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

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...

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Bibliographic Details
Published in:Molecular genetics and genomics : MGG 2007-04, Vol.277 (4), p.413-425
Main Authors: 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
Format: Article
Language:English
Subjects:
Arabidopsis - genetics
Arabidopsis thaliana
Candidate gene
Chromosomes, Plant - genetics
Comparative genomics
Fabaceae
Functional variation
Gene Duplication
Gene Library
Grasses
legumes
Medicago sativa - genetics
Medicago truncatula
Plant growth
Ploidies
Polymorphism, Single Nucleotide
Segregation analysis
Trifolium - genetics
Trifolium repens
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Summary: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.
ISSN:1617-4615
1617-4623
DOI:10.1007/s00438-006-0198-5