Via this web site and associated publications, we have placed all the data related to each and every SNP, including available flanking sequences (usually 120 base pairs or greater), into the public domain. We hope that by making this information freely available without any restrictions, it will encourage other wheat geneticists to do likewise so ensuring that all such markers are made public and free of use. Only by following this principle can we hope to ensure that wheat breeders across the world are in possession of the tools they require to create the new varieties that will be needed to help feed the World beyond 2050.
| The KASPar SNP database contains | |
|---|---|
| Varietal SNPs: | 99945 |
| Validated SNPs: | 4986 |
| Mapped SNPs (Avalon x Cadenza): | 1795 |
| Mapped SNPs (Savannah x Rialto): | 760 |
| Wheat varieties studied: | 101 |
This site has been designed with breeders in mind, and we hope that is will be easy and straightforward to use. Principally the site is aimed at those who wish to obtain information about SNP markers; e.g., the sequence upon which they are based, obtain primers used for their identification, identify the haplotypes of common UK varieties. However, there are pages that describe, in simple terms, what SNPs are and how they can be a wonderful tool for the breeder. To gather such information, please follow the links on the menu bar to the left.
Information on genetic relationships among individuals is of importance to plant breeders for line and hybrid development. Estimates on the genetic similarity of breeding materials is best obtained using DNA markers. The most abundant genetic polymorphisms between individuals are Single Nucleotide Polymorphisms. SNPs are single base pair positions at which different sequence alternatives exist between two individuals (a simple description can be found here).
The work behind this study was undertaken to mine the UK wheat germplasm for varietal SNPs. Twenty-three wheat varieties were used in the initial study (see table below). To do this, we used both the available wheat expressed sequence tags (ESTs) that are reposited in the public databases and next-generation sequencing (NGS), together with a novel sequence alignment and assembly approach to identify varietal SNPs in lines of interest to European wheat breeders. We then investigated whether these SNPs could be validated by a relatively new, high-throughput genotyping procedure, the KBioscience Competitive Allele-Specific polymerase chain reaction (KASPar) assay. Finally, we made use of the existing Avalon X Cadenza mapping population to examine whether the validated SNPs could be efficiently placed onto the existing linkage groups identified within this doubled haploid population. The details of this work are available in the article Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.).
| Wheat variety | Breeder/Source | Ploidy | Planting | Pedigree |
|---|---|---|---|---|
| Alcedo | NIAB | Hexaploid | Winter | (Record AUT x Poros) x Carstens-VIII |
| Alchemy | Limagrain UK Ltd | Hexaploid | Winter | Claire x (Consort x Woodstock) |
| Avalon | Plant Breeding International Cambridge Ltd. | Hexaploid | Winter | Maris-Ploughman x Bilbo |
| Bacanora | CIMMYT | Hexaploid | Spring | (Jupateco-73 x BlueJay) x Ures-81 |
| Brompton | Elsoms Seeds Ltd | Hexaploid | Winter | CWW 92.1 x Caxton |
| Cadenza | CPB Twyford Ltd | Hexaploid | Spring | Axona x Tonic |
| Chinese Spring (L42) | JIC | Hexaploid | Spring | A Chinese Land Race |
| Claire | Limagrain UK Ltd | Hexaploid | Winter | Wasp x Flame |
| Croc | WGGRC | Tetraploid | Spring | Triticum turgidum subsp. Dicoccoides (AB genome) |
| Hereward | RAGT seeds Ltd | Hexaploid | Winter | Norman ‘sib’ x Disponent |
| Opata | CIMMYT | Hexaploid | Spring | Bluejay x Jupateco-73 |
| Recital | C.C. Benoist | Hexaploid | Winter | Mexique-267 (R-267) x 9369 |
| Renan | INRA | Hexaploid | Winter | (Mironovskaya-808 x Maris-Huntsman) x Courtot |
| Rialto | RAGT seeds Ltd | Hexaploid | Winter | Haven x Fresco |
| Robigus | KWS UK Ltd | Hexaploid | Winter | Z836 x 1366 (PUTCH) |
| Savannah | Zeneca Seeds UK Ltd. | Hexaploid | Winter | Riband x Brigadier |
| Shamrock | Verneuil Recherche | Hexaploid | Winter | COMPL TIG 323-1-3m x CWW 4899/25 |
| Soissons | Maison Florimond Desprez France | Hexaploid | Winter | Iena (Jena) x HN35 |
| Synthetic | John Innes Centre | Hexaploid | Spring | Unknown |
| Synthetic 39 | WGGRC | Hexaploid | Spring | TA1618 x Croc |
| TA1618 | WGGRC | Diploid | Spring | Aegilops Tauschii (D genome) |
| Weebil | CIMMYT | Hexaploid | Spring | Unknown |
| Xi19 | Limagrain UK Ltd | Hexaploid | Spring | (Cadenza x Rialto) x Cadenza |