ELSEVIER Scientia Horticulturae 94 (2002) 157-170 ww.elsevier.comilocate!scihorti Defining the sources of Paradox: DNA sequence markers for North American walnut (Juglans L.) species and hybrids Daniel potter*, Fangyou Gao, Scott I3aggett1, James R. McKenna, Gale H. McGranahan Department of Pomology, 1045 Wickson Hall, University of Cal@brnia, One Shielclf Avenue, Davis, CA 95616, USA Accepted 14 September 2001 Abstract One of the most important rootstocks in the California walnut industry is Paradox, which refers to the offspring of a California black walnut pollinized by a Persian walnut (Juglans regia). Paradox was developed by Luther Burbank, who did not distinguish between northern (J. hindsii) and southern (J. californica) California black walnut. Although it is generally accepted that Paradox designates hybrids between J. hindsii and J. regia, the name is commonly applied to any black walnut-Persian walnut hybrid. Moreover, due to gene flow among black walnut species, the genealogy of Paradox hybrids may also include species such as Arizona (J. major) and Eastern black (J. nigra) walnut. Since the nuts from which Paradox seedlings are grown are collected from wild trees, their genetic backgrounds are not generally known. In conjunction with a large study aimed at evaluating Paradox hybrids from different industry sources, we have been working to develop molecular markers that can be used to infer the parentage of individual Paradox seedlings. Representatives of the five black walnut species from North America were screened for variability in the internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA and in three noncoding regions from the chloroplast genome, the tmT-tvnL, trnL-tmF, and tmD-tmT spacers. Unique sequence markers were identified for each species, and total DNA extracts from 27 Paradox source trees were tested for those markers. Chloroplast DNA profiles were used to trace the maternal lineages of the Paradox source trees, while the ITS data provided evidence as to whether or not the source trees were themselves hybrids. Our results indicate that, among industry * Corresponding author. Tel.: $- 1-530-754-6141 ; fax: 11 -530-752-8502. E-mail address: dpotter@ucdavis.edu (D. Potter). ' Present address: PkD. Program Biology, Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, NY 10458, New York. 0304-4238/02/$ - see front matter e 2002 Elsevier Science B.V. All rights reserved. PII: SO304-4238(01)00358-2