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Evolution and association analysis of Ghd7 in rice
- Source :
- PLoS ONE, PLoS ONE, Vol 7, Iss 5, p e34021 (2012)
- Publication Year :
- 2011
-
Abstract
- Plant height, heading date, and yield are the main targets for rice genetic improvement. Ghd7 is a pleiotropic gene that controls the aforementioned traits simultaneously. In this study, a rice germplasm collection of 104 accessions (Oryza sativa) and 3 wild rice varieties (O.rufipogon) was used to analyze the evolution and association of Ghd7 with plant height, heading date, and yield. Among the 104 accessions, 76 single nucleotide polymorphisms (SNPs) and six insertions and deletions were found within a 3932-bp DNA fragment of Ghd7. A higher pairwise π and θ in the promoter indicated a highly diversified promoter of Ghd7. Sixteen haplotypes and 8 types of Ghd7 protein were detected. SNP changes between haplotypes indicated that Ghd7 evolved from two distinct ancestral gene pools, and independent domestication processes were detected in indica and japonica varietals respectively. In addition to the previously reported premature stop mutation in the first exon of Ghd7, which caused phenotypic changes of multiple traits, we found another functional C/T mutation (SNP S_555) by structure-based association analysis. SNP S_555 is located in the promoter and was related to plant height probably by altering gene expression. Moreover, another seven SNP mutations in complete linkage were found to be associated with the number of spikelets per panicle, regardless of the photoperiod. These associations provide the potential for flexibility of Ghd7 application in rice breeding programs.
- Subjects :
- Germplasm
Linkage disequilibrium
Plant Evolution
Plant genetics
Molecular Sequence Data
Population genetics
lcsh:Medicine
Cereals
Single-nucleotide polymorphism
Crops
Plant Science
Biology
Breeding
Plant Genetics
Polymorphism, Single Nucleotide
Linkage Disequilibrium
Evolution, Molecular
Model Organisms
Species Specificity
Gene Expression Regulation, Plant
Plant and Algal Models
Point Mutation
lcsh:Science
Genetic association
Plant Proteins
Genetics
Plant Growth and Development
Evolutionary Biology
Multidisciplinary
Oryza sativa
Base Sequence
Population Biology
Haplotype
lcsh:R
food and beverages
Oryza
Agriculture
Organismal Evolution
Phenotype
Haplotypes
Codon, Terminator
Genetic Polymorphism
lcsh:Q
Rice
Germ Cells, Plant
Population Genetics
Research Article
Developmental Biology
Subjects
Details
- ISSN :
- 19326203
- Volume :
- 7
- Issue :
- 5
- Database :
- OpenAIRE
- Journal :
- PloS one
- Accession number :
- edsair.doi.dedup.....b1a2c186b233d40ea5d95ce3e00a89e2