Dissecting the phenotypic components and genetic architecture of maize stem vascular bundles using high-throughput phenotypic analysis.
MaizeSPD
genome-wide association studies
maize stem
micro-CT
micro-phenotype
vascular bundle
Journal
Plant biotechnology journal
ISSN: 1467-7652
Titre abrégé: Plant Biotechnol J
Pays: England
ID NLM: 101201889
Informations de publication
Date de publication:
01 2021
01 2021
Historique:
received:
10
09
2019
revised:
03
06
2020
accepted:
15
06
2020
pubmed:
23
6
2020
medline:
22
4
2021
entrez:
23
6
2020
Statut:
ppublish
Résumé
High-throughput phenotyping is increasingly becoming an important tool for rapid advancement of genetic gain in breeding programmes. Manual phenotyping of vascular bundles is tedious and time-consuming, which lags behind the rapid development of functional genomics in maize. More robust and automated techniques of phenotyping vascular bundles traits at high-throughput are urgently needed for large crop populations. In this study, we developed a standard process for stem micro-CT data acquisition and an automatic CT image process pipeline to obtain vascular bundle traits of stems including geometry-related, morphology-related and distribution-related traits. Next, we analysed the phenotypic variation of stem vascular bundles between natural population subgroup (480 inbred lines) based on 48 comprehensively phenotypic information. Also, the first database for stem micro-phenotypes, MaizeSPD, was established, storing 554 pieces of basic information of maize inbred lines, 523 pieces of experimental information, 1008 pieces of CT scanning images and processed images, and 24 192 pieces of phenotypic data. Combined with genome-wide association studies (GWASs), a total of 1562 significant single nucleotide polymorphism (SNPs) were identified for 30 stem micro-phenotypic traits, and 84 unique genes of 20 traits such as VBNum, VBAvArea and PZVBDensity were detected. Candidate genes identified by GWAS mainly encode enzymes involved in cell wall metabolism, transcription factors, protein kinase and protein related to plant signal transduction and stress response. The results presented here will advance our knowledge about phenotypic trait components of stem vascular bundles and provide useful information for understanding the genetic controls of vascular bundle formation and development.
Identifiants
pubmed: 32569428
doi: 10.1111/pbi.13437
pmc: PMC7769239
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
35-50Informations de copyright
© 2020 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
Références
Plant Physiol. 2018 Apr;176(4):2677-2690
pubmed: 29475898
J Integr Plant Biol. 2012 May;54(5):300-11
pubmed: 22463712
Mol Plant. 2017 Mar 6;10(3):359-374
pubmed: 28039028
Genome Res. 2001 Nov;11(11):1817-25
pubmed: 11691845
BMC Plant Biol. 2012 Apr 30;12:56
pubmed: 22545925
Plant J. 2017 Jan;89(2):366-380
pubmed: 27714888
J Exp Bot. 2015 Sep;66(18):5605-15
pubmed: 25796084
Theor Appl Genet. 2013 Apr;126(4):867-87
pubmed: 23471459
Theor Appl Genet. 2010 Mar;120(5):875-93
pubmed: 20151298
PLoS One. 2015 Feb 25;10(2):e0117737
pubmed: 25714370
Plant Cell Physiol. 2004 Apr;45(4):369-85
pubmed: 15111711
Science. 2009 Nov 20;326(5956):1112-5
pubmed: 19965430
PLoS One. 2014 Mar 12;9(3):e90673
pubmed: 24622152
Genome Biol. 2015 Sep 11;16:167
pubmed: 26357913
Sci Rep. 2019 Mar 5;9(1):3458
pubmed: 30837510
Plant Methods. 2014 Mar 28;10(1):8
pubmed: 24678985
J Integr Plant Biol. 2016 Jan;58(1):81-90
pubmed: 25845500
Mol Plant. 2017 Mar 6;10(3):414-426
pubmed: 27381443
Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20431-6
pubmed: 24297875
Rice (N Y). 2019 Mar 21;12(1):17
pubmed: 30900100
Proc Natl Acad Sci U S A. 2012 Jul 10;109(28):E1913-21
pubmed: 22711828
EMBO Rep. 2005 Mar;6(3):282-8
pubmed: 15723040
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W316-22
pubmed: 21715386
Bioinformatics. 2007 Oct 1;23(19):2633-5
pubmed: 17586829
Plant Biotechnol J. 2019 Nov;17(11):2106-2122
pubmed: 30963678
Mol Ecol Resour. 2009 Sep;9(5):1322-32
pubmed: 21564903
Nat Genet. 2000 May;25(1):25-9
pubmed: 10802651
J Exp Bot. 2019 Jan 7;70(2):545-561
pubmed: 30380099
Trends Plant Sci. 2010 Aug;15(8):454-61
pubmed: 20542719
Trends Biotechnol. 2019 Nov;37(11):1217-1235
pubmed: 31235329
PLoS Genet. 2014 Sep 11;10(9):e1004573
pubmed: 25211220
Database (Oxford). 2016 Apr 17;2016:
pubmed: 27087305
Theor Appl Genet. 2003 Feb;106(4):649-58
pubmed: 12595994
Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16386-91
pubmed: 18845687
Mol Biol Evol. 2015 Jul;32(7):1767-73
pubmed: 25750178
Funct Plant Biol. 2016 Feb;44(1):10-22
pubmed: 32480542
Plant Physiol. 2008 Aug;147(4):1947-59
pubmed: 18562767
Dev Cell. 2014 Aug 25;30(4):437-48
pubmed: 25132385
Front Plant Sci. 2016 Jun 15;7:833
pubmed: 27379126
Annu Rev Plant Biol. 2013;64:267-91
pubmed: 23451789
Front Plant Sci. 2019 Jun 03;10:714
pubmed: 31214228
Plant Biotechnol J. 2021 Jan;19(1):35-50
pubmed: 32569428
Curr Opin Plant Biol. 2013 May;16(2):180-7
pubmed: 23578473
Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16969-74
pubmed: 24089449
J Appl Genet. 2012 May;53(2):133-43
pubmed: 22246661
Rice (N Y). 2018 Mar 6;11(1):13
pubmed: 29511908
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W720-4
pubmed: 16845106
Nature. 2001 Jun 7;411(6838):709-13
pubmed: 11395776
Sci Rep. 2013;3:2442
pubmed: 23942574
Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):8872-7
pubmed: 22615396
Curr Opin Biotechnol. 2015 Apr;32:179-185
pubmed: 25614069
Science. 2009 Aug 7;325(5941):714-8
pubmed: 19661422
J Vis Exp. 2018 Oct 9;(140):
pubmed: 30371675
Genetics. 2014 Apr;196(4):1337-56
pubmed: 24514905
Plant J. 2016 Jun;86(5):391-402
pubmed: 27012534
Annu Rev Genet. 2004;38:37-59
pubmed: 15568971
Mol Plant. 2015 Jun;8(6):871-84
pubmed: 25620769
Nat Commun. 2014 Oct 08;5:5087
pubmed: 25295980
J Agric Food Chem. 2013 Apr 3;61(13):3186-92
pubmed: 23470249
PLoS One. 2011;6(12):e29229
pubmed: 22216221
Plant Signal Behav. 2015;10(10):e1078955
pubmed: 26340415
Plant Mol Biol. 2005 Dec;59(6):881-94
pubmed: 16307364
BMC Plant Biol. 2011 May 09;11:77
pubmed: 21554668
Nucleic Acids Res. 2017 Jan 4;45(D1):D1040-D1045
pubmed: 27924042
Plant Physiol. 2017 Mar;173(3):1554-1564
pubmed: 28153923
Plant Methods. 2015 Apr 09;11:26
pubmed: 25901177