Dynamic parent-of-origin effects on small interfering RNA expression in the developing maize endosperm

Persistent Link:
http://hdl.handle.net/10150/610088
Title:
Dynamic parent-of-origin effects on small interfering RNA expression in the developing maize endosperm
Author:
Xin, Mingming; Yang, Ruolin; Yao, Yingyin; Ma, Chuang; Peng, Huiru; Sun, Qixin; Wang, Xiangfeng; Ni, Zhongfu
Affiliation:
State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, China; School of Plant Sciences, University of Arizona, 1145 E. South Campus Drive, Tucson 85721-0036, AZ, USA
Issue Date:
2014
Publisher:
BioMed Central
Citation:
Xin et al. BMC Plant Biology 2014, 14:192 http://www.biomedcentral.com/1471-2229/14/192
Journal:
BMC Plant Biology
Rights:
© 2014 Xin et al., licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
Background:In angiosperms, the endosperm plays a crucial placenta-like role in that not only is it necessary for nurturing the embryo, but also regulating embryogenesis through complicated genetic and epigenetic interactions with other seed compartments and is the primary tissue in which genomic imprinting occurs.Results:We observed a gradual increase of paternal siRNA expression in the early stages of kernels and an expected 2:1 maternal to paternal ratio in 7-DAP endosperm via sequencing of small interfering RNA (siRNA) transcriptomes in developing kernels (0, 3 and 5 days after pollination (DAP)) and endosperms (7, 10 and 15 DAP) from the maize B73 and Mo17 reciprocal crosses. Additionally, 460 imprinted siRNA loci were identified in the endosperm, with the majority (456/460, 99.1%) being maternally expressed at 10 DAP. Moreover, 13 out of 29 imprinted genes harbored imprinted siRNA loci within their 2-kb flanking regions, a significant higher frequency than expected based on simulation analysis. Additionally, gene ontology terms of "response to auxin stimulus", "response to brassinosteroid stimulus" and "regulation of gene expression" were enriched with genes harboring 10-DAP specific siRNAs, whereas those of "nutrient reservoir activity", "protein localization to vacuole" and "secondary metabolite biosynthetic process" were enriched with genes harboring 15-DAP specific siRNAs.Conclusions:A subset of siRNAs subjected to imprinted expression pattern in maize developing endosperm, and they are likely correlated with certain imprinted gene expression. Additionally, siRNAs might influence nutrient uptake and allocation processes during maize endosperm development.
EISSN:
1471-2229
DOI:
10.1186/s12870-014-0192-8
Keywords:
siRNA; Imprinting; Maize; Endosperm; GSE52726
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2229/14/192

Full metadata record

DC FieldValue Language
dc.contributor.authorXin, Mingmingen
dc.contributor.authorYang, Ruolinen
dc.contributor.authorYao, Yingyinen
dc.contributor.authorMa, Chuangen
dc.contributor.authorPeng, Huiruen
dc.contributor.authorSun, Qixinen
dc.contributor.authorWang, Xiangfengen
dc.contributor.authorNi, Zhongfuen
dc.date.accessioned2016-05-20T08:58:17Z-
dc.date.available2016-05-20T08:58:17Z-
dc.date.issued2014en
dc.identifier.citationXin et al. BMC Plant Biology 2014, 14:192 http://www.biomedcentral.com/1471-2229/14/192en
dc.identifier.doi10.1186/s12870-014-0192-8en
dc.identifier.urihttp://hdl.handle.net/10150/610088-
dc.description.abstractBackground:In angiosperms, the endosperm plays a crucial placenta-like role in that not only is it necessary for nurturing the embryo, but also regulating embryogenesis through complicated genetic and epigenetic interactions with other seed compartments and is the primary tissue in which genomic imprinting occurs.Results:We observed a gradual increase of paternal siRNA expression in the early stages of kernels and an expected 2:1 maternal to paternal ratio in 7-DAP endosperm via sequencing of small interfering RNA (siRNA) transcriptomes in developing kernels (0, 3 and 5 days after pollination (DAP)) and endosperms (7, 10 and 15 DAP) from the maize B73 and Mo17 reciprocal crosses. Additionally, 460 imprinted siRNA loci were identified in the endosperm, with the majority (456/460, 99.1%) being maternally expressed at 10 DAP. Moreover, 13 out of 29 imprinted genes harbored imprinted siRNA loci within their 2-kb flanking regions, a significant higher frequency than expected based on simulation analysis. Additionally, gene ontology terms of "response to auxin stimulus", "response to brassinosteroid stimulus" and "regulation of gene expression" were enriched with genes harboring 10-DAP specific siRNAs, whereas those of "nutrient reservoir activity", "protein localization to vacuole" and "secondary metabolite biosynthetic process" were enriched with genes harboring 15-DAP specific siRNAs.Conclusions:A subset of siRNAs subjected to imprinted expression pattern in maize developing endosperm, and they are likely correlated with certain imprinted gene expression. Additionally, siRNAs might influence nutrient uptake and allocation processes during maize endosperm development.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2229/14/192en
dc.rights© 2014 Xin et al., licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)en
dc.subjectsiRNAen
dc.subjectImprintingen
dc.subjectMaizeen
dc.subjectEndospermen
dc.subjectGSE52726en
dc.titleDynamic parent-of-origin effects on small interfering RNA expression in the developing maize endospermen
dc.typeArticleen
dc.identifier.eissn1471-2229en
dc.contributor.departmentState Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, Chinaen
dc.contributor.departmentSchool of Plant Sciences, University of Arizona, 1145 E. South Campus Drive, Tucson 85721-0036, AZ, USAen
dc.identifier.journalBMC Plant Biologyen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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