title: Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution dwarf alleles in rice and barley.
abstract: Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5), which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis, are found in different populations from southern, western, and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection, whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore, because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes, this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants.
authors.affiliation: Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany.
authors.forename: Luis
authors.initials: L
authors.lastname: Barboza
authors.forename: Sigi
authors.initials: S
authors.lastname: Effgen
authors.forename: Carlos
authors.initials: C
authors.lastname: Alonso-Blanco
authors.forename: Rik
authors.initials: R
authors.lastname: Kooke
authors.forename: Joost J B
authors.initials: JJ
authors.lastname: Keurentjes
authors.forename: Maarten
authors.initials: M
authors.lastname: Koornneef
authors.forename: Rubén
authors.initials: R
authors.lastname: Alcázar
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000033:anatomy & histology* / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D005075:Biological Evolution; D056426:Genetic Loci / Q000235:genetics; D055106:Genome-Wide Association Study; D005838:Genotype; D005843:Geography; D001467:Hordeum / Q000235:genetics*; D006899:Mixed Function Oxygenases / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics*; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D011157:Population Dynamics; D017386:Sequence Homology, Amino Acid
chemical_list: D029681:Arabidopsis Proteins; D006899:Mixed Function Oxygenases; C108186:gibberellin 3beta-hydroxylase
keywords: Arabidopsis natural variation; dwarf accessions; gibberellin mutants
references.citation: New Phytol. 2012 Jul;195(1):58-70
references.pmid: 22510148
references.citation: Mol Ecol. 2005 Jul;14(8):2611-20
references.pmid: 15969739
references.citation: Trends Genet. 2003 Jan;19(1):5-9
references.pmid: 12493241
references.citation: Plant J. 2008 Feb;53(3):488-504
references.pmid: 18069939
references.citation: Funct Integr Genomics. 2009 May;9(2):255-62
references.pmid: 19280236
references.citation: Nat Genet. 2010 Apr;42(4):348-54
references.pmid: 20208533
references.citation: Theor Appl Genet. 1980 Nov;58(6):257-63
references.pmid: 24301503
references.citation: Nat Genet. 2010 Dec;42(12):1135-9
references.pmid: 21037570
references.citation: PLoS Genet. 2010 Feb 12;6(2):e1000843
references.pmid: 20169178
references.citation: Plant Physiol. 2005 Nov;139(3):1304-12
references.pmid: 16244146
references.citation: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references.pmid: 7984417
references.citation: Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):19120-5
references.pmid: 20956303
references.citation: Nat Genet. 2011 Aug 28;43(10):956-63
references.pmid: 21874002
references.citation: Genetics. 2005 Mar;169(3):1601-15
references.pmid: 15654111
references.citation: Genetics. 2008 Oct;180(2):1009-21
references.pmid: 18716334
references.citation: Bioinformatics. 2009 Jun 1;25(11):1451-2
references.pmid: 19346325
references.citation: Nature. 2002 Apr 18;416(6882):701-2
references.pmid: 11961544
references.citation: Proc Natl Acad Sci U S A. 1995 Jul 3;92(14):6640-4
references.pmid: 7604047
references.citation: Plant Cell. 2012 Mar;24(3):941-60
references.pmid: 22427334
references.citation: Proc Natl Acad Sci U S A. 2010 Dec 7;107(49):21199-204
references.pmid: 21078970
references.citation: Plant Physiol. 2011 Dec;157(4):1942-55
references.pmid: 21988878
references.citation: Plant Mol Biol. 2004 Mar;54(4):533-47
references.pmid: 15316288
references.citation: Plant J. 2006 Mar;45(5):804-18
references.pmid: 16460513
references.citation: BMC Evol Biol. 2009 Aug 18;9:206
references.pmid: 19689796
references.citation: Evolution. 2013 May;67(5):1235-50
references.pmid: 23617905
references.citation: Mol Ecol. 2013 Feb;22(3):699-708
references.pmid: 22420446
references.citation: Science. 2003 Oct 3;302(5642):71-2
references.pmid: 14526071
references.citation: Theor Appl Genet. 2011 May;122(8):1451-60
references.pmid: 21318371
references.citation: Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):9043-8
references.pmid: 12077303
references.citation: Genetics. 2006 Mar;172(3):1867-76
references.pmid: 16361234
references.citation: Biochem J. 2012 May 15;444(1):11-25
references.pmid: 22533671
references.citation: Mol Ecol. 2010 Nov;19(21):4753-64
references.pmid: 20887360
references.citation: Genetics. 2000 Jun;155(2):945-59
references.pmid: 10835412
references.citation: Annu Rev Plant Biol. 2008;59:225-51
references.pmid: 18173378
references.citation: Structure. 2002 Jan;10(1):93-103
references.pmid: 11796114
references.citation: Mol Ecol. 2000 Oct;9(10):1657-9
references.pmid: 11050560