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Combining genetical genomics and bulked segregant analysis-based differential expression: an approach to gene localization
- Source :
- Theoretical and Applied Genetics 122 (2011) 7, TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, Theoretical and Applied Genetics, 122(7), 1375-1383
- Publisher :
- Springer Nature
-
Abstract
- Positional gene isolation in unsequenced species generally requires either a reference genome sequence or an inference of gene content based on conservation of synteny with a genomic model. In the large unsequenced genomes of the Triticeae cereals the latter, i.e. conservation of synteny with the rice and Brachypodium genomes, provides a powerful proxy for establishing local gene content and order. However, efficient exploitation of conservation of synteny requires ‘homology bridges’ between the model genome and the target region that contains a gene of interest. As effective homology bridges are generally the sequences of genetically mapped genes, increasing the density of these genes around a target locus is an important step in the process. We used bulked segregant analysis (BSA) of transcript abundance data to identify genes located in a specific region of the barley genome. The approach is valuable because only a relatively small proportion of barley genes are currently placed on a genetic map. We analyzed eQTL datasets from the reference Steptoe × Morex doubled haploid population and showed a strong association between differential gene expression and cis-regulation, with 83% of differentially expressed genes co-locating with their eQTL. We then performed BSA by assembling allele-specific pools based on the genotypes of individuals at the partial resistance QTL Rphq11. BSA identified a total of 411 genes as differentially expressed, including HvPHGPx, a gene previously identified as a promising candidate for Rphq11. The genetic location of 276 of these genes could be determined from both eQTL datasets and conservation of synteny, and 254 (92%) of these were located on the target chromosome. We conclude that the identification of differential expression by BSA constitutes a novel method to identify genes located in specific regions of interest. The datasets obtained from such studies provide a robust set of candidate genes for the analysis and serve as valuable resources for targeted marker development and comparative mapping with other grass species. Electronic supplementary material The online version of this article (doi:10.1007/s00122-011-1538-3) contains supplementary material, which is available to authorized users.
- Subjects :
- Candidate gene
chromosome addition lines
Quantitative Trait Loci
Genomics
Locus (genetics)
partial resistance
Biology
Quantitative trait locus
Genes, Plant
maize
Synteny
Genome
Laboratorium voor Plantenveredeling
Gene Expression Regulation, Plant
puccinia-hordei
wheat
Databases, Genetic
Gene Order
Genetics
hordeum-vulgare l
Gene
Original Paper
EPS-2
Bulked segregant analysis
Chromosome Mapping
Hordeum
Oryza
General Medicine
Microarray Analysis
Plant Breeding
arabidopsis
RNA, Plant
barley genes
reveals
Agronomy and Crop Science
Genome, Plant
Brachypodium
transcript-level variation
Biotechnology
Subjects
Details
- Language :
- English
- ISSN :
- 00405752
- Volume :
- 122
- Issue :
- 7
- Database :
- OpenAIRE
- Journal :
- Theoretical and Applied Genetics
- Accession number :
- edsair.doi.dedup.....0bf3d64b4ea760d715bd95bd7e762aae
- Full Text :
- https://doi.org/10.1007/s00122-011-1538-3