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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 #324346

Title: Open chromatin reveals the functional maize genome

item RODGERS-MELNICK, ELI - Cornell University
item VERA, DANIEL - Florida State University
item KELLOGG, ELIZABETH - Danforth Plant Science Center
item BASS, HANK - Florida State University
item Buckler, Edward - Ed

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/18/2016
Publication Date: 5/16/2016
Citation: Rodgers-Melnick, E., Vera, D.L., Kellogg, E.A., Bass, H.W., Buckler IV, E.S. 2016. Open chromatin reveals the functional maize genome. Proceedings of the National Academy of Sciences. 113(22):E3177-E3184.

Interpretive Summary: DNA is a very long molecule that needs to be wrapped up very tightly in order to fit within a cell. Only the open regions of the DNA are accessible to the proteins that turn on and off genes. This study uses a novel approach to measure DNA accessibility across the maize genome. Surprisingly, we have identified that only 2% of the maize genome is accessible to regulatory proteins. This accessible region of the genome is where DNA recombination occurs naturally and is associated with expression of genes. In addition, this accessible portion of the genome explains nearly half of the genetic variability in the field for over 40 traits. These accessible regions of the genome are likely controlling phenotypic variation by controlling the expression of genes. The focusing of the recombination in these regions of genome is also producing a mutagenic effect in the middle of genes that may be preventing our crops from being a vigorous as possible. Overall, the combining of detailed analyses of DNA accessibility with quantitative genetics will have long reaching implications for accelerating crop breeding.

Technical Abstract: Every cellular process mediated through nuclear DNA must contend with chromatin. As results from ENCODE show, open chromatin assays can efficiently integrate across diverse regulatory elements, revealing functional non-coding genome. In this study, we use a MNase hypersensitivity assay to discover open chromatin regions in the maize reference genome, B73. We show that maize MNase hypersensitive (MNase HS) regions localize around active genes and within recombination hotspots. We also demonstrate that they focus biased gene conversion at their flanks. Finally, we show that MNase HS regions – comprising less than 1% of the genome – consistently explain approximately 40% of the heritable phenotypic variance in diverse quantitative traits, with the remainder of the variance primarily explained by the coding sequence. Altogether, our results imply that less than 3% of the maize genome may explain most of the variation in both molecular and organismal-level phenotypes, greatly narrowing the scope of the functional genome.