Putatively mapped varietal SNPs

The NimbleGen array capture/Illumina NGS sequencing of the 8 varieties Alchemy, Avalon, Cadenza, Hereward, Rialto, Robigus, Savannah and Xi19 produced a large number of putative SNPs (511,439): see articles by Allen et al. (2011) and Winfield et al. (2012). These included both homoeologous (411,494 = 80.5%) and varietal SNPs (99,945 = 19.5%) - see explanatory image below. Of these 99,945 varietal SNPs, only a relatively small number have been validated and mapped (c. 7,000; see the KASP SNP database page of this web site for precise numbers). However, we have provisionally mapped many of the non-validated, putative varietal SNPs. As we fully recognise the potential importance of these, we are making them available here. Please be aware, however, that the chromosome locations provided are only putative and, as further work is carried out, they may be revised.

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The table below gives the number of putative varietal SNPs between any two varieties. To obtain an Excel spreadsheet containing a list of these and the chromosomes to which they are provisionally located click on the blue, underlined numbers in the table below.

Alchemy Avalon Cadenza Hereward Rialto Robigus Savannah Xi19
Alchemy 19,346 14,836 21,528 24,921 16,815 28,776 7,822
Avalon 19,346 7,886 11,735 13,507 9,282 16,307 4,097
Cadenza 14,836 7,886 9,083 355 7,223 11,944 658
Hereward 21,528 11,735 9,083 16,429 11,489 21,965 4,100
Rialto 24,921 13,507 355 16,429 11,831 21,472 1,357
Robigus 16,815 9,282 7,223 11,489 11,831 15,031 3,371
Savannah 28,776 16,307 11,944 21,965 21,472 15,031 6,309
Xi19 7,822 4,097 658 4,100 1,357 3,371 6,309

When considering the numbers presented in the table above, one needs to be aware that the read depth, and thus the number of missing reads, was very different between the eight varieties. The varieties Alchemy and Savannah had the highest read depth and Xi19 had the lowest: the number of missing reads was inversely proportional to the read depth (see bar chart below).

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