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Genome‐wide screen of genes imprinted in sorghum endosperm, and the roles of allelic differential cytosine methylation
Author(s) -
Zhang Meishan,
Li Ning,
He Wenan,
Zhang Huakun,
Yang Wei,
Liu Bao
Publication year - 2016
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.13116
Subject(s) - biology , endosperm , genomic imprinting , genetics , gene , imprinting (psychology) , dna methylation , epigenetics , allele , gene expression
Summary Imprinting 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 F 1 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 ( MEG s) and 16 paternal expressed genes ( PEG s). 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 MEG s and five PEG s) was validated by pyrosequencing using independent sources of RNA from various developmental stages and dissected parts of endosperm. Forty‐six imprinted genes (30 MEG s and 16 PEG s) 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 PEG s were associated with hypomethylation of maternal alleles, no MEG was associated with allele‐differential methylation.