Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency

Abstract

Background: Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. A lack of recombination limits breeding efforts in crops; therefore, increasing recombination rates can reduce linkage drag and generate new genetic combinations.

Results: We use computational analysis of 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat (Triticum aestivum). We observe that high-frequency crossover sites are shared between populations and that closely related parents lead to populations with more similar crossover patterns. We demonstrate that gene conversion is more prevalent and covers more of the genome in wheat than in other plants, making it a critical process in the generation of new haplotypes, particularly in centromeric regions where crossovers are rare. We identify quantitative trait loci for altered gene conversion and crossover frequency and confirm functionality for a novel RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages including Arabidopsis.

Conclusions: This is the first gene to be demonstrated to be involved in gene conversion in wheat. Harnessing the RecQ helicase has the potential to break linkage drag utilizing widespread gene conversions.

Keywords: Crossover; Gene conversion; QTL; Recombination; Wheat.

Fig. 1

Recombination landscape of wheat. a The number of COs recorded for each RIL in the Paragon × Chinese Spring population (CO frequency per sample) as a frequency histogram. b The number of RILs sharing each recorded CO (number of samples with each CO) as a frequency histogram for the Paragon × Chinese Spring population. c For all analyzed COs, the location of the CO (the start of the window that shows a different predominant parental allele compared to the previous window) is plotted on the x-axis with the number of samples in the population that share the CO on the y axis. d The intersection of two 20-Mbp windows defines a CO. Therefore, for all windows of 40 Mbp encompassing a central defined CO, the number of high-confidence genes that are found within each interval is plotted alongside the number of RILs within each population showing the CO. e Parents for the 13 populations clustered according to their representative alleles from the 35K SNP array. f The 13 populations clustered according to their individual CO profiles, i.e., number of RILs with each recorded CO in the population. The dendrograms in e and f were produced using the R package pvclust average linkage method with correlation-based dissimilarity matrix and the value of this distance metric between clusters is represented as height on the y-axis. AU (approximately unbiased) p values were computed by multiscale bootstrap resampling (bootstrap number of 1000). Landraces are highlighted with blue boxes and pure breeding lines are highlighted with pink boxes

Fig. 2

Fine-scale analysis of sequence exchange events. a The number of COs and/or GCs recorded for each RIL in the Paragon × Chinese Spring population (GC/CO frequency per sample) as a frequency histogram. b Line plots separately for the number of COs (COs), GCs (GCs), and array SNPs per 20-Mbp window across the genome. All chromosomes are normalized to 500 Mbp in length to be displayed in a single plot. The moving average of each dataset is displayed (period = 15). c Schematic of methodology for calling gene conversions (GCs) and crossovers (COs) in the skim sequencing data using pre-defined Paragon and Chinese Spring-specific homozygous SNPs. d Immunolocalization of the chromosome axis protein ASY1 (blue) and yH2A.X (red) a marker for DNA DSB on hexaploid wheat leptotene male meiotic nuclei. Scale bar = 10 μM. e Original nuclei as per d; however, yH2A.X foci are marked that co-localize with ASY1. Mean number of yH2A.X foci across five replicates are shown from the displayed image n = 1673. f Line plots separately for the number of GCs 20 bp–2 kbp, 2–10 kbp, 10–500 kbp, and > 500 kbp in length per 20-Mbp window across the genome. Chromosomes are normalized as per b and the average frequency per window is displayed

Fig. 3

Output from QTL analysis from the Paragon × Chinese Spring population. QTL analysis output for the Paragon × Chinese Spring population that yielded significant associations for either a CO-Phenotype or b GC-Phenotype (p < 0.05). Detailing LOD scores plotted over the respective linkage groups, i.e., chromosomes. Increased resolution of QTL peaks for c CO-Phenotype and d GC-Phenotype. e Finally, the locations of the array SNPs showing the peak associations are marked in red surrounded by a red box while also showing all other array SNP locations per chromosome

Fig. 4

Examination of candidate genes from QTL analysis RecQ-7 and RuvB. a Box plot comparison of the knockout RuvB lines with the control lines, defining CO frequency using collapsed linkage windows as per CO-Phenotype. b Box plot comparison of the knockout RecQ-7 lines with the control lines, defining CO/GC frequency using GC-Phenotype. c Box plot comparison of the knockout RecQ-7 lines with the control lines, defining CO frequency using CO-Phenotype. d Phylogenetic tree of identified genes across multiple species (Arabidopsis, rice and wheat) with sequence similarity to the RecQ helicase family, including our wheat candidate RecQ-7 gene for comparison. Bootstrap values ≥ 90% are shown as green dots on the branches