Epigenetic modification contributes to the expression divergence of three TaEXPA1 homoeologs in hexaploid wheat (Triticum aestivum).
Common wheat is a hexaploid species with most of the genes present as triplicate homoeologs. Expression divergences of homoeologs are frequently observed in wheat, as well as in other polyploid plants. However, the mechanisms underlying this phenomenon are poorly understood. Expansin genes play important roles in the regulation of cell size, as well as organ size. We found that all three TaEXPA1 homoeologs were silenced in seedling roots. In seedling leaves, TaEXPA1-A and TaEXPA1-D were expressed, but TaEXPA1-B was silenced. Further analysis revealed that silencing of TaEXPA1-B in leaves occurred after the formation of the hexaploid. Chromatin immunoprecipitation assays revealed that the transcriptional silencing of three TaEXPA1 homoeologs in roots was correlated with an increased level of H3K9 dimethylation and decreased levels of H3K4 trimethylation and H3K9 acetylation. Reactivation of TaEXPA1-A and TaEXPA1-D expression in leaves was correlated with increased levels of H3K4 trimethylation and H3K9 acetylation, and decreased levels of H3K9 dimethylation in their promoters, respectively. Moreover, a higher level of cytosine methylation was detected in the promoter region of TaEXPA1-B, which may contribute to its silencing in leaves. We demonstrated that epigenetic modifications contribute to the expression divergence of three TaEXPA1 homoeologs during wheat development.
State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.|National Plant Gene Research Centre (Beijing), Beijing, 100193, China.|Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China.
Zhaorong
Z
Hu
State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.|National Plant Gene Research Centre (Beijing), Beijing, 100193, China.|Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China.
Zongfu
Z
Han
State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.|National Plant Gene Research Centre (Beijing), Beijing, 100193, China.|Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China.
Na
N
Song
State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.|National Plant Gene Research Centre (Beijing), Beijing, 100193, China.|Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China.
Lingling
L
Chai
State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.|National Plant Gene Research Centre (Beijing), Beijing, 100193, China.|Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China.
Yingyin
Y
Yao
State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.|National Plant Gene Research Centre (Beijing), Beijing, 100193, China.|Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China.
Huiru
H
Peng
State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.|National Plant Gene Research Centre (Beijing), Beijing, 100193, China.|Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China.
Zhongfu
Z
Ni
State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.|National Plant Gene Research Centre (Beijing), Beijing, 100193, China.|Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China.
Qixin
Q
Sun
D000107:Acetylation; D001483:Base Sequence; D047369:Chromatin Immunoprecipitation; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D020868:Gene Silencing; D006657:Histones / Q000737:chemistry / Q000378:metabolism*; D008745:Methylation; D008969:Molecular Sequence Data; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D016415:Sequence Alignment; D014908:Triticum / Q000235:genetics* / Q000378:metabolism
D006657:Histones; D010940:Plant Proteins