NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE145586 Query DataSets for GSE145586
Status Public on Sep 23, 2020
Title Evolutionary and functional genomics of DNA methylation in maize domestication and improvement
Organism Zea mays
Experiment type Other
Methylation profiling by high throughput sequencing
Summary DNA methylation is a ubiquitous chromatin feature — in maize, more than 25% of cytosines in the genome are methylated. Recently, major progress has been made in describing the molecular mechanisms driving methylation, yet variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here we leveraged whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to investigate the adaptive and phenotypic consequences of methylation variations in maize. By using a novel estimation approach, we inferred the methylome site frequency spectrum (mSFS) to estimate forward and backward methylation mutation rates and selection coefficients. We only found weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) were identified in population-wide that are correlated with recent selection. Further investigation revealed that DMRs are enriched in 5’ untranslated regions, and that maize hypomethylated DMRs likely helped rewire distal gene regulation. For two trait-associated DMRs, vgt1-DMR and tb1DMR, our HiChIP data indicated that the interactive loops between DMRs and respective downstream genes were present in B73, a modern maize line, but absent in teosinte. Functional analyses suggested that these DMRs likely served as cis-acting elements that modulated gene regulation after domestication. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.
 
Overall design We collected whole-genome sequencing and bisulfite sequencing data of 51 samples, including the wild ancestor of maize — teosinte (Zea mays ssp. parviglumis, N=20), Mexican landraces (N=17),and modern maize inbred lines (N=14) to understand the impact of epigenetics on maize domestication.
The "modern maize inbred lines (N=14)" were downloaded from NCBI. The descriptive details for all 51 samples are in supplementary file metadata_51samples.xls.
 
Contributor(s) Xu G, Lyu J, Li Q, Liu H, Wang D, Zhang M, M.Springer N, Ross-Ibarra J, Yang J
Citation(s) 33139747
Submission date Feb 20, 2020
Last update date Nov 13, 2020
Contact name GEN XU
E-mail(s) jsycxugen@gmail.com
Organization name University of Nebraska-Lincoln
Street address 383 Plant Science Hall Department of Agronomy and Horticulture
City Lincoln
State/province Nebraska
ZIP/Postal code 68503
Country USA
 
Platforms (2)
GPL15463 Illumina HiSeq 2000 (Zea mays)
GPL17628 Illumina HiSeq 2500 (Zea mays)
Samples (74)
GSM4321815 Teosinte WGS_JRIAL2A
GSM4321816 Teosinte WGS_JRIAL2B
GSM4321817 Teosinte WGS_JRIAL2C
Relations
BioProject PRJNA607675
SRA SRP250084

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE145586_Table_S1_DMR.bed.gz 60.4 Kb (ftp)(http) BED
GSE145586_Table_S2_Selective_sweep.bed.gz 57.2 Kb (ftp)(http) BED
GSE145586_metadata_51samples.xls.gz 15.0 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap