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

Paul Bailey,Bernardo J. Clavijo,Jonathan Wright,Laura-Jayne Gardiner,James D. Higgins,Anthony Hall,Thomas Brabbs,Ryan Joynson,Luzie U. Wingen,Neil Hall,Simon Griffiths

doi:10.1186/s13059-019-1675-6

Paul Bailey, Bernardo J. Clavijo + Show 9 more

Open Access

https://doi.org/10.1186/s13059-019-1675-6

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Abstract

BackgroundSequence 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.ResultsWe 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.ConclusionsThis 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.

Highlights

There is an evolutionary requirement for genetic diversity across a species
gene conversions (GCs) contribute to breaking up linkage groups, and it has been observed that GCs are prevalent in centromeric regions suggesting that centromeres do experience genetic change but that double-strand breaks (DSBs) in these regions are converted preferentially to GCs [41, 43]
Analysis of the CO landscape in wheat For each of the 13 populations, the number of COs per recombinant inbred line (RIL) was recorded across the 21 chromosomes (Fig. 1a; Additional file 1: Figure S2; CO-Phenotype, “Materials and methods”)

Summary

Introduction

Shuffling of material between homologous chromosomes, or genetic recombination, breaks linkage between genes resulting in offspring that have combinations of alleles that differ from those found in either of the parents. It is important for us to understand recombination and GC if we are to alter their rates to accelerate the induction of novel allelic combinations or to generate stable cultivars This is important in bread wheat where recombination frequency is low and skewed towards the ends of chromosomes [9]. 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; increasing recombination rates can reduce linkage drag and generate new genetic combinations

Methods

Results

Conclusion