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

Polyploidization in peanut (Arachis hypogaea L.) provided evolutionary advantages by increasing heterosis, the response to selection, and enhancing adaptability. However, it also caused a genetic bottleneck by 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 segregation pattern restricted to polyploids, in which a single-dosage locus yields duplex gametes. It requires multivalent formation and crossing over between non-sister chromatids, both of which are associated with homoeologous exchange. 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, a high-density phased linkage map was constructed using a backcross population from a cross between a neoallotetraploid [A. magna K 30097 x A. stenosperma V 15076]4x (MagSten) and cultivated peanut. The final map included 9,717 SNP markers with an average spacing of 0.22 centiMorgans. Some progenies showed unbalanced genomic compositions, creating artifacts in linkage analysis. Removing these progenies improved the map and suggested a common origin for artifacts previously observed in other linkage maps, revealing a novel aspect of mapping in allotetraploid peanut. Analysis of the phased map revealed double reduction in 12% of progenies. Notably, one event produced a genomic composition consistent with theoretical predictions, supporting the expectation that double reduction causes unbalanced genomes in allopolyploids. These results indicate that double reduction is a low but significant frequency genetic phenomenon in the segmental allotetraploid peanut, contributing to the genetic instability and evolutionary dynamics of this and likely other allopolyploid genomes. Article SummaryThis study investigated double reduction, a rare genetic event in segmental allopolyploid peanut, which can create unbalanced genomic compositions and affect genetic diversity. We generated a backcross population using neoallotetraploid and cultivated peanuts, then constructed a high-density phased linkage map. Analysis revealed unbalanced genomic compositions in some progenies caused by homoeologous exchanges, which reduced map quality. Double reduction was estimated to occur in approximately 12% of progenies, aligning with theoretical expectations for genomic imbalance. These results demonstrate that double reduction contributes to genetic instability, inheritance patterns, and genome evolution in allopolyploid organisms such as peanut.