INTRODUCTION: Meiotic recombination is one of the most important processes of evolution and adaptation to environmental conditions. Even though there is substantial knowledge about proteins involved in the process, targeting specific DNA loci by the recombination machinery is not well understood. OBJECTIVES: This study aims to investigate a wheat recombination hotspot (H1) in comparison with a "regular" recombination site (Rec7) on the sequence and epigenetic level in conditions with functional and non-functional Ph1 locus. METHODS: The DNA sequence, methylation pattern, and recombination frequency were analyzed for the H1 and Rec7 in three mapping populations derived by crossing introgressive wheat line 8.1 with cv. Chinese Spring (with Ph1 and ph1 alleles) and cv. Tähti. RESULTS: The H1 and Rec7 loci are 1.586 kb and 2.538 kb long, respectively. High-density mapping allowed to delimit the Rec7 and H1 to 19 and 574 bp and 593 and 571 bp CO sites, respectively. A new method (ddPing) allowed screening recombination frequency in almost 66 thousand gametes. The screening revealed a 5.94-fold higher recombination frequency at the H1 compared to the Rec7. The H1 was also found out of the Ph1 control, similarly as gamete distortion. The recombination was strongly affected by larger genomic rearrangements but not by the SNP proximity. Moreover, chromatin markers for open chromatin and DNA hypomethylation were found associated with crossover occurrence except for the CHH methylation. CONCLUSION: Our results, for the first time, allowed study of wheat recombination directly on sequence, shed new light on chromatin landmarks associated with particular recombination sites, and deepened knowledge about role of the Ph1 locus in control of wheat recombination processes. The results are suggesting more than one recombination control pathway. Understanding this phenomenon may become a base for more efficient wheat genome manipulation, gene pool enrichment, breeding, and study processes of recombination itself.

Institute of Experimental Botany Czech Academy of Sciences Centre of the Region Haná for Biotechnological and Agricultural Research Šlechtitelů 31 Olomouc 779 00 Czech Republic

Institute of Experimental Botany Czech Academy of Sciences Centre of the Region Haná for Biotechnological and Agricultural Research Šlechtitelů 31 Olomouc 779 00 Czech Republic; Department of Cell Biology and Genetics Faculty of Science Palacký University 17 listopadu 1192 12 Olomouc 779 00 Czech Republic

Institute of Experimental Botany Czech Academy of Sciences Centre of the Region Haná for Biotechnological and Agricultural Research Šlechtitelů 31 Olomouc 779 00 Czech Republic; Department of Computer Science Faculty of Science Palacký University 17 listopadu 1192 12 Olomouc 779 00 Czech Republic; Department of Physical Chemistry Faculty of Science Palacký University 17 listopadu 1192 12 Olomouc 779 00 Czech Republic

Institute of Experimental Botany Czech Academy of Sciences Centre of the Region Haná for Biotechnological and Agricultural Research Šlechtitelů 31 Olomouc 779 00 Czech Republic; Polish Academy of Sciences Institute of Plant Genetics Strzeszyńska 34 Poznań 60 479 Poland

Tallinn University of Technology Department of Chemistry and Biotechnology Akadeemia tee 15 Tallinn 19086 Estonia

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