This article is part of a special issue on plant genomics.

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Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids

Guangming He1*, Beibei Chen23, Xuncheng Wang4, Xueyong Li25, Jigang Li12, Hang He1, Mei Yang1, Lu Lu6, Yijun Qi7, Xiping Wang6 and Xing Wang Deng12*

Author Affiliations

1 Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China

2 Department of Molecular, Cellular and Developmental Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA

3 Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China

4 Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Tsinghua Park No. 1, Haidian District, Beijing 100084, China

5 National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agriculture Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing 100081, China

6 College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing 100875, China

7 National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China

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Genome Biology 2013, 14:R57  doi:10.1186/gb-2013-14-6-r57

Published: 12 June 2013



Recent genome-wide studies suggested that in addition to genetic variations, epigenetic variations may also be associated with differential gene expression and growth vigor in plant hybrids. Maize is an ideal model system for the study of epigenetic variations in hybrids given the significant heterotic performance, the well-known complexity of the genome, and the rich history in epigenetic studies. However, integrated comparative transcriptomic and epigenomic analyses in different organs of maize hybrids remain largely unexplored.


Here, we generated integrated maps of transcriptomes and epigenomes of shoots and roots of two maize inbred lines and their reciprocal hybrids, and globally surveyed the epigenetic variations and their relationships with transcriptional divergence between different organs and genotypes. We observed that whereas histone modifications vary both between organs and between genotypes, DNA methylation patterns are more distinguishable between genotypes than between organs. Histone modifications were associated with transcriptomic divergence between organs and between hybrids and parents. Further, we show that genes up-regulated in both shoots and roots of hybrids were significantly enriched in the nucleosome assembly pathway. Interestingly, 22- and 24-nt siRNAs were shown to be derived from distinct transposable elements, and for different transposable elements in both shoots and roots, the differences in siRNA activity between hybrids and patents were primarily driven by different siRNA species.


These results suggest that despite variations in specific genes or genomic loci, similar mechanisms may account for the genome-wide epigenetic regulation of gene activity and transposon stability in different organs of maize hybrids.

maize hybrids; transcriptome; epigenome