Meiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potato

Meiotic recombination is the foundation for genetic variation in natural and artificial populations of eukaryotes. Although genetic maps have been developed for numerous plant species since the late 1980s, few of these maps have provided the necessary resolution needed to investigate the genomic and...

Full description

Saved in:
Bibliographic Details
Published in:Genome Biology 2017-10, Vol.18 (1), p.203-203, Article 203
Main Authors: Marand, Alexandre P, Jansky, Shelley H, Zhao, Hainan, Leisner, Courtney P, Zhu, Xiaobiao, Zeng, Zixian, Crisovan, Emily, Newton, Linsey, Hamernik, Andy J, Veilleux, Richard E, Buell, C Robin, Jiang, Jiming
Format: Article
Language:English
Subjects:
Bioinformatics
Chromatin
Chromosomes
Cloning
Deoxyribonuclease
Deoxyribonucleic acid
DNA
DNA methylation
Gene mapping
Genetic diversity
Genetic engineering
Genomes
Genotype & phenotype
Haplotypes
Insects
Meiosis
Nucleosomes
Population
Population genetics
Potatoes
Recombination
Transposons
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Meiotic recombination is the foundation for genetic variation in natural and artificial populations of eukaryotes. Although genetic maps have been developed for numerous plant species since the late 1980s, few of these maps have provided the necessary resolution needed to investigate the genomic and epigenomic features underlying meiotic crossovers. Using a whole genome sequencing-based approach, we developed two high-density reference-based haplotype maps using diploid potato clones as parents. The vast majority (81%) of meiotic crossovers were mapped to less than 5 kb. The fine-scale accuracy of crossover detection was validated by Sanger sequencing for a subset of ten crossover events. We demonstrate that crossovers reside in genomic regions of "open chromatin", which were identified based on hypersensitivity to DNase I digestion and association with H3K4me3-modified nucleosomes. The genomic regions spanning crossovers were significantly enriched with the Stowaway family of miniature inverted-repeat transposable elements (MITEs). The occupancy of Stowaway elements in gene promoters is concomitant with an increase in recombination rate. A generalized linear model identified the presence of Stowaway elements as the third most important genomic or chromatin feature behind genes and open chromatin for predicting crossover formation over 10-kb windows. Collectively, our results suggest that meiotic crossovers in potato are largely determined by the local chromatin status, marked by accessible chromatin, H3K4me3-modified nucleosomes, and the presence of Stowaway transposons.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-017-1326-8