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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #346737

Research Project: Development and Application of Genetic, Genomic, and Bioinformatic Resources in Maize

Location: Plant, Soil and Nutrition Research

Title: Genomic features shaping the landscape of meiotic double-strand break hotspots in maize

Author
item HE, YAN - China Agricultural University
item WANG, MINGHUI - Cornell University - New York
item DUKOWIC-SCHULZE, STEFANIE - University Of Minnesota
item ZHOU, ADELE - Cornell University - New York
item TIANG, CHOON-LIN - Cornell University - New York
item SHILO, SHAY - Weizmann Institite Of Science
item SIDH SIDHU, GAGANPREET - Columbia University Medical Center
item EICHTEN, STEVEN - University Of Minnesota
item Bradbury, Peter
item SPRINGER, NATHAN - University Of Minnesota
item Buckler, Edward - Ed
item LEVY, AVRAHAM - Weizmann Institite Of Science
item SUN, QI - Cornell University - New York
item PILLARDY, JAROSLAW - Cornell University - New York
item KIANIAN, PENNY - University Of Minnesota
item Kianian, Shahryar
item CHEN, CHANGBIN - University Of Minnesota
item PAWLOWSKI, WOJCIECH - Cornell University - New York

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/12/2017
Publication Date: 11/14/2017
Citation: He, Y., Wang, M., Dukowic-Schulze, S., Zhou, A., Tiang, C., Shilo, S., Sidh Sidhu, G., Eichten, S., Bradbury, P., Springer, N., Buckler IV, E.S., Levy, A., Sun, Q., Pillardy, J., Kianian, P., Kianian, S., Chen, C., Pawlowski, W. 2017. Genomic features shaping the landscape of meiotic double-strand break hotspots in maize. Proceedings of the National Academy of Sciences. 114(46):12231-12236.

Interpretive Summary: Meiotic recombination is a process in plants, animals, and fungi, during which chromosomes exchange their parts. It generates new genetic variation in the progeny, and is one of the reasons why progeny is both similar and different from their parents. Recombination is initiated by formation of breaks in chromosomal DNA. We generated a high-resolution map of sites where these breaks are formed in the genome of maize. Surprisingly, we found that the DNA breaks are abundant in all genome regions, including sites where recombination was thought to be limited, such as repetitive DNA. The map will allow understanding of how recombination patterns shape the genome, and aid development of more efficient breeding methods.

Technical Abstract: Meiotic recombination is the most important source of genetic variation in higher eukaryotes. It is initiated by formation of double-strand breaks (DSBs) in chromosomal DNA in early meiotic prophase. The DSBs are subsequently repaired, resulting in crossovers and non-crossovers. Recombination events are not distributed evenly along chromosomes but cluster at recombination hotspots. How specific sites become hotspots is poorly understood. Studies in yeast and mammals linked initiation of meiotic recombination to active chromatin features present upstream from genes, such as absence of nucleosomes and presence of trimethylation of lysine 4 in histone H3 (H3K4me3). Core recombination components are conserved among eukaryotes but it is unclear whether this conservation results in universal characteristics of recombination landscapes shared by a wide range of species. To address this question, we mapped meiotic DSBs in maize, a higher eukaryote with a large genome that is rich in repetitive DNA. We found DSBs in maize to be frequent in all chromosome regions, including sites lacking COs, such as centromeres and pericentromeric regions. Furthermore, most DSB are formed in repetitive DNA, predominantly Gypsy retrotransposons, and only one-quarter of DSB hotspots are near genes. Genic and non-genic hotspots differ in several characteristics, and only genic DSBs contribute to crossover formation. Maize hotspots overlap regions of low nucleosome occupancy but show only limited association with H3K4me3 sites. Overall, maize DSB hotspots exhibit distribution patterns and characteristics not reported previously in other species. Understanding recombination patterns in maize will shed light on mechanisms affecting dynamics of the plant genome.