Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution dwarf alleles in rice and barley
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 m...
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| Veröffentlicht in: | Proceedings of the National Academy of Sciences - PNAS 2013-09, Vol.110 (39), p.15818-15823 |
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| creator | Barboza, Luis Effgen, Sigi Alonso-Blanco, Carlos Kooke, Rik Keurentjes, Joost J. B. Koornneef, Maarten Alcázar, Rubén |
| description | 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. |
| doi_str_mv | 10.1073/pnas.1314979110 |
| format | Article |
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B. ; Koornneef, Maarten ; Alcázar, Rubén</creator><creatorcontrib>Barboza, Luis ; Effgen, Sigi ; Alonso-Blanco, Carlos ; Kooke, Rik ; Keurentjes, Joost J. B. ; Koornneef, Maarten ; Alcázar, Rubén</creatorcontrib><description>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.</description><identifier>ISSN: 0027-8424</identifier><identifier>EISSN: 1091-6490</identifier><identifier>DOI: 10.1073/pnas.1314979110</identifier><identifier>PMID: 24023067</identifier><language>eng</language><publisher>United States: National Academy of Sciences</publisher><subject>adaptation ; Alleles ; allelism ; Arabidopsis - anatomy & histology ; Arabidopsis - genetics ; Arabidopsis Proteins - genetics ; Arabidopsis Proteins - metabolism ; Arabidopsis thaliana ; association ; Barley ; Biological Evolution ; Biological Sciences ; biosynthesis ; Central Asia ; evolutionary adaptation ; gene ; Genes ; Genetic loci ; Genetic Loci - genetics ; Genetic mutation ; Genetic variation ; Genome-Wide Association Study ; Genotype ; Genotype & phenotype ; Geography ; gibberellin biosynthesis ; Gibberellins ; Haplotypes ; Hordeum - genetics ; Hordeum vulgare ; Hormones ; Japan ; loci ; Mixed Function Oxygenases - genetics ; Mixed Function Oxygenases - metabolism ; Molecular Sequence Data ; Mutation ; Mutation - genetics ; natural variation ; Northern European region ; Oryza - genetics ; Oryza sativa ; Phenotypes ; Phenotypic traits ; phenotypic variation ; Phylogeny ; Plant biology ; plant hormones ; Plants ; pleiotropy ; polymorphism ; Population Dynamics ; populations ; quantitative trait loci ; Rice ; Sequence Homology, Amino Acid ; statistics ; thaliana</subject><ispartof>Proceedings of the National Academy of Sciences - PNAS, 2013-09, Vol.110 (39), p.15818-15823</ispartof><rights>Copyright National Academy of Sciences</rights><rights>Copyright National Academy of Sciences Sep 24, 2013</rights><rights>Wageningen University & Research</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c609t-fba7add76121aeeb298d49693df0c9e0d5326906a9575ffc879f75226c4697463</citedby><cites>FETCH-LOGICAL-c609t-fba7add76121aeeb298d49693df0c9e0d5326906a9575ffc879f75226c4697463</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://www.pnas.org/content/110/39.cover.gif</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/42713417$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/42713417$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,723,776,780,799,881,27901,27902,53766,53768,57992,58225</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24023067$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Barboza, Luis</creatorcontrib><creatorcontrib>Effgen, Sigi</creatorcontrib><creatorcontrib>Alonso-Blanco, Carlos</creatorcontrib><creatorcontrib>Kooke, Rik</creatorcontrib><creatorcontrib>Keurentjes, Joost J. B.</creatorcontrib><creatorcontrib>Koornneef, Maarten</creatorcontrib><creatorcontrib>Alcázar, Rubén</creatorcontrib><title>Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution dwarf alleles in rice and barley</title><title>Proceedings of the National Academy of Sciences - PNAS</title><addtitle>Proc Natl Acad Sci U S A</addtitle><description>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.</description><subject>adaptation</subject><subject>Alleles</subject><subject>allelism</subject><subject>Arabidopsis - anatomy & histology</subject><subject>Arabidopsis - genetics</subject><subject>Arabidopsis Proteins - genetics</subject><subject>Arabidopsis Proteins - metabolism</subject><subject>Arabidopsis thaliana</subject><subject>association</subject><subject>Barley</subject><subject>Biological Evolution</subject><subject>Biological Sciences</subject><subject>biosynthesis</subject><subject>Central Asia</subject><subject>evolutionary adaptation</subject><subject>gene</subject><subject>Genes</subject><subject>Genetic loci</subject><subject>Genetic Loci - genetics</subject><subject>Genetic mutation</subject><subject>Genetic variation</subject><subject>Genome-Wide Association Study</subject><subject>Genotype</subject><subject>Genotype & phenotype</subject><subject>Geography</subject><subject>gibberellin biosynthesis</subject><subject>Gibberellins</subject><subject>Haplotypes</subject><subject>Hordeum - genetics</subject><subject>Hordeum vulgare</subject><subject>Hormones</subject><subject>Japan</subject><subject>loci</subject><subject>Mixed Function Oxygenases - genetics</subject><subject>Mixed Function Oxygenases - metabolism</subject><subject>Molecular Sequence Data</subject><subject>Mutation</subject><subject>Mutation - genetics</subject><subject>natural variation</subject><subject>Northern European region</subject><subject>Oryza - genetics</subject><subject>Oryza sativa</subject><subject>Phenotypes</subject><subject>Phenotypic traits</subject><subject>phenotypic variation</subject><subject>Phylogeny</subject><subject>Plant biology</subject><subject>plant hormones</subject><subject>Plants</subject><subject>pleiotropy</subject><subject>polymorphism</subject><subject>Population Dynamics</subject><subject>populations</subject><subject>quantitative trait loci</subject><subject>Rice</subject><subject>Sequence Homology, Amino Acid</subject><subject>statistics</subject><subject>thaliana</subject><issn>0027-8424</issn><issn>1091-6490</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNks2PEyEYhydG49bVsyeVxIsHu8sLDB8eTJqNriabeNA9E2aG6dJQqDDTumf_cZltrR8Xvbwk8PyewMtbVU8BnwEW9HwTTD4DCkwJBYDvVTPACuacKXy_mmFMxFwywk6qRzmvMMaqlvhhdUIYJhRzMau-L5JpXBc32WWU7dp1O5P6jOw2-q3tUJ_iGrnQ2Y0tJQxoPQ5mcDHksosuFwTHb_AaxTTcRB-XaIhomawNKE2GcSLRnRIZ7623d7HkWotM6FBjkre3j6sHvfHZPjmsp9X1-3dfLj7Mrz5dfrxYXM1bjtUw7xsjTNcJDgSMtQ1RsmOKK9r1uFUWdzUlXGFuVC3qvm-lUL2oCeEt40owTk-rN3vvzixtcKEUHUxqXdbROO1dk0y61bsx6eCnZTM2WTOmqJIl_HYfLptr27WlF8l4vUluPYUmwZ8nwd3oZdxqKmS5DxTBq4Mgxa-jzYNeu9xa702wccwaJKYAda34v1HGJAElavYfKBUAnIu6oC__QldxTKF0fKKkVEDwJDzfU22KOSfbH58IWE8zp6eZ079mriSe_96ZI_9zyAqADsCUPOqKjyoNtYSpu8_2yCoPMR0ZRgRQBpPixf68N1GbZSpfdv2ZYOAYAwMpOf0BvALyXw</recordid><startdate>20130924</startdate><enddate>20130924</enddate><creator>Barboza, Luis</creator><creator>Effgen, Sigi</creator><creator>Alonso-Blanco, Carlos</creator><creator>Kooke, Rik</creator><creator>Keurentjes, Joost J. 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B.</au><au>Koornneef, Maarten</au><au>Alcázar, Rubén</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution dwarf alleles in rice and barley</atitle><jtitle>Proceedings of the National Academy of Sciences - PNAS</jtitle><addtitle>Proc Natl Acad Sci U S A</addtitle><date>2013-09-24</date><risdate>2013</risdate><volume>110</volume><issue>39</issue><spage>15818</spage><epage>15823</epage><pages>15818-15823</pages><issn>0027-8424</issn><eissn>1091-6490</eissn><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.</abstract><cop>United States</cop><pub>National Academy of Sciences</pub><pmid>24023067</pmid><doi>10.1073/pnas.1314979110</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | adaptation Alleles allelism Arabidopsis - anatomy & histology Arabidopsis - genetics Arabidopsis Proteins - genetics Arabidopsis Proteins - metabolism Arabidopsis thaliana association Barley Biological Evolution Biological Sciences biosynthesis Central Asia evolutionary adaptation gene Genes Genetic loci Genetic Loci - genetics Genetic mutation Genetic variation Genome-Wide Association Study Genotype Genotype & phenotype Geography gibberellin biosynthesis Gibberellins Haplotypes Hordeum - genetics Hordeum vulgare Hormones Japan loci Mixed Function Oxygenases - genetics Mixed Function Oxygenases - metabolism Molecular Sequence Data Mutation Mutation - genetics natural variation Northern European region Oryza - genetics Oryza sativa Phenotypes Phenotypic traits phenotypic variation Phylogeny Plant biology plant hormones Plants pleiotropy polymorphism Population Dynamics populations quantitative trait loci Rice Sequence Homology, Amino Acid statistics thaliana |
| title | Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution dwarf alleles in rice and barley |
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