Supporting Information (SI) Appendix - Proceedings of the National ...

Supplementary Text
Biases in grape germplasm collections: a cautionary note
The conclusions from the present study are based on samples from the USDA grape germplasm
collection. The USDA grape germplasm collection harbors one of the most (if not the most)
extensive collection of grape genetic diversity in the world. Nevertheless, it is unclear to what
extent this collection represents an unbiased sample of the worldwide genetic diversity of
vinifera. It is possible, for example, that the proportion of the morphological diversity in the
collection that is represented by clonal mutants is a poor representation of this proportion in
vinifera worldwide. It is also possible that the extent to which vinifera cultivars are related by
first degree relationships is less or more than expected from an exhaustive survey of vinifera
worldwide. All germplasm collections are biased in complex and often unknown ways. This
study is therefore an evaluation of genetic diversity in the USDA grape germplasm collection
and is not an unbiased survey of worldwide genetic variation within vinifera. The reader should
take this cautionary note into consideration when interpreting the results of the present study.
Potential misnaming of cultivars
The cultivar names associated with each DNA sample are, in some cases, clearly incorrect.
There are numerous examples of such mismatches between names and their inferred genetic
relatedness (see ftp://ftp.gramene.org/pub/vitis_2010_files/): Kyoho (DVIT 616) is actually
Affenthaler; Mamelon (DVIT 586) is in fact Perle de Csaba; Gamay (DVIT 732) is likely not a
true Gamay because of its inferred pedigree relationships. We have therefore not only provided
the name associated with each DNA sample, but also the DVIT number, which is a unique
identifier carried by each grapevine in the USDA grape germplasm collection. The naming
inaccuracies may be due to curation error, sample mix-up or other synonym and homonym
problems, which are common in germplasm collections. However, DNA sample mix-up is an
unlikely explanation for most inaccuracies because sample processing was done primarily with
robotics and we observed no discordance for 145 pairwise comparisons between replicate
samples placed randomly across sample plates. Thus, we conclude that the cases of cultivar
misidentification in the USDA grape germplasm collection are likely often due to curation error.
We are confident that our main conclusions will not be strongly influenced by these inaccuracies