{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T06:44:49Z","timestamp":1791787489163,"version":"4.3.4"},"reference-count":84,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2026,10,11]],"date-time":"2026-10-11T00:00:00Z","timestamp":1791676800000},"content-version":"vor","delay-in-days":10,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100022709","name":"Cluster of Excellence on Plant Sciences","doi-asserted-by":"publisher","award":["EXC 2048\/1"],"award-info":[{"award-number":["EXC 2048\/1"]}],"id":[{"id":"10.13039\/100022709","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100022709","name":"Cluster of Excellence on Plant Sciences","doi-asserted-by":"publisher","award":["390686111"],"award-info":[{"award-number":["390686111"]}],"id":[{"id":"10.13039\/100022709","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003484","name":"Heinrich-Heine-Universit\u00e4t D\u00fcsseldorf","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003484","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Plant Journal"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>SUMMARY<\/jats:title>\n                  <jats:p>Meiotic recombination is not only a key mechanism for sexual adaptation in eukaryotes but crucial for the accumulation of beneficial alleles in breeding populations. The effective manipulation of recombination requires, however, a better understanding of the mechanisms regulating the rate and distribution of recombination events in genomes. Here, we identified the genomic features that best explain the recombination variation among a diverse set of segregating populations of barley at a resolution of 1 Mbp and investigated how methylation and structural variants (SVs) determine crossover (CO) hotspots and coldspots at a high resolution of 10\u2009kb. Hotspots were found to be in proximity to genes, and the genetic effects not assigned to methylation were found to be the most important factor explaining differences in recombination rates among populations, along with the methylation and the parental sequence divergence. Interestingly, coldspots were associated with the inheritance of a highly methylated genomic fragment from one parent only, but hotspots were identified at genomic segments where both parents were equally low methylated. The parental sequence divergence was shown to have a sigmoidal correlation with recombination, indicating an upper limit of mismatch among homologous chromosomes for CO formation. SVs were shown to be correlated with CO suppression, and their type and size were not found to influence that effect. The joint act of methylation and SVs was associated with the location of coldspots in barley, and the weight of their relative effect depends on the genomic region. Our findings suggest that recombination in barley is highly predictable, occurring mostly in multiple short sections located in proximity to genes and being modulated by local levels of methylation and SV load.<\/jats:p>","DOI":"10.1111\/tpj.71171","type":"journal-article","created":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T05:48:59Z","timestamp":1791784139000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The role of methylation and structural variants in shaping the recombination landscape of barley"],"prefix":"10.1111","volume":"128","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0006-4536","authenticated-orcid":false,"given":"Federico","family":"Casale","sequence":"first","affiliation":[{"name":"Institute of Quantitative Genetics and Genomics of Plants Heinrich Heine University  Universit\u00e4tsstra\u00dfe 1 D\u00fcsseldorf 40225 Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8735-5549","authenticated-orcid":false,"given":"Christopher","family":"Arlt","sequence":"additional","affiliation":[{"name":"Institute of Quantitative Genetics and Genomics of Plants Heinrich Heine University  Universit\u00e4tsstra\u00dfe 1 D\u00fcsseldorf 40225 Germany"},{"name":"Julius K\u00fchn\u2010Institut, Federal Research Center for Cultivated Plants Institute for Breeding Research on Agricultural Crops  Sanitz 18190 Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marius","family":"K\u00fchl","sequence":"additional","affiliation":[{"name":"Institute of Quantitative Genetics and Genomics of Plants Heinrich Heine University  Universit\u00e4tsstra\u00dfe 1 D\u00fcsseldorf 40225 Germany"},{"name":"Julius K\u00fchn\u2010Institut, Federal Research Center for Cultivated Plants Institute for Breeding Research on Agricultural Crops  Sanitz 18190 Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinquan","family":"Li","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Plant Breeding Research  K\u00f6ln 50829 Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6680-3012","authenticated-orcid":false,"given":"Julia","family":"Engelhorn","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Plant Breeding Research  K\u00f6ln 50829 Germany"},{"name":"Institute for Molecular Physiology Heinrich Heine University  Universit\u00e4tsstra\u00dfe 1 D\u00fcsseldorf 40225 Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2707-2771","authenticated-orcid":false,"given":"Thomas","family":"Hartwig","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Plant Breeding Research  K\u00f6ln 50829 Germany"},{"name":"Institute for Molecular Physiology Heinrich Heine University  Universit\u00e4tsstra\u00dfe 1 D\u00fcsseldorf 40225 Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6791-8068","authenticated-orcid":false,"given":"Benjamin","family":"Stich","sequence":"additional","affiliation":[{"name":"Institute of Quantitative Genetics and Genomics of Plants Heinrich Heine University  Universit\u00e4tsstra\u00dfe 1 D\u00fcsseldorf 40225 Germany"},{"name":"Julius K\u00fchn\u2010Institut, Federal Research Center for Cultivated Plants Institute for Breeding Research on Agricultural Crops  Sanitz 18190 Germany"},{"name":"Max Planck Institute for Plant Breeding Research  K\u00f6ln 50829 Germany"},{"name":"Cluster of Excellence on Plant Sciences, From Complex Traits Towards Synthetic Modules  Universit\u00e4tsstra\u00dfe 1 D\u00fcsseldorf 40225 Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,11]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1534\/g3.119.400504","article-title":"Inferring the genomic landscape of recombination rate variation in European aspen (Populus tremula)","volume":"10","author":"Apuli R.P.","year":"2020","journal-title":"G3: Genes, Genomes, Genetics"},{"key":"e_1_2_9_3_1","doi-asserted-by":"crossref","first-page":"2109","DOI":"10.1073\/pnas.1416622112","article-title":"Crossovers are associated with mutation and biased gene conversion at recombination hotspots","volume":"112","author":"Arbeithuber B.","year":"2015","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"e_1_2_9_4_1","doi-asserted-by":"crossref","first-page":"2241","DOI":"10.1111\/pbi.14126","article-title":"Affordable, accurate and unbiased RNA sequencing by manual library miniaturization: a case study in barley","volume":"21","author":"Arlt C.","year":"2023","journal-title":"Plant Biotechnology Journal"},{"key":"e_1_2_9_5_1","doi-asserted-by":"crossref","DOI":"10.3389\/fpls.2021.706560","article-title":"An induced mutation in HvRECQL4 increases the overall recombination and restores fertility in a barley HvMLH3 mutant background","volume":"12","author":"Arrieta M.","year":"2021","journal-title":"Frontiers in Plant Science"},{"key":"e_1_2_9_6_1","doi-asserted-by":"crossref","first-page":"1986","DOI":"10.1126\/science.281.5385.1986","article-title":"Why sex and recombination?","volume":"281","author":"Barton N.H.","year":"1998","journal-title":"Science"},{"key":"e_1_2_9_7_1","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1007\/s10577-007-1140-3","article-title":"Regulating double\u2010stranded DNA break repair towards crossover or non\u2010crossover during mammalian meiosis","volume":"15","author":"Baudat F.","year":"2007","journal-title":"Chromosome Research: An 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dissect adaptive traits in global sorghum diversity using a nested association mapping population","volume":"206","author":"Bouchet S.","year":"2017","journal-title":"Genetics"},{"key":"e_1_2_9_15_1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1010141","article-title":"Diversity and determinants of recombination landscapes in flowering plants","volume":"18","author":"Brazier T.","year":"2022","journal-title":"PLoS Genetics"},{"key":"e_1_2_9_16_1","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1016\/j.ajhg.2018.07.015","article-title":"A one\u2010penny imputed genome from next\u2010generation reference panels","volume":"103","author":"Browning B.L.","year":"2018","journal-title":"American Journal of Human Genetics"},{"key":"e_1_2_9_17_1","first-page":"337","article-title":"Perspective: sex, recombination, and the efficacy of selection \u2013 was Weismann right?","volume":"54","author":"Burt 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and domesticated barley","volume":"228","author":"Dreissig S.","year":"2020","journal-title":"New Phytologist"},{"key":"e_1_2_9_27_1","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1534\/genetics.107.080622","article-title":"Using crossover breakpoints in recombinant inbred lines to identify quantitative trait loci controlling the global recombination frequency","volume":"177","author":"Esch E.","year":"2007","journal-title":"Genetics"},{"key":"e_1_2_9_28_1","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s13059-024-03163-4","article-title":"Structural variation and DNA methylation shape the centromere\u2010proximal meiotic crossover landscape in Arabidopsis","volume":"25","author":"Fernandes J.B.","year":"2024","journal-title":"Genome Biology"},{"key":"e_1_2_9_29_1","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s13059-019-1675-6","article-title":"Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency","volume":"20","author":"Gardiner L.J.","year":"2019","journal-title":"Genome Biology"},{"key":"e_1_2_9_30_1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1093\/bioinformatics\/btv562","article-title":"RegioneR: an R\/Bioconductor package for the association analysis of genomic regions based on permutation tests","volume":"32","author":"Gel B.","year":"2016","journal-title":"Bioinformatics"},{"key":"e_1_2_9_31_1","first-page":"1","article-title":"Genome\u2010wide variation in recombination rate in Eucalyptus","volume":"17","author":"Gion J.\u2010M.","year":"2016","journal-title":"BMC Genomics"},{"key":"e_1_2_9_32_1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1002354","article-title":"Genome\u2010wide crossover distribution in Arabidopsis thaliana meiosis reveals sex\u2010specific patterns along chromosomes","volume":"7","author":"Giraut L.","year":"2011","journal-title":"PLoS 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James F. Ewels P. Afyounian E. Weinstein M. Schuster\u2010Boeckler B.et\u00a0al. 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after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis","volume":"22","author":"Lu P.","year":"2012","journal-title":"Genome Research"},{"key":"e_1_2_9_51_1","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1038\/nature07135","article-title":"High\u2010resolution mapping of meiotic crossovers and noncrossovers in yeast","volume":"454","author":"Mancera E.","year":"2009","journal-title":"Nature"},{"key":"e_1_2_9_52_1","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1105\/tpc.18.00750","article-title":"Historical meiotic crossover hotspots fueled patterns of evolutionary divergence in rice","volume":"31","author":"Marand A.P.","year":"2019","journal-title":"Plant Cell"},{"key":"e_1_2_9_53_1","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.cell.2006.05.044","article-title":"Crossover homeostasis in yeast meiosis","volume":"126","author":"Martini 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America"},{"key":"e_1_2_9_57_1","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1146\/annurev-arplant-050213-035923","article-title":"The molecular biology of meiosis in plants","volume":"66","author":"Mercier R.","year":"2015","journal-title":"Annual Review of Plant Biology"},{"key":"e_1_2_9_58_1","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1042\/BST0340531","article-title":"Meiotic recombination hotspots in plants","volume":"34","author":"M\u00e9zard C.","year":"2006","journal-title":"Biochemical Society Transactions"},{"key":"e_1_2_9_59_1","doi-asserted-by":"crossref","first-page":"5880","DOI":"10.1073\/pnas.1120841109","article-title":"Loss of DNA methylation affects the recombination landscape in Arabidopsis","volume":"109","author":"Mirouze M.","year":"2012","journal-title":"Proceedings of the National Academy of Sciences of the United States of 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