Abstract
Meiotic recombination is a fundamental mechanism to generate novel allelic combinations which can be harnessed by breeders to achieve crop improvement. The recombination landscape of many crop species, including the major crop barley, is characterized by a dearth of recombination in 65% of the genome. In addition, segregation distortion caused by selection on genetically linked loci is a frequent and undesirable phenomenon in double haploid populations which hampers genetic mapping and breeding. Here, we present an approach to directly investigate recombination at the DNA sequence level by combining flow-sorting of haploid pollen nuclei of barley with single-cell genome sequencing. We confirm the skewed distribution of recombination events toward distal chromosomal regions at megabase resolution and show that segregation distortion is almost absent if directly measured in pollen. Furthermore, we show a bimodal distribution of inter-crossover distances, which supports the existence of two classes of crossovers which are sensitive or less sensitive to physical interference. We conclude that single pollen nuclei sequencing is an approach capable of revealing recombination patterns in the absence of segregation distortion.
Highlights
Meiotic recombination is a key mechanism in eukaryotic reproduction which enables novel combinations of alleles and provides a mechanism for plant breeders to achieve crop improvement
“Morex” (Mascher et al, 2017) and genotypes were called at single-nucleotide polymorphism (SNP) sites known to segregate in the “Morex” × “Barke” population (Mascher et al, 2013a)
Our results show that segregation distortion is almost absent in pollen grains which supports the conclusion that meiosis alone is not the main cause of this phenomenon
Summary
Meiotic recombination is a key mechanism in eukaryotic reproduction which enables novel combinations of alleles and provides a mechanism for plant breeders to achieve crop improvement. Recombination patterns are shaped by genetic, epigenetic and environmental factors (MelamedBessudo and Levy, 2012; Mirouze et al, 2012; Yelina et al, 2012; Ziolkowski et al, 2015, 2017; Ritz et al, 2017). Several approaches were shown to be successful, including the increase of crossovers via mutation of an anti-crossover factor (Crismani et al, 2012), epigenetic remodeling of crossover frequency via reduced DNA methylation (Melamed-Bessudo and Levy, 2012; Mirouze et al, 2012; Yelina et al, 2012; Habu et al, 2015), and shifting of crossover positions via increased or decreased temperatures (Higgins et al, 2012; Phillips et al, 2015; Martin et al, 2017). Natural diversity of recombination patterns was shown to exist in Arabidopsis, maize, and Hordeum (Gale et al, 1970; Sall, 1990; Sall et al, 1990; Nilsson and Pelger, 1991; Sidhu et al, 2015; Ziolkowski et al, 2015, 2017)
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