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Characterization of imprinted genes in rice reveals post-fertilization regulation and conservation at some loci of imprinting in plant species

Chen Chen, Tingting Li, Shan Zhu, Zehou Liu, Zhenyuan Shi, Xiaoming Zheng, Rui Chen, Jianfeng Huang, Yi Shen, Shiyou Luo, Lei Wang, Qiao-Quan Liu, E Zhiguo
doi: https://doi.org/10.1101/143214
Chen Chen
aJiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
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  • For correspondence: chenchen@yzu.edu.cn ezhiguo@caas.cn
Tingting Li
bChina National Rice Research Institute, Hangzhou, China
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Shan Zhu
cRice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
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Zehou Liu
dChengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Zhenyuan Shi
aJiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
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Xiaoming Zheng
eInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facilities for Crop Gene Resources and Genetic Improvement, Beijing, China
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Rui Chen
fTianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, China
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Jianfeng Huang
gShanghai Biotechnology Corporation, Shanghai, China
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Yi Shen
hInstitute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Shiyou Luo
cRice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
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Lei Wang
bChina National Rice Research Institute, Hangzhou, China
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Qiao-Quan Liu
aJiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
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E Zhiguo
bChina National Rice Research Institute, Hangzhou, China
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  • For correspondence: chenchen@yzu.edu.cn ezhiguo@caas.cn
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Abstract

Genomic imprinting is an epigenetic phenomenon by which certain genes display monoallelic expression in a parent-of-origin-dependent manner. Hundreds of imprinted genes have been identified from several plant species. Here we identified, with a high level of confidence, 208 imprinted candidates from rice. Imprinted genes of rice showed limited association to the transposable elements, which is contrast to the findings in Arabidopsis. Generally, imprinting of rice is conserved within species, but intraspecific variations were confirmed here. Imprinting between cultivated rice and wild rice are likely similar. The imprinted genes of rice do not show significant selective signatures overall, which suggests that domestication imposes limited evolutionary effects on genomic imprinting of rice. Though the conservation of imprinting in plants is limited, here we prove that some loci tend to be imprinted in different species. In addition, our results suggest that differential epigenetic regulation between parental alleles can be established either prior to or post-fertilization. The imprinted 24-nt small RNAs, but not the 21-nt ones, likely involve the regulation of imprinting in an opposite parental-allele targeting manner. Together, our findings suggest that regulation of imprinting can be very diverse, and genomic imprinting as well as imprinted genes have essential evolutionary and biological significance.

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Posted May 28, 2017.
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Characterization of imprinted genes in rice reveals post-fertilization regulation and conservation at some loci of imprinting in plant species
Chen Chen, Tingting Li, Shan Zhu, Zehou Liu, Zhenyuan Shi, Xiaoming Zheng, Rui Chen, Jianfeng Huang, Yi Shen, Shiyou Luo, Lei Wang, Qiao-Quan Liu, E Zhiguo
bioRxiv 143214; doi: https://doi.org/10.1101/143214
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Characterization of imprinted genes in rice reveals post-fertilization regulation and conservation at some loci of imprinting in plant species
Chen Chen, Tingting Li, Shan Zhu, Zehou Liu, Zhenyuan Shi, Xiaoming Zheng, Rui Chen, Jianfeng Huang, Yi Shen, Shiyou Luo, Lei Wang, Qiao-Quan Liu, E Zhiguo
bioRxiv 143214; doi: https://doi.org/10.1101/143214

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