COmapper high-resolution mapping of meiotic crossovers by long-read sequencing in Arabidopsis

COmapper : high-resolution mapping of meiotic crossovers by long-read sequencing in Arabidopsis

© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.

Détails bibliographiques
Publié dans:The New phytologist. - 1979. - 247(2025), 4 vom: 19. Juli, Seite 1942-1957
Auteur principal: Byun, Dohwan (Auteur)
Autres auteurs: Son, Namil, Kim, Heejin, Kim, Jaeil, Park, Jihye, Park, Sang-Jun, Kim, Hyein, Kim, Jaebeom, Kim, Juhyun, Lee, Seula, Hyun, Youbong, Ziolkowski, Piotr A, Henderson, Ian R, Choi, Kyuha
Format: Article en ligne
Langue:English
Publié: 2025
Accès à la collection:The New phytologist
Sujets:Journal Article Arabidopsis thaliana RECQ4 crossover long‐read sequencing meiosis polymorphism
Description
Résumé:© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.
Meiotic crossovers rearrange existing genetic variation between homologous chromosomes, profoundly affecting genomic diversity. Crossovers are typically constrained to one to three events per chromosome pair, and their distribution is shaped by chromatin accessibility and DNA polymorphisms. Genome-wide crossover maps can be generated in plants by high-throughput short-read sequencing or linked-read sequencing. Here, we use long-read nanopore sequencing technology to develop a crossover mapping pipeline, COmapper, for high-resolution mapping of genome-wide crossovers from pooled DNA of F1 hybrid pollen and F2 recombinant seedlings derived from a cross between Arabidopsis thaliana accessions Col and Ler. We validate the high accuracy of COmapper by applying nanopore long-read sequencing to the pooled DNA of Arabidopsis F2 individuals with crossovers mapped by short-read sequencing. Using the COmapper, we constructed high-resolution genomic maps of crossovers using F1 hybrid pollen and F2 seedlings in wild-type (WT) and crossover-elevated recq4a recq4b mutants, showing results comparable to short-read sequencing. Crossovers were enriched at gene-proximal promoters in WT and increased but reshaped by high polymorphism density in recq4a recq4b. We propose that COmapper will be widely applicable for exploring the effects of genetic, epigenetic, and environmental changes on the crossover patterns across diverse plant species
Description:Date Completed 17.07.2025
Date Revised 19.07.2025
published: Print-Electronic
Citation Status MEDLINE
ISSN:1469-8137
DOI:10.1111/nph.70304