Linked Life Data

20456226

Source:http://linkedlifedata.com/resource/pubmed/id/20456226

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
6
pubmed:dateCreated
2010-5-11
pubmed:abstractText
Association studies utilize the action of recombination over numerous generations to identify loci that underlie quantitative traits. We use a candidate-gene association approach, segregation analyses and analyses of local linkage disequilibrium (LD) to evaluate the potentially causal effects of molecular variation at PIF4 (PHYTOCROME INTERACTING FACTOR 4) on ecologically important traits in Arabidopsis thaliana. A preliminary analysis of sequence diversity in 14 natural genotypes revealed one intermediate-frequency replacement polymorphism at PIF4. A sample of 161 natural accessions was genotyped at PIF4 and screened for average length of early internodes, inflorescence length, days to flowering and flowering interval (days between bolting and flowering) under high- and low-density environments to test for genotype-phenotype associations. PIF4 was associated with early internode lengths, while the PIF4x treatment interaction was associated with flowering interval in the panel of 161 accessions. Further, in a set of recombinant inbred lines that segregate for the PIF4 polymorphism, nucleotide substitutions at PIF4 co-segregated with early internode lengths, days to flowering and fruit set, suggesting that cryptic population structure in the association-mapping panel and attendant LD with a physically distant locus do not account for the observed association. Finally, in a panel of pseudochromosomes from 20 re-sequenced genotypes, LD appeared to decay rapidly in the immediate vicinity of PIF4, suggesting that flanking loci contribute little to the observed association. In sum, the results suggest that PIF4 causally affects early internode lengths on the primary inflorescence, potentially via effects on reproductive timing and that these traits in turn affect fitness.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Mar
pubmed:issn
1365-294X
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
19
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1187-99
pubmed:meshHeading
pubmed-meshheading:20456226-Arabidopsis, pubmed-meshheading:20456226-Arabidopsis Proteins, pubmed-meshheading:20456226-Basic Helix-Loop-Helix Transcription Factors, pubmed-meshheading:20456226-DNA, Plant, pubmed-meshheading:20456226-Flowers, pubmed-meshheading:20456226-Fruit, pubmed-meshheading:20456226-Gene Expression Regulation, Plant, pubmed-meshheading:20456226-Genes, Plant, pubmed-meshheading:20456226-Genetic Association Studies, pubmed-meshheading:20456226-Genetic Variation, pubmed-meshheading:20456226-Genotype, pubmed-meshheading:20456226-Linkage Disequilibrium, pubmed-meshheading:20456226-Models, Genetic, pubmed-meshheading:20456226-Polymorphism, Single Nucleotide, pubmed-meshheading:20456226-Quantitative Trait, Heritable, pubmed-meshheading:20456226-Sequence Analysis, DNA, pubmed-meshheading:20456226-Time Factors
pubmed:year
2010
pubmed:articleTitle
Genes underlying quantitative variation in ecologically important traits: PIF4 (phytochrome interacting factor 4) is associated with variation in internode length, flowering time, and fruit set in Arabidopsis thaliana.
pubmed:affiliation
Department of Botany, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82071, USA. mbrock2@uwyo.edu
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, Non-P.H.S.