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ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #336647

Research Project: Resources for the Genetic Improvement of Potato

Location: Vegetable Crops Research

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

Author
item Marand, Alexandre - University Of Wisconsin
item Jansky, Shelley
item Zhao, Hainan - University Of Wisconsin
item Leisner, Courtney - Michigan State University
item Zhu, Xiaobiao - University Of Wisconsin
item Zeng, Zixian - University Of Wisconsin
item Crisovan, Emily - Michigan State University
item Newton, Linsey - Michigan State University
item Hamernik, Andy
item Veilleux, Richard - Virginia Tech
item Buell, C - Michigan State University
item Jiang, Jiming - University Of Wisconsin

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/12/2017
Publication Date: 3/5/2018
Citation: Marand, A., Jansky, S.H., Zhao, H., Leisner, C., Zhu, X., Zeng, Z., Crisovan, E., Newton, L., Hamernik, A.J., Veilleux, R.E., Buell, C.R., Jiang, J. 2018. Meiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potato. Genome Biology. 18:203. https://doi.org/10.1186/s13059-017-1326-8.
DOI: https://doi.org/10.1186/s13059-017-1326-8

Interpretive Summary: Geneticists are interested in patterns of meiotic recombination. Knowledge of positions of recombination are especially important to plant breeders interested in introgressing new genes via sexual reproduction. This study found that recombination breakpoints in potato are associated with a class of transposable elements.

Technical Abstract: Meiotic recombination is the foundation for genetic variation in natural and artificial populations of eukaryotes. Although genetic recombination maps have been developed in numerous plant species since late the 1980s, very few of these maps have provided the necessary resolution needed to investigate the genomic and epigenomic features underlying meiotic recombination. Using a whole genome sequencing based approach, we developed an ultra-high resolution reference-based haplotype map using two diploid potato clones as parents. The vast majority (~80%) of maternal meiotic recombination breakpoints were mapped to less than 2 kilobases. We demonstrate that these breakpoints reside in genomic regions of “open chromatin”, which were identified based on their hypersensitivity to DNase I digestion. The genomic regions spanning recombination breakpoints were significantly enriched with the TcMar-Stowaway family of miniature inverted-repeat transposable elements (MITEs). TcMar-Stowaways were also associated with features consistent with cis-regulatory function and their presence in gene promoters is concomitant with an increase in the local recombination rate. Collectively, our results suggest that maternal meiotic recombination breakpoints in potato are largely determined by the local chromatin status, marked by accessible chromatin, and are associated with TcMar- Stowaway transposons.