Genome-wide atlas of loci involved in chromosomal recombination in common wheat

Chromosomal recombination is a pivotal biological mechanism for generating novel genetic diversity, essential for plant breeding and genetic research endeavors. This study investigated the genetic loci involved in chromosomal recombination through analyzing five published recombinant inbred line (RIL) populations and four double haploid (DH) populations. Great phenotypic variations in recombination frequency were observed between populations and chromosomes. A total of 29 QTL were mapped, which were predominantly located on the B genome. Notably, one QTL on chromosome 6AL was identified from two RIL populations and one QTL on chromosome 3B was identified in both RIL and DH populations. Additionally, a map delineating recombination hotspot regions was developed, and these regions were observed on all chromosomes except for 6B. Recombination hotspot regions tended to locate on chromosomes 1D, 3A, 3B, 6A, and 7D compared to chromosomes 1B, 5B, and 6B. In addition, most hotspot regions were located at chromosome termini, with some clustering in specific regions. Besides genetic factors, the study also explored the impact of chip size and population type on the number of identifiable chromosomal recombination events. Overall, this work improves our understanding of the molecular mechanisms for the chromosomal recombination rate and may contribute to the optimization of breeding strategies in wheat.