Targeted exome sequencing of unselected heavy-ion beam-irradiated populations reveals less-biased mutation characteristics in the rice genome.
Base Sequence
DNA Mutational Analysis
DNA, Plant
/ genetics
Dose-Response Relationship, Radiation
Exome
/ genetics
Gene Expression Regulation, Plant
/ radiation effects
Heavy Ions
Mutagenesis
/ radiation effects
Mutation
/ radiation effects
Mutation Rate
Oryza
/ genetics
Seeds
/ genetics
Exome Sequencing
heavy-ion beam
mutagenesis
mutation rate
rice (Oryza sativa)
whole-exome sequencing
Journal
The Plant journal : for cell and molecular biology
ISSN: 1365-313X
Titre abrégé: Plant J
Pays: England
ID NLM: 9207397
Informations de publication
Date de publication:
04 2019
04 2019
Historique:
received:
09
08
2018
revised:
20
11
2018
accepted:
18
12
2018
pubmed:
26
12
2018
medline:
28
4
2020
entrez:
26
12
2018
Statut:
ppublish
Résumé
Heavy-ion beams have been widely utilized as a novel and effective mutagen for mutation breeding in diverse plant species, but the induced mutation spectrum is not fully understood at the genome scale. We describe the development of a multiplexed and cost-efficient whole-exome sequencing procedure in rice, and its application to characterize an unselected population of heavy-ion beam-induced mutations. The bioinformatics pipeline identified single-nucleotide mutations as well as small and large (>63 kb) insertions and deletions, and showed good agreement with the results obtained with conventional polymerase chain reaction (PCR) and sequencing analyses. We applied the procedure to analyze the mutation spectrum induced by heavy-ion beams at the population level. In total, 165 individual M
Identifiants
pubmed: 30584677
doi: 10.1111/tpj.14213
pmc: PMC6850588
doi:
Substances chimiques
DNA, Plant
0
Banques de données
GENBANK
['OID37934', 'SRP145251']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
301-314Informations de copyright
© 2019 The Authors The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.
Références
BMC Plant Biol. 2011 Nov 15;11:161
pubmed: 22085561
PLoS One. 2015 Apr 14;10(4):e0123872
pubmed: 25875648
Am J Hum Genet. 2012 Oct 5;91(4):597-607
pubmed: 23040492
Mutat Res. 2012 Jul 1;735(1-2):19-31
pubmed: 22579628
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
PLoS One. 2013 Aug 14;8(8):e70107
pubmed: 23967070
Plant J. 2015 Apr;82(1):93-104
pubmed: 25690092
Plant Cell. 2007 Jan;19(1):211-25
pubmed: 17209125
Int J Radiat Biol. 1994 Nov;66(5):427-32
pubmed: 7983426
Genes Genet Syst. 2013;88(3):189-97
pubmed: 24025247
Mutat Res. 2018 Jan;807:21-30
pubmed: 29268080
Mol Plant. 2016 Jul 6;9(7):1078-81
pubmed: 27018389
J Biol Chem. 1992 Jan 5;267(1):166-72
pubmed: 1730583
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Plant J. 2004 Apr;38(1):152-63
pubmed: 15053768
J Radiat Res. 2010;51(3):223-33
pubmed: 20505261
Nat Rev Genet. 2011 Sep 27;12(11):745-55
pubmed: 21946919
Genome Res. 2012 May;22(5):939-46
pubmed: 22267522
Plant J. 2017 Dec;92(6):1020-1030
pubmed: 29024116
J Radiat Res. 1999 Dec;40 Suppl:1-13
pubmed: 10804988
Fly (Austin). 2012 Apr-Jun;6(2):80-92
pubmed: 22728672
Rice (N Y). 2013 Feb 06;6(1):4
pubmed: 24280374
Bioinformatics. 2009 Nov 1;25(21):2865-71
pubmed: 19561018
J Zhejiang Univ Sci B. 2016 Dec.;17(12):905-915
pubmed: 27921396
Sci Rep. 2018 Jan 23;8(1):1394
pubmed: 29362368
Plant Cell. 2014 Apr 11;26(4):1382-1397
pubmed: 24728647
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
BMC Genomics. 2012 Nov 14;13:618
pubmed: 23148716
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
Genes Genet Syst. 2017 Mar 17;91(4):229-233
pubmed: 27452041