Abstract
SummaryRecombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence‐based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome‐wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans‐acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans‐acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low‐recombining pericentromeric regions of chromosomes.
Highlights
Besides playing a critical role in meiotic division, recombination is one of the major factors that influences the precision of gene mapping studies, and along with random drift and effective population size, defines the fate of genetic variation in populations by affecting the efficiency of selection acting on linked alleles
We showed that the recombination rate variation along the chromosomes and among the genomes affects the distribution of deleterious genetic load
Additional high-density single nucleotide polymorphisms (SNPs) and InDel data was generated for founder lines using the wheat exome capture assay (WEC) (Jordan et al, 2015) and the 420K Axiom array
Summary
Besides playing a critical role in meiotic division, recombination is one of the major factors that influences the precision of gene mapping studies, and along with random drift and effective population size, defines the fate of genetic variation in populations by affecting the efficiency of selection acting on linked alleles. The ability to control the rate and distribution of recombination events has the potential to substantially accelerate the development of new varieties by allowing quick assembly of novel beneficial multi-allelic complexes and by fixing desirable haplotypes in fewer generations. While these findings hold great promise for plant breeding, their practical applications are hindered by the limited understanding of the genetics of recombination rate control in specific crops that may differ in genomic organization, genome size, or ploidy level from those of the model species (Mercier et al, 2015). The identification of genetic factors that can shift CO distribution toward the pericentromeric chromosomal regions would be important for making all genomic regions accessible for selection
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