Mapping recombination cold spots in wheat via meiotic recombination in a large biparental population

Crossover (CO) recombination during meiosis is the fundamental driver of success in conventional plant breeding and a key determinant of genetic discoveries. Despite its importance, the fine-scale recombination landscape across the wheat genome remains partially characterized. Here, we constructed a dense genetic map by using 2,826 genotyping-by-sequencing SNP markers in a population of 345 F2:6 recombinant inbred lines, derived from a Penny x Yecora-Rojo cross. We constructed linkage maps spanning ∼3,507 cM across all 21 wheat chromosomes, and generated chromosome-wide recombination profiles and quantified local recombination rates in 5 Mb non-overlapping windows anchored to the reference genome. COs in wheat are overwhelmingly concentrated in distal and gene-rich regions, while the extensive pericentromeric cold spots span up to 77% of physical length. Low-recombination tracts (<0.1 cM/Mb) occupied 29.9 to 77.0% of chromosome physical length for all chromosomes. Average recombination rates ranged from 0.21 to 0.32 cM/Mb across the A subgenome, while local rates exceeded 5 cM/Mb in distal arms but dropped below 0.1 cM/Mb in centromeric regions. Chromosome 5A exhibited the longest genetic length (226 cM) but pronounced suppression in its subtelomeric and pericentromeric domains, whereas 4B showed the most extreme recombination desert, with 77% of its sequence nearly devoid of COs. These findings identified regions producing extended haplotype blocks and linkage drag in low-recombination regions that often constrain QTL resolution and limit access to allelic variation underlying key agronomic traits. The findings can also guide population design and inform strategies to redistribute COs through genetic, molecular, or epigenetic interventions by various genome rearrangement techniques in the future to unlock the hidden genetic diversity.