TaqMan® SNPs Summary Statistics
Total number of markers available: 4,800
Mapped markers available: 4,735
TaqMan® Assays are a gold standard in qPCR applications and the technology is based on 5’ nuclease chemistry using specific fluorescent probes to discriminate SNP variants. These assays come as single tube, pre-formulated primer and probe sets which can be used right out of the box requiring no optimization or laborious setup. Assays are available from ThermoFisher Scientific.
TaqMan® Assays were used on a 'core marker set' of 960 SNPs which, based on the Avalon x Cadenza genetic map, were selected to be evenly distributed across the wheat genome.
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | Total | |
|---|---|---|---|---|---|---|---|---|
| A | 227 (224) | 278 (252) | 232 (232) | 128 (240) | 262 (232) | 265 (201) | 243 (228) | 1635 (1609) |
| B | 414 (238) | 356 (260) | 281 (278) | 156 (230) | 362 (244) | 249 (254) | 113 (252) | 1931 (1756) |
| D | 386 (169) | 207 (204) | 46 (216) | 66 (181) | 227 (210) | 117 (177) | 120 (204) | 1169 (1361) |
| Total | 1027 | 841 | 559 | 350 | 851 | 631 | 476 | 4735 |
Table showing the number of TaqMan® 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 (4,735), 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 article 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.
Maintained by Mark Winfield.