A genome-wide association study identifies variants underlying the Arabidopsis thaliana shade avoidance response.
Shade avoidance is an ecologically and molecularly well-understood set of plant developmental responses that occur when the ratio of red to far-red light (R:FR) is reduced as a result of foliar shade. Here, a genome-wide association study (GWAS) in Arabidopsis thaliana was used to identify variants...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2012-01-01
|
| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC3305432?pdf=render |
| _version_ | 1818271723769823232 |
|---|---|
| author | Daniele L Filiault Julin N Maloof |
| author_facet | Daniele L Filiault Julin N Maloof |
| author_sort | Daniele L Filiault |
| collection | DOAJ |
| description | Shade avoidance is an ecologically and molecularly well-understood set of plant developmental responses that occur when the ratio of red to far-red light (R:FR) is reduced as a result of foliar shade. Here, a genome-wide association study (GWAS) in Arabidopsis thaliana was used to identify variants underlying one of these responses: increased hypocotyl elongation. Four hypocotyl phenotypes were included in the study, including height in high R:FR conditions (simulated sun), height in low R:FR conditions (simulated shade), and two different indices of the response of height to low R:FR. GWAS results showed that variation in these traits is controlled by many loci of small to moderate effect. A known PHYC variant contributing to hypocotyl height variation was identified and lists of significantly associated genes were enriched in a priori candidates, suggesting that this GWAS was capable of generating meaningful results. Using metadata such as expression data, GO terms, and other annotation, we were also able to identify variants in candidate de novo genes. Patterns of significance among our four phenotypes allowed us to categorize associations into three groups: those that affected hypocotyl height without influencing shade avoidance, those that affected shade avoidance in a height-dependent fashion, and those that exerted specific control over shade avoidance. This grouping allowed for the development of explicit hypotheses about the genetics underlying shade avoidance variation. Additionally, the response to shade did not exhibit any marked geographic distribution, suggesting that variation in low R:FR-induced hypocotyl elongation may represent a response to local conditions. |
| first_indexed | 2024-12-12T21:30:43Z |
| format | Article |
| id | doaj.art-c3222b54a397492f830a26296b6c7d6e |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-12T21:30:43Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-c3222b54a397492f830a26296b6c7d6e2022-12-22T00:11:20ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042012-01-0183e100258910.1371/journal.pgen.1002589A genome-wide association study identifies variants underlying the Arabidopsis thaliana shade avoidance response.Daniele L FiliaultJulin N MaloofShade avoidance is an ecologically and molecularly well-understood set of plant developmental responses that occur when the ratio of red to far-red light (R:FR) is reduced as a result of foliar shade. Here, a genome-wide association study (GWAS) in Arabidopsis thaliana was used to identify variants underlying one of these responses: increased hypocotyl elongation. Four hypocotyl phenotypes were included in the study, including height in high R:FR conditions (simulated sun), height in low R:FR conditions (simulated shade), and two different indices of the response of height to low R:FR. GWAS results showed that variation in these traits is controlled by many loci of small to moderate effect. A known PHYC variant contributing to hypocotyl height variation was identified and lists of significantly associated genes were enriched in a priori candidates, suggesting that this GWAS was capable of generating meaningful results. Using metadata such as expression data, GO terms, and other annotation, we were also able to identify variants in candidate de novo genes. Patterns of significance among our four phenotypes allowed us to categorize associations into three groups: those that affected hypocotyl height without influencing shade avoidance, those that affected shade avoidance in a height-dependent fashion, and those that exerted specific control over shade avoidance. This grouping allowed for the development of explicit hypotheses about the genetics underlying shade avoidance variation. Additionally, the response to shade did not exhibit any marked geographic distribution, suggesting that variation in low R:FR-induced hypocotyl elongation may represent a response to local conditions.http://europepmc.org/articles/PMC3305432?pdf=render |
| spellingShingle | Daniele L Filiault Julin N Maloof A genome-wide association study identifies variants underlying the Arabidopsis thaliana shade avoidance response. PLoS Genetics |
| title | A genome-wide association study identifies variants underlying the Arabidopsis thaliana shade avoidance response. |
| title_full | A genome-wide association study identifies variants underlying the Arabidopsis thaliana shade avoidance response. |
| title_fullStr | A genome-wide association study identifies variants underlying the Arabidopsis thaliana shade avoidance response. |
| title_full_unstemmed | A genome-wide association study identifies variants underlying the Arabidopsis thaliana shade avoidance response. |
| title_short | A genome-wide association study identifies variants underlying the Arabidopsis thaliana shade avoidance response. |
| title_sort | genome wide association study identifies variants underlying the arabidopsis thaliana shade avoidance response |
| url | http://europepmc.org/articles/PMC3305432?pdf=render |
| work_keys_str_mv | AT danielelfiliault agenomewideassociationstudyidentifiesvariantsunderlyingthearabidopsisthalianashadeavoidanceresponse AT julinnmaloof agenomewideassociationstudyidentifiesvariantsunderlyingthearabidopsisthalianashadeavoidanceresponse AT danielelfiliault genomewideassociationstudyidentifiesvariantsunderlyingthearabidopsisthalianashadeavoidanceresponse AT julinnmaloof genomewideassociationstudyidentifiesvariantsunderlyingthearabidopsisthalianashadeavoidanceresponse |