Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: cross-species 2D GWAS reveals the underlying genetics.
Adaptation, Physiological
/ genetics
Disease Resistance
/ genetics
Gene Expression Regulation, Bacterial
Gene Expression Regulation, Plant
Genome, Bacterial
Genome, Plant
Genome-Wide Association Study
Host-Pathogen Interactions
/ genetics
Linkage Disequilibrium
Oryza
/ genetics
Phylogeny
Plant Breeding
Plant Diseases
/ genetics
Polymorphism, Single Nucleotide
Virulence
/ genetics
Whole Genome Sequencing
Xanthomonas
/ genetics
Journal
The Plant cell
ISSN: 1532-298X
Titre abrégé: Plant Cell
Pays: England
ID NLM: 9208688
Informations de publication
Date de publication:
31 08 2021
31 08 2021
Historique:
received:
01
06
2021
accepted:
15
05
2021
entrez:
1
9
2021
pubmed:
2
9
2021
medline:
31
12
2021
Statut:
ppublish
Résumé
A 1D/2D genome-wide association study strategy was adopted to investigate the genetic systems underlying the reciprocal adaptation of rice (Oryza sativa) and its bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) using the whole-genome sequencing and large-scale phenotyping data of 701 rice accessions and 23 diverse Xoo strains. Forty-seven Xoo virulence-related genes and 318 rice quantitative resistance genes (QR-genes) mainly located in 41 genomic regions, and genome-wide interactions between the detected virulence-related genes and QR genes were identified, including well-known resistance genes/virulence genes plus many previously uncharacterized ones. The relationship between rice and Xoo was characterized by strong differentiation among Xoo races corresponding to the subspecific differentiation of rice, by strong shifts toward increased resistance/virulence of rice/Xoo populations and by rich genetic diversity at the detected rice QR-genes and Xoo virulence genes, and by genome-wide interactions between many rice QR-genes and Xoo virulence genes in a multiple-to-multiple manner, presumably resulting either from direct protein-protein interactions or from genetic epistasis. The observed complex genetic interaction system between rice and Xoo likely exists in other crop-pathogen systems that would maintain high levels of diversity at their QR-loci/virulence-loci, resulting in dynamic coevolutionary consequences during their reciprocal adaptation.
Identifiants
pubmed: 34467412
pii: 6291252
doi: 10.1093/plcell/koab146
pmc: PMC8408478
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2538-2561Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of American Society of Plant Biologists.
Références
Mol Plant. 2017 Sep 12;10(9):1246-1249
pubmed: 28624544
PLoS One. 2013 Oct 07;8(10):e75230
pubmed: 24116030
Metallomics. 2009;1(3):249-55
pubmed: 20161024
Microbiol Spectr. 2016 Apr;4(2):
pubmed: 27227310
Plant Sci. 2019 Feb;279:3-18
pubmed: 30709490
Int J Mol Sci. 2018 Oct 02;19(10):
pubmed: 30279356
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Mol Plant. 2015 Jun;8(6):946-57
pubmed: 25747843
Nat Commun. 2011 Sep 13;2:467
pubmed: 21915109
Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):E5163-71
pubmed: 27535938
ISME J. 2017 May;11(5):1189-1204
pubmed: 28117833
Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):8113-8118
pubmed: 28698366
Proc Natl Acad Sci U S A. 2018 Jun 12;115(24):E5440-E5449
pubmed: 29848634
PLoS Comput Biol. 2006 Sep 1;2(9):e115
pubmed: 16948529
Nat Genet. 2002 Dec;32(4):569-77
pubmed: 12457190
Sci Rep. 2020 Jul 28;10(1):12642
pubmed: 32724216
J Microbiol. 2015 Mar;53(3):201-8
pubmed: 25732741
Genome Med. 2014 Nov 15;6(11):101
pubmed: 25484920
Front Plant Sci. 2017 May 23;8:763
pubmed: 28588588
Sci Rep. 2016 Sep 26;6:34137
pubmed: 27667260
Science. 2012 Aug 17;337(6096):815
pubmed: 22767897
Gigascience. 2018 Jan 1;7(1):1-9
pubmed: 29220485
PLoS One. 2007 Feb 21;2(2):e224
pubmed: 17311090
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
BMC Genomics. 2012 Jan 31;13:49
pubmed: 22289642
Nature. 2018 May;557(7703):43-49
pubmed: 29695866
Proc Natl Acad Sci U S A. 2006 May 23;103(21):7994-9
pubmed: 16702555
Microb Genom. 2016 Oct 21;2(10):e000089
pubmed: 28348830
Nucleic Acids Res. 2017 Jan 4;45(D1):D1075-D1081
pubmed: 27899667
Front Plant Sci. 2017 Jul 25;8:1301
pubmed: 28791038
Annu Rev Phytopathol. 2015;53:541-63
pubmed: 26047564
Nucleic Acids Res. 2017 Jan 25;45(2):597-605
pubmed: 27940610
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
Phytopathology. 2010 Mar;100(3):262-70
pubmed: 20128700
Annu Rev Plant Biol. 2005;56:509-31
pubmed: 15862106
Theor Appl Genet. 2018 Dec;131(12):2733-2743
pubmed: 30225642
J Bacteriol. 2011 Jul;193(14):3606-17
pubmed: 21602354
Plant J. 1994 Aug;6(2):271-82
pubmed: 7920717
Plant Biotechnol J. 2017 Mar;15(3):306-317
pubmed: 27539813
Sci Rep. 2017 Jan 13;7:40694
pubmed: 28084432
Hum Genet. 2012 May;131(5):747-56
pubmed: 22143225
Mol Plant. 2015 Aug;8(8):1274-84
pubmed: 25917172
Mol Plant Pathol. 2009 Nov;10(6):735-47
pubmed: 19849781
Nature. 2005 Jun 23;435(7045):1122-5
pubmed: 15973413
Plant Cell. 1997 Aug;9(8):1279-87
pubmed: 9286106
Breed Sci. 2016 Sep;66(4):636-645
pubmed: 27795689
Gigascience. 2014 May 28;3:7
pubmed: 24872877
Bioinformatics. 2019 May 15;35(10):1786-1788
pubmed: 30321304
Mol Microbiol. 2014 Mar;91(5):950-64
pubmed: 24444429
Nucleic Acids Res. 2019 Jul 2;47(W1):W256-W259
pubmed: 30931475
BMC Genomics. 2008 May 01;9:204
pubmed: 18452608
Nat Genet. 2010 Apr;42(4):348-54
pubmed: 20208533
Science. 2018 Jun 22;360(6395):1300-1301
pubmed: 29930125
Antimicrob Agents Chemother. 1998 Sep;42(9):2225-31
pubmed: 9736539
Annu Rev Phytopathol. 2010;48:419-36
pubmed: 19400638
Genetics. 2001 Oct;159(2):757-65
pubmed: 11606550
Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8525-8534
pubmed: 30948631
Biochim Biophys Acta. 2013 Aug;1834(8):1660-70
pubmed: 23748134
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
BMC Genomics. 2014 Feb 26;15:162
pubmed: 24571581
Rice (N Y). 2013 Feb 06;6(1):4
pubmed: 24280374
Mol Plant Pathol. 2006 Sep;7(5):303-24
pubmed: 20507449
Phytopathology. 2016 Oct;106(10):1177-1185
pubmed: 27442533
PLoS Genet. 2006 Dec;2(12):e190
pubmed: 17194218
Phytopathology. 2003 Oct;93(10):1258-62
pubmed: 18944325
Plant Cell Environ. 2011 Nov;34(11):1958-69
pubmed: 21726237
Plant J. 2015 Nov;84(4):694-703
pubmed: 26426417
Sci Adv. 2015 Jul 24;1(6):e1500245
pubmed: 26601222
Mol Plant. 2012 Jan;5(1):281-90
pubmed: 21930802
Am J Hum Genet. 2007 Sep;81(3):559-75
pubmed: 17701901
Theor Appl Genet. 2020 Mar;133(3):689-705
pubmed: 31811315
Nat Genet. 2014 Jul;46(7):714-21
pubmed: 24908251
Mol Plant Pathol. 2018 Jan;19(1):3-6
pubmed: 29226559
Curr Opin Plant Biol. 2019 Aug;50:1-8
pubmed: 30861483
Plant Cell. 2014 Jan;26(1):497-515
pubmed: 24488961
PLoS One. 2019 Feb 12;14(2):e0211775
pubmed: 30753229
Nature. 2006 Nov 16;444(7117):323-9
pubmed: 17108957
Nat Commun. 2016 Oct 31;7:13308
pubmed: 27796364
Mol Plant. 2011 Mar;4(2):300-9
pubmed: 21208999
Genetics. 2000 Jun;155(2):945-59
pubmed: 10835412
Front Genet. 2015 Jun 10;6:208
pubmed: 26113860
Proc Natl Acad Sci U S A. 2000 Dec 5;97(25):13500-5
pubmed: 11095723
Theor Appl Genet. 2015 Oct;128(10):1933-43
pubmed: 26081948
Plant Physiol. 2009 Aug;150(4):1677-86
pubmed: 19458115
Plant J. 2004 Feb;37(4):517-27
pubmed: 14756760
Nucleic Acids Res. 2017 Jul 3;45(W1):W122-W129
pubmed: 28472432
Syst Biol. 2010 May;59(3):307-21
pubmed: 20525638
Bioinformatics. 2005 Jun 1;21(11):2791-3
pubmed: 15814564
Mol Plant. 2015 Feb;8(2):290-302
pubmed: 25616388
Int J Mol Sci. 2017 Sep 21;18(10):
pubmed: 28934168
Plant Cell. 1998 Nov;10(11):1817-32
pubmed: 9811791
Annu Rev Plant Biol. 2014;65:531-51
pubmed: 24274033
Plant J. 2015 May;82(4):632-43
pubmed: 25824104
Annu Rev Plant Physiol Plant Mol Biol. 1997 Jun;48:575-607
pubmed: 15012275
Annu Rev Phytopathol. 2014;52:213-41
pubmed: 24906128