The complex genetic architecture of shoot growth natural variation in Arabidopsis thaliana.
Journal
PLoS genetics
ISSN: 1553-7404
Titre abrégé: PLoS Genet
Pays: United States
ID NLM: 101239074
Informations de publication
Date de publication:
04 2019
04 2019
Historique:
received:
16
07
2018
accepted:
11
01
2019
entrez:
23
4
2019
pubmed:
23
4
2019
medline:
9
5
2019
Statut:
epublish
Résumé
One of the main outcomes of quantitative genetics approaches to natural variation is to reveal the genetic architecture underlying the phenotypic space. Complex genetic architectures are described as including numerous loci (or alleles) with small-effect and/or low-frequency in the populations, interactions with the genetic background, environment or age. Linkage or association mapping strategies will be more or less sensitive to this complexity, so that we still have an unclear picture of its extent. By combining high-throughput phenotyping under two environmental conditions with classical QTL mapping approaches in multiple Arabidopsis thaliana segregating populations as well as advanced near isogenic lines construction and survey, we have attempted to improve our understanding of quantitative phenotypic variation. Integrative traits such as those related to vegetative growth used in this work (highlighting either cumulative growth, growth rate or morphology) all showed complex and dynamic genetic architecture with respect to the segregating population and condition. The more resolutive our mapping approach, the more complexity we uncover, with several instances of QTLs visible in near isogenic lines but not detected with the initial QTL mapping, indicating that our phenotyping accuracy was less limiting than the mapping resolution with respect to the underlying genetic architecture. In an ultimate approach to resolve this complexity, we intensified our phenotyping effort to target specifically a 3Mb-region known to segregate for a major quantitative trait gene, using a series of selected lines recombined every 100kb. We discovered that at least 3 other independent QTLs had remained hidden in this region, some with trait- or condition-specific effects, or opposite allelic effects. If we were to extrapolate the figures obtained on this specific region in this particular cross to the genome- and species-scale, we would predict hundreds of causative loci of detectable phenotypic effect controlling these growth-related phenotypes.
Identifiants
pubmed: 31009456
doi: 10.1371/journal.pgen.1007954
pii: PGENETICS-D-18-01430
pmc: PMC6476473
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1007954Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Plant Cell. 1999 May;11(5):949-56
pubmed: 10330478
Science. 2000 Oct 13;290(5490):344-7
pubmed: 11030654
Nat Genet. 2001 Dec;29(4):435-40
pubmed: 11726930
Plant J. 2002 Aug;31(3):355-64
pubmed: 12164814
Plant Physiol. 2003 Jan;131(1):345-58
pubmed: 12529542
Theor Appl Genet. 2002 May;104(6-7):1173-1184
pubmed: 12582628
Bioinformatics. 2003 May 1;19(7):889-90
pubmed: 12724300
Plant Physiol. 2003 Dec;133(4):1547-56
pubmed: 14605225
Genes Dev. 2004 Mar 15;18(6):700-14
pubmed: 15031265
Plant J. 2004 Apr;38(1):193-202
pubmed: 15053772
Plant Physiol. 2004 May;135(1):444-58
pubmed: 15122039
Bioinformatics. 2005 Jan 1;21(1):128-30
pubmed: 15319261
Theor Appl Genet. 2005 Feb;110(4):742-53
pubmed: 15678326
Nat Genet. 2005 May;37(5):501-6
pubmed: 15806101
Planta. 2005 Oct;222(3):418-27
pubmed: 15864638
Nature. 2005 May 5;435(7038):95-8
pubmed: 15875023
Plant Physiol. 2005 Jun;138(2):1163-73
pubmed: 15908596
Nature. 2005 Aug 11;436(7052):866-70
pubmed: 16007076
New Phytol. 2006;169(3):623-35
pubmed: 16411964
Theor Appl Genet. 2006 Jul;113(2):206-24
pubmed: 16791688
New Phytol. 2007;174(2):447-55
pubmed: 17388907
PLoS Biol. 2007 Sep;5(9):e236
pubmed: 17803357
Genetics. 2008 Jan;178(1):539-51
pubmed: 18202393
Genetics. 2008 Apr;178(4):2253-64
pubmed: 18430947
Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):17193-8
pubmed: 18971337
Science. 2009 Feb 20;323(5917):1060-3
pubmed: 19150812
BMC Plant Biol. 2009 Jun 26;9:79
pubmed: 19558640
Plant Cell. 2009 Jul;21(7):1877-96
pubmed: 19574434
Nature. 2010 Jun 3;465(7298):627-31
pubmed: 20336072
PLoS Genet. 2010 May 06;6(5):e1000940
pubmed: 20463887
PLoS Genet. 2010 May 13;6(5):e1000945
pubmed: 20485571
Nature. 2010 Jun 3;465(7298):632-6
pubmed: 20520716
Plant Cell Environ. 2010 Nov;33(11):1875-87
pubmed: 20545881
Genetics. 2010 Sep;186(1):395-404
pubmed: 20592258
Plant Cell. 2010 Aug;22(8):2660-79
pubmed: 20798329
Plant Physiol. 2010 Nov;154(3):1361-71
pubmed: 20826703
Bioinformatics. 2010 Dec 1;26(23):2990-2
pubmed: 20966004
Nat Biotechnol. 2011 Mar;29(3):212-4
pubmed: 21390020
Genetics. 2011 Jun;188(2):421-33
pubmed: 21406681
Genetics. 2011 Jul;188(3):673-81
pubmed: 21515578
Curr Opin Plant Biol. 2011 Jun;14(3):225-31
pubmed: 21536479
PLoS One. 2012;7(2):e32319
pubmed: 22384215
G3 (Bethesda). 2012 Jan;2(1):29-34
pubmed: 22384379
BMC Genomics. 2012 Mar 27;13:117
pubmed: 22453064
New Phytol. 2013 Mar;197(4):1321-31
pubmed: 23311994
Plant J. 2013 May;74(3):534-44
pubmed: 23452317
Curr Opin Plant Biol. 2013 Jun;16(3):274-81
pubmed: 23462639
Plant Cell. 2013 Apr;25(4):1304-13
pubmed: 23590882
Plant Cell. 2013 Jun;25(6):2132-54
pubmed: 23898029
Genetics. 2013 Nov;195(3):1077-86
pubmed: 23979570
Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15818-23
pubmed: 24023067
Evolution. 2013 Oct;67(10):2923-35
pubmed: 24094343
Nat Genet. 2014 Jan;46(1):77-81
pubmed: 24212884
Nat Rev Genet. 2014 Jan;15(1):34-48
pubmed: 24296534
Plant J. 2014 Apr;78(1):121-33
pubmed: 24479634
Trends Plant Sci. 2014 Jun;19(6):390-8
pubmed: 24491827
Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):2836-41
pubmed: 24550314
Curr Opin Plant Biol. 2014 Apr;18:37-43
pubmed: 24565952
Elife. 2014 Apr 29;3:e02252
pubmed: 24843021
Genetics. 2014 Sep;198(1):345-53
pubmed: 24950893
Mol Ecol. 2014 Sep;23(17):4291-303
pubmed: 25039363
Plant Cell. 2014 Nov;26(11):4298-310
pubmed: 25428981
Genetics. 2015 Feb;199(2):359-61
pubmed: 25527287
J Exp Bot. 2015 Feb;66(4):1045-54
pubmed: 25601785
Plant Physiol. 2015 Mar;167(3):800-16
pubmed: 25604532
Plant Sci. 2015 May;234:155-62
pubmed: 25804818
J Exp Bot. 2015 Sep;66(18):5567-80
pubmed: 25922493
Plant Cell Environ. 2016 Jan;39(1):88-102
pubmed: 26138664
Plant Physiol. 2015 Sep;169(1):647-59
pubmed: 26195568
J Exp Bot. 2015 Nov;66(21):6863-75
pubmed: 26272902
New Phytol. 2016 Feb;209(3):921-44
pubmed: 26465351
Plant Physiol. 2016 Apr;170(4):2187-203
pubmed: 26869705
Plant Methods. 2016 Feb 15;12:14
pubmed: 26884806
Genetics. 2016 Jul;203(3):1453-67
pubmed: 27182953
Genetics. 2016 Sep;204(1):21-33
pubmed: 27356613
Plant Sci. 2016 Oct;251:12-22
pubmed: 27593459
Plant J. 2017 Jan;89(2):366-380
pubmed: 27714888
Plant Cell. 2016 Oct;28(10):2417-2434
pubmed: 27729396
PLoS Biol. 2016 Dec 6;14(12):e2000322
pubmed: 27923039
Plant J. 2017 Mar;89(6):1225-1235
pubmed: 27995664
Plant Physiol. 2017 Mar;173(3):1554-1564
pubmed: 28153923
Annu Rev Plant Biol. 2017 Apr 28;68:435-455
pubmed: 28226236
Plant Cell Environ. 2017 Aug;40(8):1429-1441
pubmed: 28252189
Genetics. 2017 Jun;206(2):527-529
pubmed: 28592493
Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2431-2436
pubmed: 29183972
Nat Ecol Evol. 2018 Feb;2(2):352-358
pubmed: 29255303
Cell. 2018 Jan 25;172(3):478-490.e15
pubmed: 29373829
Nat Commun. 2018 Feb 7;9(1):541
pubmed: 29416032
Plant Cell Environ. 2018 Aug;41(8):1806-1820
pubmed: 29520809