Dissecting meiotic recombination based on tetrad analysis by single-microspore sequencing in maize

Abstract

Meiotic recombination drives eukaryotic sexual reproduction and the generation of genome diversity. Tetrad analysis, which examines the four chromatids resulting from a single meiosis, is an ideal method to study the mechanisms of homologous recombination. Here we develop a method to isolate the four microspores from a single tetrad in maize for the purpose of whole-genome sequencing. A high-resolution recombination map reveals that crossovers are unevenly distributed across the genome and are more likely to occur in the genic than intergenic regions, especially common in the 5′- and 3′-end regions of annotated genes. The direct detection of genomic exchanges suggests that conversions likely occur in most crossover tracts. Negative crossover interference and weak chromatid interference are observed at the population level. Overall, our findings further our understanding of meiotic recombination with implications for both basic and applied research.

DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis

“…This is consistent with low levels of DNA methylation observed at Arabidopsis and maize crossover hot spots (Choi et al 2013;Wijnker et al 2013;RodgersMelnick et al 2015) and the widespread suppression of recombination in plant heterochromatin (Copenhaver et al 1999;Fu et al 2002;Liu et al 2009;Giraut et al 2011;Mayer et al 2012;Salomé et al 2012; The Tomato Genome Consortium 2012; Bauer et al 2013;Choulet et al 2014;Li et al 2015;Rodgers-Melnick et al 2015). We show that RdDM is associated with acquisition of H3K9me2 and increased nucleosome occupancy at the targeted hot spots.…”

“…Plant hot spots are observed at gene transcriptional start sites (TSSs) and transcriptional termination sites (TTSs) and require the histone variant H2A.Z for wild-type activity (Brown and Sundaresan 1991;Fu et al 2001;Saintenac et al 2011;Choi et al 2013;Drouaud et al 2013;Hellsten et al 2013;Li et al 2015). In contrast, crossovers are largely suppressed in repeat-rich heterochromatic regions in plant genomes (Copenhaver et al 1999;Wei et al 2009;Mayer et al 2012; The Tomato Genome Consortium 2012; Yelina et al 2012;Choulet et al 2014;Rodgers-Melnick et al 2015).…”

Understanding and Manipulating Meiotic Recombination in Plants

“…Thus, historical CO events can be deduced from linkage disequilibrium analysis that measures the association of sets of markers on chromosomes in a population. Recently, whole-genome sequencing of four products of meiotic tetrads allowed fine-scale mapping of recombination break points (Wijnker et al, 2013;Li et al, 2015). COs also can be scored cytologically by counting chiasmata or recombination nodules, seen as electron-dense structures at recombination sites by electron microscopy (Anderson et al, 2003).…”

DNA Crossover Motifs Associated with Epigenetic Modifications Delineate Open Chromatin Regions in Arabidopsis

“…It is also possible to map recombination events at high resolution, by crossing strains with defined sequence polymorphisms, followed by wholegenome sequencing of the resulting progenies. High-resolution maps of genome-wide recombination events are now available for Saccharomyces cerevisiae, Drosophila, maize, and Theileria parva (Mancera et al, 2008;Comeron et al, 2012;Henson et al, 2012;Li et al, 2015;Rodgers-Melnick et al, 2015). Furthermore, highthroughput sequencing, combined with single-cell technology, contributed to the detection of meiotic recombination of single sperm (Lu et al, 2012b;Wang et al, 2012) and single oocyte (Hou et al, 2013) genotyping.…”