Deep Genome-Wide Measurement of Meiotic Gene Conversion Using Tetrad Analysis in Arabidopsis thaliana

Abstract

Gene conversion, the non-reciprocal exchange of genetic information, is one of the potential products of meiotic recombination. It can shape genome structure by acting on repetitive DNA elements, influence allele frequencies at the population level, and is known to be implicated in human disease. But gene conversion is hard to detect directly except in organisms, like fungi, that group their gametes following meiosis. We have developed a novel visual assay that enables us to detect gene conversion events directly in the gametes of the flowering plant Arabidopsis thaliana. Using this assay we measured gene conversion events across the genome of more than one million meioses and determined that the genome-wide average frequency is 3.5×10−4 conversions per locus per meiosis. We also detected significant locus-to-locus variation in conversion frequency but no intra-locus variation. Significantly, we found one locus on the short arm of chromosome 4 that experienced 3-fold to 6-fold more gene conversions than the other loci tested. Finally, we demonstrated that we could modulate conversion frequency by varying experimental conditions.

Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping

“…Optimally, predicted GCs would be validated by using PCR and conventional sequencing, but in this case, the relevant plant material was not available. The small number of GCs detected here is consistent with previous findings (31,34,53) and suggests relatively small sizes of the gaps repaired by NCOs, although an underestimation of GCs due to the stringent criteria here cannot be ruled out.…”

Formation of interference-sensitive meiotic cross-overs requires sufficient DNA leading-strand elongation

“…Meiotic recombination not only ensures physical association of homologs to form bivalents but also, promotes their accurate segregation, and it is initiated by the formation of SPO11-programmed DNA double-strand breaks (DSBs) (1). Repair of meiotic DSBs is evolutionarily important, because it redistributes genetic variants in regions flanking the site of recombination [cross-overs (COs)] or gene conversion without flanking exchange [non-COs (NCOs)], resulting in offspring that are genetically distinct from parents and siblings (2,3). Although DNA synthesis is thought to be essential for DSB repair (DSBR) (4), molecular genetic studies are quite limited.…”

“…Although DNA synthesis is thought to be essential for DSB repair (DSBR) (4), molecular genetic studies are quite limited. Recent genome-wide studies provide evidence that meiotic COs and NCOs may require different amounts of DNA synthesis (2,3,(5)(6)(7), but the underlying mechanism remains unknown.…”

“…These findings suggest that DNA synthesis likely affects the length of strand exchange intermediates and influences their resolution toward different CO pathways. Moreover, genome-wide analyses in both yeast and plants showed that meiotic gene conversion tracts vary in length, ranging from several hundreds to thousands of nucleotides, and that CO-associated tracts are usually longer than those of NCOs (2,3,(5)(6)(7). This difference raises a question of whether there is any difference in DNA synthesis among CO-associated tracts with different lengths; however, this hypothesis has not been tested experimentally.…”

Polarized gene conversion at the bz locus of maize

“…A notable exception is the Arabidospsis quartet1 (qrt1) mutant that allows pollen tetrad analysis and has been used to demonstrate gene conversion events unambiguously by their classic 3:1 segregation (10) to estimate genome-wide conversion frequencies (11,12) and to measure the tract lengths of such conversion events (12,13). Usually, however, gene conversions have been identified by the flanking marker arrangement of intragenic recombinants (IGRs).…”