut mainly exhibits disomic pairing, occasional multivalents theoretically allow low-frequency double reduction. To estimate double reduction and examine its relationship with genetic instability, we constructed a high-density phased linkage map (9,717 markers, 0.22 cM average spacing) from a backcross population between cultivated peanut and the neoallotetraploid [A. magna × A. stenosperma]4x (MagSten). Initial maps showed distinctive double linkage group artifacts, and some progenies displayed abnormal genotyping patterns linked to unbalanced chromosomal compositions, outcomes of homoeologous exchange. Removing these progenies resolved the artifacts, revealing a previously unrecognized mapping artifact in allotetraploid peanut and suggesting a common origin for similar artifacts observed in other linkage maps. Analysis of the phased map detected double reduction in 12% of progenies; one event was confirmed as producing a genomic composition matching theoretical predictions, supporting the hypothesis that double reduction causes unbalanced genomic compositions in allopolyploids as well. These results indicate that double reduction is a rare but recurrent phenomenon in segmental allotetraploid peanut that, together with homoeologous exchange, contributes to genetic instability and generates new allelic combinations in this and likely other allopolyploid genomes.