Genome‐wide screen of genes imprinted in sorghum endosperm, and the roles of allelic differential cytosine methylation

Meishan Zhang; Ning Li; Wenan He; Huakun Zhang; Wei Yang; Bao Liu

doi:10.1111/tpj.13116

journal article Jan 30, 2016

Genome‐wide screen of genes imprinted in sorghum endosperm, and the roles of allelic differential cytosine methylation

Meishan Zhang Ning Li

Wenan He Huakun Zhang

Wei Yang

Bao Liu

The Plant Journal Vol. 85 No. 3 pp. 424-436 · Wiley

View at Publisher Save 10.1111/tpj.13116

Abstract

SummaryImprinting is an epigenetic phenomenon referring to allele‐biased expression of certain genes depending on their parent of origin. Accumulated evidence suggests that, while imprinting is a conserved mechanism across kingdoms, the identities of the imprinted genes are largely species‐specific. Using deep RNA sequencing of endosperm 14 days after pollination in sorghum, 5683 genes (29.27% of the total 19 418 expressed genes) were found to harbor diagnostic single nucleotide polymorphisms between two parental lines. The analysis of parent‐of‐origin expression patterns in the endosperm of a pair of reciprocal F1 hybrids between the two sorghum lines led to identification of 101 genes with ≥ fivefold allelic expression difference in both hybrids, including 85 maternal expressed genes (MEGs) and 16 paternal expressed genes (PEGs). Thirty of these genes were previously identified as imprinted in endosperm of maize (Zea mays), rice (Oryza sativa) or Arabidopsis, while the remaining 71 genes are sorghum‐specific imprinted genes relative to these three plant species. Allele‐biased expression of virtually all of the 14 tested imprinted genes (nine MEGs and five PEGs) was validated by pyrosequencing using independent sources of RNA from various developmental stages and dissected parts of endosperm. Forty‐six imprinted genes (30 MEGs and 16 PEGs) were assayed by quantitative RT–PCR, and the majority of them showed endosperm‐specific or preferential expression relative to embryo and other tissues. DNA methylation analysis of the 5’ upstream region and gene body for seven imprinted genes indicated that, while three of the four PEGs were associated with hypomethylation of maternal alleles, no MEG was associated with allele‐differential methylation.

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Details

Published: Jan 30, 2016
Vol/Issue: 85(3)
Pages: 424-436
License: View

Authors

M

Meishan Zhang

Department of Agronomy Jilin Agricultural University Changchun 130118 China; Key Laboratory of Molecular Epigenetics of the Ministry of Education Northeast Normal University Changchun 130024 China

N

Ning Li

Key Laboratory of Molecular Epigenetics of the Ministry of Education Northeast Normal University Changchun 130024 China

W

Wenan He

Department of Agronomy Jilin Agricultural University Changchun 130118 China

H

Huakun Zhang

Key Laboratory of Molecular Epigenetics of the Ministry of Education Northeast Normal University Changchun 130024 China

W

Wei Yang

Department of Agronomy Jilin Agricultural University Changchun 130118 China

B

Bao Liu

Key Laboratory of Molecular Epigenetics of the Ministry of Education Northeast Normal University Changchun 130024 China

Funding

National Natural Science Foundation of China Award: 31370341

Cite This Article

Meishan Zhang, Ning Li, Wenan He, et al. (2016). Genome‐wide screen of genes imprinted in sorghum endosperm, and the roles of allelic differential cytosine methylation. The Plant Journal, 85(3), 424-436. https://doi.org/10.1111/tpj.13116

Genome‐wide screen of genes imprinted in sorghum endosperm, and the roles of allelic differential cytosine methylation

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