RNA Sequencing-Based Transcriptome Analysis in Response to Different Types and Doses of Ionizing Radiation in Rice

Ionizing radiation (IR) is regarded as an abiotic stressor for plants because it causes oxidative stress and changes the expression of genes. We investigated RNA sequencing-based global transcriptome changes induced by three different types of IR (gamma rays (GR), ion beams (IB), and proton beams (P...

Full description

Saved in:
Bibliographic Details
Published inPlant breeding and biotechnology Vol. 9; no. 3; pp. 213 - 226
Main Authors Park, Jae Wan, Lee, Gileung, Kim, Jin-Baek, Choi, Hong-Il
Format Journal Article
LanguageEnglish
Published 한국육종학회 01.09.2021
Subjects
농학
Online AccessGet full text
ISSN2287-9358
2287-9366
DOI10.9787/PBB.2021.9.3.213

Cover

Abstract Ionizing radiation (IR) is regarded as an abiotic stressor for plants because it causes oxidative stress and changes the expression of genes. We investigated RNA sequencing-based global transcriptome changes induced by three different types of IR (gamma rays (GR), ion beams (IB), and proton beams (PB)) at different doses in rice. On average, 489 upregulated and 234 downregulated differentially expressed genes (DEGs) were found per sample. The union of the DEGs for each IR type was collected to simplify the comparison of effects among the different IR treatments. This resulted to a total of 1,558 DEGs after GR irradiation, 1,865 DEGs after IB irradiation, and 1,347 DEGs after PB irradiation. The gene ontology (GO) enrichment analysis of the union DEG sets revealed 69 and 12 commonly enriched GO terms for up- and downregulated DEGs, respectively, many of which were closely related to oxidative stress responses. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway mapping and enrichment analysis of the union DEG sets also showed that most of the DEGs fell into common pathways related to oxidative stress, stress signaling, and redox reactions. A total of 137 transcription factor (TF) genes were differentially expressed, and many belong to families associated with stress responses. Our results suggest that different types and doses of IR can induce universal gene expression changes in response to oxidative stress. This study contributes to our understanding of the molecular response mechanisms to IR in plants. KCI Citation Count: 0
AbstractList Ionizing radiation (IR) is regarded as an abiotic stressor for plants because it causes oxidative stress and changes the expression of genes. We investigated RNA sequencing-based global transcriptome changes induced by three different types of IR (gamma rays (GR), ion beams (IB), and proton beams (PB)) at different doses in rice. On average, 489 upregulated and 234 downregulated differentially expressed genes (DEGs) were found per sample. The union of the DEGs for each IR type was collected to simplify the comparison of effects among the different IR treatments. This resulted to a total of 1,558 DEGs after GR irradiation, 1,865 DEGs after IB irradiation, and 1,347 DEGs after PB irradiation. The gene ontology (GO) enrichment analysis of the union DEG sets revealed 69 and 12 commonly enriched GO terms for up- and downregulated DEGs, respectively, many of which were closely related to oxidative stress responses. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway mapping and enrichment analysis of the union DEG sets also showed that most of the DEGs fell into common pathways related to oxidative stress, stress signaling, and redox reactions. A total of 137 transcription factor (TF) genes were differentially expressed, and many belong to families associated with stress responses. Our results suggest that different types and doses of IR can induce universal gene expression changes in response to oxidative stress. This study contributes to our understanding of the molecular response mechanisms to IR in plants. KCI Citation Count: 0
Author Lee, Gileung
Park, Jae Wan
Choi, Hong-Il
Kim, Jin-Baek
Author_xml – sequence: 1
  givenname: Jae Wan
  surname: Park
  fullname: Park, Jae Wan
  organization: Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea
– sequence: 2
  givenname: Gileung
  surname: Lee
  fullname: Lee, Gileung
  organization: Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea
– sequence: 3
  givenname: Jin-Baek
  surname: Kim
  fullname: Kim, Jin-Baek
  organization: Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea
– sequence: 4
  givenname: Hong-Il
  surname: Choi
  fullname: Choi, Hong-Il
  organization: Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea
BackLink https://www.kci.go.kr/kciportal/ci/sereArticleSearch/ciSereArtiView.kci?sereArticleSearchBean.artiId=ART002747088$$DAccess content in National Research Foundation of Korea (NRF)
BookMark eNp1kD1PwzAYhC1UJErpzuiVIcGO4yQe05aPShWgEGbLdezKtLWLHYby63FbxICE9Ep3wz0nvXcJBtZZBcA1Rikrq_L2ZTJJM5ThlKUkzTA5A8Msq8qEkaIY_HpaXYBxCO8IIYwRRSwfAt881fBVfXwqK41dJRMRVAdbL2yQ3ux6t1WwtmKzDyZAY2Gjws7ZoGDv4MxorbyyPWz3OxWgsB2cuRCd03DurPmKjbARnRG9cfaIG6muwLkWm6DGPzoCb_d37fQxWTw_zKf1IpGYZX2Cl5iQospxV3WIEoyWrGQqz3BJSkVLvew0zTUpScUkUiRmtCRZheIJKmlHRuDm1Gu95mtpuBPmqCvH157XTTvnrKKkoDRm0SkrvQvBK8133myF33OM-GFiHifmh4k544THiSNS_EGk6Y-P9l6Yzf_gN1ARgYc
CitedBy_id crossref_primary_10_3390_ijms222112088
Cites_doi 10.3390/plants9111515
10.1104/pp.106.077073
10.1186/s13059-014-0550-8
10.1016/j.jenvrad.2018.09.018
10.1007/s11032-019-1052-x
10.1111/tpj.15010
10.1186/1471-2164-8-242
10.1186/s12864-019-5617-1
10.1038/srep27752
10.3389/fpls.2015.01092
10.1111/j.1467-7652.2004.00090.x
10.1269/jrr.40.59
10.1186/1471-2229-11-174
10.3390/f9060326
10.1016/j.gene.2010.03.011
10.1016/j.jenvrad.2019.02.001
10.1111/ppl.12121
10.1093/jxb/erh005
10.3390/qubs3020007
10.1038/srep23719
10.1093/bioinformatics/btu638
10.1007/s11071-011-0314-x
10.1186/s12864-015-1373-z
10.1111/j.1365-313X.2004.02016.x
10.1093/nar/gkx382
10.1111/pce.13907
10.1016/j.ejbt.2019.02.004
10.4061/2010/592980
10.3390/antiox9050454
10.1093/nar/gkp805
10.1016/j.plantsci.2011.05.015
10.1093/nar/gkw199
10.1016/j.bbagrm.2011.10.005
10.1371/journal.pone.0030619
10.3390/plants10030439
10.1534/genetics.106.061374
10.1038/srep22783
10.1093/bioinformatics/btp324
10.3389/fpls.2018.00847
10.1186/s12870-016-0766-8
10.3390/ijms19113298
10.1186/1471-2164-13-544
10.1002/pro.3711
10.1016/j.gene.2019.02.037
10.1007/s11033-012-2034-9
10.1007/s13205-019-1742-4
10.3389/fpls.2016.00187
10.3389/fpls.2015.00678
10.3389/fpls.2014.00206
10.1007/s12042-016-9170-7
10.1111/nph.12797
10.1186/s12870-016-0771-y
10.3389/fpls.2018.01771
10.1016/S0014-5793(01)02460-7
10.1016/j.envexpbot.2010.01.007
10.1590/1678-4685-gmb-2017-0284
10.1016/j.tplants.2004.08.009
ContentType Journal Article
DBID AAYXX
CITATION
ACYCR
DOI 10.9787/PBB.2021.9.3.213
DatabaseName CrossRef
Korean Citation Index
DatabaseTitle CrossRef
DatabaseTitleList
DeliveryMethod fulltext_linktorsrc
EISSN 2287-9366
EndPage 226
ExternalDocumentID oai_kci_go_kr_ARTI_9853655
10_9787_PBB_2021_9_3_213
GroupedDBID AAYXX
ALMA_UNASSIGNED_HOLDINGS
CITATION
DYU
OK1
OZF
P5Y
ACYCR
ID FETCH-LOGICAL-c192t-1b1336841d8d05310b979e421737e57fbdf54f37389c0e3d05fc3280280a5c5d3
ISSN 2287-9358
IngestDate Fri May 09 03:29:03 EDT 2025
Thu Apr 24 23:03:37 EDT 2025
Tue Jul 01 01:15:39 EDT 2025
IsPeerReviewed true
IsScholarly true
Issue 3
Language English
LinkModel OpenURL
MergedId FETCHMERGED-LOGICAL-c192t-1b1336841d8d05310b979e421737e57fbdf54f37389c0e3d05fc3280280a5c5d3
Notes https://doi.org/10.9787/PBB.2021.9.3.213
PageCount 14
ParticipantIDs nrf_kci_oai_kci_go_kr_ARTI_9853655
crossref_primary_10_9787_PBB_2021_9_3_213
crossref_citationtrail_10_9787_PBB_2021_9_3_213
ProviderPackageCode CITATION
AAYXX
PublicationCentury 2000
PublicationDate 2021-09
PublicationDateYYYYMMDD 2021-09-01
PublicationDate_xml – month: 09
  year: 2021
  text: 2021-09
PublicationDecade 2020
PublicationTitle Plant breeding and biotechnology
PublicationYear 2021
Publisher 한국육종학회
Publisher_xml – name: 한국육종학회
References ref13
ref57
ref12
ref56
ref15
ref14
ref53
ref52
ref11
ref55
ref10
ref54
ref17
ref16
ref19
ref18
ref51
ref50
ref46
ref45
ref48
ref47
ref42
ref41
ref44
ref43
ref49
ref8
ref7
ref9
ref4
ref3
ref6
ref5
ref40
ref35
ref34
ref37
ref36
ref31
ref30
ref33
ref32
ref2
ref1
ref39
ref38
ref24
ref23
ref26
ref25
ref20
ref22
ref21
ref28
ref27
ref29
References_xml – ident: ref26
  doi: 10.3390/plants9111515
– ident: ref13
  doi: 10.1104/pp.106.077073
– ident: ref28
  doi: 10.1186/s13059-014-0550-8
– ident: ref51
  doi: 10.1016/j.jenvrad.2018.09.018
– ident: ref55
  doi: 10.1007/s11032-019-1052-x
– ident: ref6
  doi: 10.1111/tpj.15010
– ident: ref2
  doi: 10.1186/1471-2164-8-242
– ident: ref9
  doi: 10.1186/s12864-019-5617-1
– ident: ref11
  doi: 10.1038/srep27752
– ident: ref53
  doi: 10.3389/fpls.2015.01092
– ident: ref22
  doi: 10.1111/j.1467-7652.2004.00090.x
– ident: ref46
  doi: 10.1269/jrr.40.59
– ident: ref32
  doi: 10.1186/1471-2229-11-174
– ident: ref8
  doi: 10.3390/f9060326
– ident: ref29
  doi: 10.1016/j.gene.2010.03.011
– ident: ref12
  doi: 10.1016/j.jenvrad.2019.02.001
– ident: ref17
  doi: 10.1111/ppl.12121
– ident: ref4
  doi: 10.1093/jxb/erh005
– ident: ref18
  doi: 10.3390/qubs3020007
– ident: ref42
  doi: 10.1038/srep23719
– ident: ref1
  doi: 10.1093/bioinformatics/btu638
– ident: ref40
  doi: 10.1007/s11071-011-0314-x
– ident: ref50
  doi: 10.1186/s12864-015-1373-z
– ident: ref47
  doi: 10.1111/j.1365-313X.2004.02016.x
– ident: ref48
  doi: 10.1093/nar/gkx382
– ident: ref27
  doi: 10.1111/pce.13907
– ident: ref21
  doi: 10.1016/j.ejbt.2019.02.004
– ident: ref37
  doi: 10.4061/2010/592980
– ident: ref34
  doi: 10.3390/antiox9050454
– ident: ref36
  doi: 10.1093/nar/gkp805
– ident: ref7
  doi: 10.1016/j.plantsci.2011.05.015
– ident: ref38
  doi: 10.1093/nar/gkw199
– ident: ref33
  doi: 10.1016/j.bbagrm.2011.10.005
– ident: ref35
  doi: 10.1371/journal.pone.0030619
– ident: ref5
  doi: 10.3390/plants10030439
– ident: ref45
  doi: 10.1534/genetics.106.061374
– ident: ref15
  doi: 10.1038/srep22783
– ident: ref25
  doi: 10.1093/bioinformatics/btp324
– ident: ref3
  doi: 10.3389/fpls.2018.00847
– ident: ref39
  doi: 10.1186/s12870-016-0766-8
– ident: ref56
  doi: 10.3390/ijms19113298
– ident: ref20
  doi: 10.1186/1471-2164-13-544
– ident: ref19
  doi: 10.1002/pro.3711
– ident: ref54
  doi: 10.1016/j.gene.2019.02.037
– ident: ref23
  doi: 10.1007/s11033-012-2034-9
– ident: ref52
  doi: 10.1007/s13205-019-1742-4
– ident: ref41
  doi: 10.3389/fpls.2016.00187
– ident: ref57
  doi: 10.3389/fpls.2015.00678
– ident: ref16
  doi: 10.3389/fpls.2014.00206
– ident: ref30
  doi: 10.1007/s12042-016-9170-7
– ident: ref44
  doi: 10.1111/nph.12797
– ident: ref49
  doi: 10.1186/s12870-016-0771-y
– ident: ref14
  doi: 10.3389/fpls.2018.01771
– ident: ref24
  doi: 10.1016/S0014-5793(01)02460-7
– ident: ref10
  doi: 10.1016/j.envexpbot.2010.01.007
– ident: ref43
  doi: 10.1590/1678-4685-gmb-2017-0284
– ident: ref31
  doi: 10.1016/j.tplants.2004.08.009
SSID ssj0001105094
Score 2.1629632
Snippet Ionizing radiation (IR) is regarded as an abiotic stressor for plants because it causes oxidative stress and changes the expression of genes. We investigated...
SourceID nrf
crossref
SourceType Open Website
Enrichment Source
Index Database
StartPage 213
SubjectTerms 농학
Title RNA Sequencing-Based Transcriptome Analysis in Response to Different Types and Doses of Ionizing Radiation in Rice
URI https://www.kci.go.kr/kciportal/ci/sereArticleSearch/ciSereArtiView.kci?sereArticleSearchBean.artiId=ART002747088
Volume 9
hasFullText 1
inHoldings 1
isFullTextHit
isPrint
ispartofPNX Plant Breeding and Biotechnology, 2021, 9(3), , pp.213-226
link http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3da9swEBdp97KXsbGNdV-IMT2MYtdfsqVHO8loByujNNA9idqWRmgXj8x96R8_difZjpN90A2CEfLp7Oh-0t3JpxMhbzGJXCmE8SKwRsFBSY0ntJFeajiMPa2TzOYp-HiaHi-SDxf8YjL5MYpaumlLv7r97b6S_5Eq1IFccZfsP0h2YAoVUAb5whUkDNc7yfjsNIfBbmOhQQN5BWik2qUrt3NB83WUdGRpl-oxHtYeljHrDkZpD9ETdYmaZ813l4L2BAb6rY3Lw8wFfTjkWRcm19uyeN5RewgutdV_lkO5bNpf1urZvGBFwCRn8ymTc5ZPbaFgMtiQQMWMFQmb56wQ-HM1MtyQwB2JgRlwJ8-YSDq-RTjmUnAmgT-0BNpZz3c6XtyIwiF6y8HRkrt2OTLIXTt4TGgfFjHBexppCzkT080UGoE_6OGXXqftxnXp9rQdjyyAyO3h31Uu4G_j5-1PReHjq_rSj_2h4TiP945-3crkfVUt1ZdGXa0V-CsnSoK1lHK-R-5FWebCDD4vNmuEIWbnwcCI4Y-4L-34Kke7L7JlWe2t1mZkKJ0_JA86D4fmDq6PyESvHpM1QJXuQpVuQZX2UKXLFe2hStuGDlClFqoUgEYtVGljaA9VOkDVNgeoPiGL9_Pz6bHXHffhVeBmtF5YhnGciiSsRY2qIShlJnUCPnOcaZ6ZsjY8MZiJS1aBjoHGVHEkMDbgkle8jp-S_VWz0s8ITXkNlnkKzngikiqpZC2kKE0ktbksg1gfkKO-q1TV5cLHI1muFfjE2LkKOldh5yqpYgWde0DeDS2-uTwwf6F9A71vRf1nkT-_C9ELcn8zKl6S_XZ9o1-BEdyWry1SfgJ3L50h
linkProvider CAB International
openUrl ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=RNA+Sequencing-Based+Transcriptome+Analysis+in+Response+to+Different+Types+and+Doses+of+Ionizing+Radiation+in+Rice&rft.jtitle=Plant+breeding+and+biotechnology&rft.au=%EB%B0%95%EC%9E%AC%EC%9B%90&rft.au=%EC%9D%B4%EA%B8%B8%EC%9D%91&rft.au=%EA%B9%80%EC%A7%84%EB%B0%B1&rft.au=%EC%B5%9C%ED%99%8D%EC%9D%BC&rft.date=2021-09-01&rft.pub=%ED%95%9C%EA%B5%AD%EC%9C%A1%EC%A2%85%ED%95%99%ED%9A%8C&rft.issn=2287-9358&rft.eissn=2287-9366&rft.spage=213&rft.epage=226&rft_id=info:doi/10.9787%2FPBB.2021.9.3.213&rft.externalDBID=n%2Fa&rft.externalDocID=oai_kci_go_kr_ARTI_9853655
thumbnail_l http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2287-9358&client=summon
thumbnail_m http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2287-9358&client=summon
thumbnail_s http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2287-9358&client=summon