CGN18108 it is

Simon Foster very kindly took the trouble to post a comment setting the record straight on the source of that blight gene:

Apologies, a previous tweet from ourselves erroneously confirmed the accession as CGN18000. It is in fact CGN18108 which is still listed in the database as Solanum okadae (was subsequently found to be S. venturii in DNA fingerprinting studies).

The origin of Rpi-vnt1 is detailed in the original research paper describing the cloning and characterisation of the gene and which is cited in the Roy. Soc. paper published yesterday. All acknowledgement of sources was published in that paper.

Foster SJ, Park T-H, Pel M, Brigneti G, Sliwka J, Jagger L, van der Vossen E, Jones JDG. 2009 Rpi- vnt1.1, a Tm-2(2) homolog from Solanum venturii, confers resistance to potato late blight. MPMI 22, 589 – 600. (doi:10.1094/MPMI-22-5-0589)

Here’s the relevant bit of that paper:

Accessions of S. venturii and S. okadae were obtained from the Centre for Genetics Resources in Wageningen, the Netherlands (CGN) (Table 1). The S. venturii accessions were originally listed as S. okadae in the CGN database but have recently been reclassified based on work using amplified fragment length polymorphism (AFLP) markers to study the validity of species labels in Solanum section Petota (Jacobs 2008; Jacobs et al. 2008).

So my apologies to Dr Foster. There is indeed a very full and proper acknowledgement of the source of the gene in the earlier paper. However, I do still think that it would not really have taken much effort to also include an acknowledgement in the later paper. The confusion over which accession was actually used that I fell into, admittedly without taking the trouble of following the references, is evidence of why it’s important to do so.

Now to suggest to CGN that they may want to change the species name of CGN18108 in their database…

LATER: Just realized we started talking about all this quite a while ago.

2 Replies to “CGN18108 it is”

  1. In general gene banks should be conservative in renaming accessions and not follow the latest publication, unless there is a clear misclassification. Solanum venturii was published in 1960 and S. okadae in 1983 both by Hawkes & Hjerting. After 1983 most of the venturii accessions were renamed into okadae (by the Argentinian potato taxonomist K.A. Okada). S. venturii acc are all from ARG, whereas okadae acc originate from ARG as well as BOL. Hawkes (1990) indicates that these two species are closely related. Therefore, it should not be surprising to find VNT genes in S. okadae. AFLP and morphological studies (Van den Berg & Groendijk-Wilders, 2007; Van den Berg & Groendijk-Wilders, unpublished; Jacobs et all 2011), indicate that the two species are difficult to distinguish and that the okadae acc form an ARG and a BOL group, where the ARG group seems to cluster closer with S. venturii. Spooner suggests to rename the Argentinian okadea acc into venturii. See this on S. venturii and this on S. okadae. So far none of the gene banks (incl. the US potato genebank in Sturgeon Bay) followed this option.

    The suggestion on this Weblog, that CGN should rename accessions CGN18108 (from ARG) into S. venturii should probably include all okadae’s from ARG. However, taxonomy is a sensitive issue. So far, CGN was reluctant to rename okadae accessions, in particular as long as Sturgeon Bay does not rename them. Too much renaming may confuse/annoy the users of the germplasm. The discussion on this Weblog at least triggers to take a look into the available data again. Personally, I would not be surprised to once find these two species reunited again…

    Roel Hoekstra, CGN, Wageningen, the Netherlands

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