Variations of five eIF4E genes across cassava accessions exhibiting tolerant and susceptible responses to cassava brown streak disease

Persistent Link:
http://hdl.handle.net/10150/625479
Title:
Variations of five eIF4E genes across cassava accessions exhibiting tolerant and susceptible responses to cassava brown streak disease
Author:
Shi, Shanshan; Zhang, Xiuchun; Mandel, M. Alejandra; Zhang, Peng; Zhang, Yuliang; Ferguson, Morag; Amuge, Teddy; Rounsley, Steve; Liu, Zhixin; Xiong, Zhongguo ( 0000-0002-2999-0840 )
Affiliation:
Univ Arizona, Sch Plant Sci; Univ Arizona, Inst BIO5
Issue Date:
2017-08-03
Publisher:
PUBLIC LIBRARY SCIENCE
Citation:
Variations of five eIF4E genes across cassava accessions exhibiting tolerant and susceptible responses to cassava brown streak disease 2017, 12 (8):e0181998 PLOS ONE
Journal:
PLOS ONE
Rights:
© 2017 Shi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License.
Collection Information:
This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.
Abstract:
Cassava (Manihot esculenta) is an important tropical subsistence crop that is severely affected by cassava brown streak disease (CBSD) in East Africa. The disease is caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Both have a (+)-sense single-stranded RNA genome with a 5' covalently-linked viral protein, which functionally resembles the cap structure of mRNA, binds to eukaryotic translation initiation factor 4E (eIF4E) or its analogues, and then enable the translation of viral genomic RNA in host cells. To characterize cassava eIF4Es and their potential role in CBSD tolerance and susceptibility, we cloned five eIF4E transcripts from cassava (accession TMS60444). Sequence analysis indicated that the cassava eIF4E family of proteins consisted of one eIF4E, two eIF(iso) 4E, and two divergent copies of novel cap-binding proteins (nCBPs). Our data demonstrated experimentally the coding of these five genes as annotated in the published cassava genome and provided additional evidence for refined annotations. Illumina resequencing data of the five eIF4E genes were analyzed from 14 cassava lines tolerant or susceptible to CBSD. Abundant single nucleotide polymorphisms (SNP) and biallelic variations were observed in the eIF4E genes; however, most of the SNPs were located in the introns and non-coding regions of the exons. Association studies of non-synonymous SNPs revealed no significant association between any SNP of the five eIF4E genes and the tolerance or susceptibility to CBSD. However, two SNPs in two genes were weakly associated with the CBSD responses but had no direct causal-effect relationship. SNPs in an intergenic region upstream of eIF4E_me showed a surprising strong association with CBSD responses. Digital expression profile analysis showed differential expression of different eIF4E genes but no significant difference in gene expression was found between susceptible and tolerant cassava accessions despite the association of the intergenic SNPs with CBSD responses.
Note:
Open access journal.
ISSN:
1932-6203
PubMed ID:
28771520
DOI:
10.1371/journal.pone.0181998
Version:
Final published version
Sponsors:
Bill and Melinda Gates Foundation [OPP1068522]; Natural Science Foundation of China [31461143016]; Genus plc
Additional Links:
http://dx.plos.org/10.1371/journal.pone.0181998

Full metadata record

DC FieldValue Language
dc.contributor.authorShi, Shanshanen
dc.contributor.authorZhang, Xiuchunen
dc.contributor.authorMandel, M. Alejandraen
dc.contributor.authorZhang, Pengen
dc.contributor.authorZhang, Yuliangen
dc.contributor.authorFerguson, Moragen
dc.contributor.authorAmuge, Teddyen
dc.contributor.authorRounsley, Steveen
dc.contributor.authorLiu, Zhixinen
dc.contributor.authorXiong, Zhongguoen
dc.date.accessioned2017-09-12T23:47:37Z-
dc.date.available2017-09-12T23:47:37Z-
dc.date.issued2017-08-03-
dc.identifier.citationVariations of five eIF4E genes across cassava accessions exhibiting tolerant and susceptible responses to cassava brown streak disease 2017, 12 (8):e0181998 PLOS ONEen
dc.identifier.issn1932-6203-
dc.identifier.pmid28771520-
dc.identifier.doi10.1371/journal.pone.0181998-
dc.identifier.urihttp://hdl.handle.net/10150/625479-
dc.description.abstractCassava (Manihot esculenta) is an important tropical subsistence crop that is severely affected by cassava brown streak disease (CBSD) in East Africa. The disease is caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Both have a (+)-sense single-stranded RNA genome with a 5' covalently-linked viral protein, which functionally resembles the cap structure of mRNA, binds to eukaryotic translation initiation factor 4E (eIF4E) or its analogues, and then enable the translation of viral genomic RNA in host cells. To characterize cassava eIF4Es and their potential role in CBSD tolerance and susceptibility, we cloned five eIF4E transcripts from cassava (accession TMS60444). Sequence analysis indicated that the cassava eIF4E family of proteins consisted of one eIF4E, two eIF(iso) 4E, and two divergent copies of novel cap-binding proteins (nCBPs). Our data demonstrated experimentally the coding of these five genes as annotated in the published cassava genome and provided additional evidence for refined annotations. Illumina resequencing data of the five eIF4E genes were analyzed from 14 cassava lines tolerant or susceptible to CBSD. Abundant single nucleotide polymorphisms (SNP) and biallelic variations were observed in the eIF4E genes; however, most of the SNPs were located in the introns and non-coding regions of the exons. Association studies of non-synonymous SNPs revealed no significant association between any SNP of the five eIF4E genes and the tolerance or susceptibility to CBSD. However, two SNPs in two genes were weakly associated with the CBSD responses but had no direct causal-effect relationship. SNPs in an intergenic region upstream of eIF4E_me showed a surprising strong association with CBSD responses. Digital expression profile analysis showed differential expression of different eIF4E genes but no significant difference in gene expression was found between susceptible and tolerant cassava accessions despite the association of the intergenic SNPs with CBSD responses.en
dc.description.sponsorshipBill and Melinda Gates Foundation [OPP1068522]; Natural Science Foundation of China [31461143016]; Genus plcen
dc.language.isoenen
dc.publisherPUBLIC LIBRARY SCIENCEen
dc.relation.urlhttp://dx.plos.org/10.1371/journal.pone.0181998en
dc.rights© 2017 Shi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License.en
dc.titleVariations of five eIF4E genes across cassava accessions exhibiting tolerant and susceptible responses to cassava brown streak diseaseen
dc.typeArticleen
dc.contributor.departmentUniv Arizona, Sch Plant Scien
dc.contributor.departmentUniv Arizona, Inst BIO5en
dc.identifier.journalPLOS ONEen
dc.description.noteOpen access journal.en
dc.description.collectioninformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen

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