Validation of in silico-predicted genic SNPs in white clover (Trifolium repens L.), an outbreeding allopolyploid species

Cogan N.O.I., Drayton M.C., Ponting R.C., Vecchies A.C., Bannan N.R., Sawbridge T.I., Smith K.F., Spangenberg G.C. and Forster J.W. (2007) Validation of in silico-predicted genic SNPs in white clover (Trifolium repens L.), an outbreeding allopolyploid species. Molecular Genetics and Genomics, 277 4: 413-425. doi:10.1007/s00438-006-0198-5


Author Cogan N.O.I.
Drayton M.C.
Ponting R.C.
Vecchies A.C.
Bannan N.R.
Sawbridge T.I.
Smith K.F.
Spangenberg G.C.
Forster J.W.
Title Validation of in silico-predicted genic SNPs in white clover (Trifolium repens L.), an outbreeding allopolyploid species
Journal name Molecular Genetics and Genomics   Check publisher's open access policy
ISSN 1617-4615
Publication date 2007
Sub-type Article (original research)
DOI 10.1007/s00438-006-0198-5
Volume 277
Issue 4
Start page 413
End page 425
Total pages 13
Subject 1311 Genetics
Abstract White clover (Trifolium repens L.) is an obligate outbreeding allotetraploid forage legume. Gene-associated SNPs provide the optimum genetic system for improvement of such crop species. An EST resource obtained from multiple cDNA libraries constructed from numerous genotypes of a single cultivar has been used for in silico SNP discovery and validation. A total of 58 from 236 selected sequence clusters (24.5%) were fully validated as containing polymorphic SNPs by genotypic analysis across the parents and progeny of several two-way pseudo-testcross mapping families. The clusters include genes belonging to a broad range of predicted functional categories. Polymorphic SNP-containing ESTs have also been used for comparative genomic analysis by comparison with whole genome data from model legume species, as well as Arabidopsis thaliana. A total of 29 (50%) of the 58 clusters detected putative ortholoci with known chromosomal locations in Medicago truncatula, which is closely related to white clover within the Trifolieae tribe of the Fabaceae. This analysis provides access to translational data from model species. The efficiency of in silico SNP discovery in white clover is limited by paralogous and homoeologous gene duplication effects, which are resolved unambiguously by the transmission test. This approach will also be applicable to other agronomically important cross-pollinating allopolyploid plant species.
Keyword Candidate gene
Comparative genomics
Functional variation
Legume
Segregation analysis
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collection: Scopus Import
 
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