High-resolution crossover mapping reveals similarities and differences in the patterns of male and female recombination in maize

Authors: KIANIAN, PENNY - University Of Minnesota; WANG, MINGHUI - Cornell University; SIMONS, KRISTIN - North Dakota State University; GHAVAMI, FARHAD - Eurofins Scientific, Inc; HE, YAN - China Agricultural University; DUKOWIC-SCHULZE, STEFANIE - University Of Minnesota; SUNDARARAJAN, ANITHA - National Center For Genome Resources; SUN, QI - Cornell University; PILLARDY, JAROSLAW - Cornell University; MUDGE, JOANN - National Center For Genome Resources; CHEN, CHANGBIN - University Of Minnesota; Kianian, Shahryar; PAWLOWSKI, WOJCIECH - Cornell University

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/4/2018
Publication Date: 6/18/2018
Citation: Kianian, P.M., Wang, M., Simons, K.J., Ghavami, F., He, Y., Dukowic-Schulze, S., Sundararajan, A., Sun, Q., Pillardy, J., Mudge, J., Chen, C., Kianian, S., Pawlowski, W. 2018. High-resolution crossover mapping reveals similarities and differences in the patterns of male and female recombination in maize. Nature Communications. 9(1):2370. https://doi.org/10.1038/s41467-018-04562-5.
DOI: https://doi.org/10.1038/s41467-018-04562-5

Interpretive Summary: Meiotic recombination is a key source of genetic variation in eukaryotes. However, it does not affect the genome uniformly, as recombination events are unevenly distributed along chromosomes. Factors affecting the location of recombination events are poorly understood. Several factors have been found to affect CO location, including the chromatin state and the local DNA sequence context. Some of these factors vary among species. One of the least understood aspects of CO distribution are differences between male and female meioses. To examine differences in CO patterns between male and female meioses, we combined Illumina sequencing with innovative bioinformatics strategies to generate high-resolution maps of COs in maize. This approach allowed us to examine CO locations with unprecedented precision. Despite its relatively large genome size, maize is an excellent system for CO mapping due to the high number of intra-specific single nucleotide polymorphisms (SNPs). We found that CO numbers and distribution in maize were fairly similar in male and female meioses. There were however, differences at the local level, as CO positions in the two sexes differed relative to open chromatin marks and transcription start sites (TSS) in gene promoter regions. These observations suggest that even in species in which recombination patterns are similar in male and female meiosis, sex-specific factors affect CO positioning.

Technical Abstract: Meiotic crossovers (COs) are not uniformly distributed across the genome. Factors affecting CO landscape are not well understood. Particularly poorly elucidated are sex-specific aspects of CO patterns. To investigate them, we conducted high-resolution CO mapping in maize. We found that CO numbers and their overall distribution were similar in the sexes. There were, however, dissimilarities at local scale. Male and female COs differed in their locations relative to chromatin marks, including nucleosome occupancy and tri-methylation of lysine 4 of histone H3 (H3K4me3), and transcription start sites in gene promoters. These data suggest that sex-specific features of CO landscape in many species may be affected by CO number disparities as well as local differences. As meiotic recombination is the main source of genetic variation, differences between male and female CO landscapes indicate that recombination has different implications for population structure and gene evolution in male and in female meioses.