KASP SNPs Summary Statistics
- Total number of varietal SNPs in SNP database: 99,945
- Markers for which assays have been developed: 8,700
- Marker assays that have been validated: 7,228
- Markers that have been mapped: 4,992
This study was undertaken to mine UK wheat germplasm for varietal SNPs. 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 (23 wheat varieties were used in the initial study). We then investigated whether these SNPs could be validated by the LGC Genomics (formerly KBioscience) high-throughput genotyping procedure, Competitive Allele-Specific polymerase chain reaction (KASP) 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.).
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | Total | |
|---|---|---|---|---|---|---|---|---|
| A | 236 (236) | 286 (266) | 239 (244) | 130 (253) | 267 (244) | 269 (212) | 248 (240) | 1675 (1695) |
| B | 428 (251) | 369 (274) | 290 (293) | 156 (242) | 374 (257) | 253 (268) | 116 (266) | 1986 (1851) |
| D | 438 (178) | 240 (215) | 53 (227) | 69 (191) | 256 (221) | 141 (187) | 134 (215) | 1331 (1434) |
| Total | 1102 | 895 | 582 | 355 | 897 | 663 | 498 | 4992 |
Table showing the number of KASP SNPs that have been mapped to each of the 21 wheat chromosomes; the expected number, given the relative lengths* of each chromosome and the total number of mapped SNPs (4,992), is shown in parentheses. These data clearly show that far fewer SNPs have been mapped to the D genome than would be expected were the SNPs to be evenly distributed across the genome.
*The total length of the wheat genome (234.4 μm) and the percentage length of each chromosome and genome (A = 34.0% , B = 37.2%, C = 28.8%) were taken from Gill, B.S., Friebe, B. and Endo, T.R. (1991) Standard karyotype and nomenclature system for description of chromosome bands and structural aberrations in wheat, Genome 34: 830-839; the paper reports on the relative length in the variety Chinese Spring, which may differ from that for the varieties used in this study.
Based at the University of Bristol with support from BBSRC.
