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. Electronic supplementary material The online version of this article (10.1186/s13059-019-1675-6) contains supplementary material, which is available to authorized users.

MutS homologue 4 and MutS homologue 5 Maintain the Obligate Crossover in Wheat Despite Stepwise Gene Loss following Polyploidization

“…The mean number of bivalents per cell was 20.97 6 0.03 (n 5 36) and the total number of chiasmata per cell was 40 6 0.28 (n 5 36), which are predominantly distally distributed (76.5%). This is consistent with a computational analysis of 13 recombinant inbred mapping populations, which gave values of 40.8 to 51.9 COs per line, typically clustered toward the ends of chromosomes (Gardiner et al, 2019).…”

A co-expression network in hexaploid wheat reveals mostly balanced expression and lack of significant gene loss of homeologous meiotic genes upon polyploidization

“…Thus, in comparison to model plants (Arabidopsis and rice), few MGs have been functionally characterized in wheat. Characterised wheat MGs include TaASY1 [ 54,55 ], TaMSH7 [ 56 ], TaRAD51 [ 57,58 ], TaDMC1 [ 57,58 ], TaPSH1 [ 59 ], TaZIP4 [ 31-33 ] and RecQ-7 [ 60 ]. Given that, the assessment of whether the three modules contain known MGs was undertaken using orthology informed approaches.…”

Bread wheat TaSPO11‐1 exhibits evolutionarily conserved function in meiotic recombination across distant plant species

“…Until now, only a dozen of genes (TaRAD51,TaRAD51C,TaRAD51D,TaDMC1,TaMRE11,TaRAD50,TaASY1,TaZYP1,TaPHS1,TaPh1,, among more than 100 known as involved in meiotic recombination in plants, have been cloned and significantly analysed in wheat. These analyses have mainly been limited to comparisons of sequences of homoeologous copies, expression analyses and immunolocalization (Boden et al, 2007;de Bustos et al, 2007;Boden et al, 2009;Devisetty et al, 2010;Perez et al, 2011;Khoo et al, 2012a;Khoo et al, 2012b;Ma et al, 2018;Gardiner et al, 2019). TaPh1, which controls homoeologous recombination in wheat, remains the best-defined locus involved in meiosis in wheat (Griffiths et al, 2006;Moore, 2014;Martin et al, 2017).…”