Four cleaved amplified polymorphic sequence (CAPS) markers for the detection of the Juglans ailantifolia chloroplast in putatively native J. cinerea populations

Abstract

Hybridization between butternut (Juglans cinerea), a forest tree native to eastern North America, and Japanese walnut (J. ailantifolia), a tree tolerant to the lethal fungal disease butternut canker, casts doubt on the genetic identity of the remaining butternuts. We report a diagnostic test to distinguish the J. cinerea chloroplast from the J. ailantifolia chloroplast using cleaved amplified polymorphic sequences resolvable in 1.5% agarose gels. J. ailantifolia maternal ancestry in naturally regenerated stands provides a site selection criterion for studies of introgression dynamics when the non-native parent and the hybrids tolerate a disease to which the native species is susceptible.

DNA markers identify hybrids between butternut (Juglans cinerea L.) and Japanese walnut (Juglans ailantifolia Carr.)

“…The trnT UGU -trnF GAA region, like other regions of the chloroplast, has been used extensively in plant systematic to differentiate among taxa (Olmstead and Palmer 1994;Won and Renner 2005). There are only a few species-specific markers for the Juglandaceae (Germain et al 1993;Potter et al 2002;McCleary et al 2009). Now that the regeneration of butternut has become a pressing concern, there is a need to develop concomitant molecular methods to identify nonhybrid butternut (Ostry and Woeste 2004).…”

“…They are simple to use, produce results quickly, and do not require any prior information concerning the DNA template, but they are sensitive to minor changes in reaction conditions during polymerase chain reaction (PCR) amplification, which can result in irreproducible results ). RAPD markers can be made more robust by converting them into sequence-specific, PCR-based markers such as a sequence characterized amplified regions (SCAR; Yang and Korban 1996;Yan et al 2005;Rahman et al 2007) or cleaved amplified polymorphic sequences (CAPS; Konieczny and Ausubel 1993;Farinhό et al 2007;McCleary et al 2009). …”

“…Chloroplast polymorphisms are powerful genetic tools for identifying matrilineal family groups, studying intraspecific population structure and gene flow from seed versus pollen movement and reconstructing phylogeographic colonization (Marshall et al 2002). To detect introgression of J. ailantifolia into native J. cinerea populations, McCleary et al (2009) developed four chloroplast markers polymorphic between the two species. We focused on the fast-evolving trnT UGUtrnF GAA region of the chloroplast, which contains the trnL UAA exon and intron, as well as a pair of spacer regions (Borsch, et al 2003).…”

Geographically extensive hybridization between the forest trees American butternut and Japanese walnut

“…We genotyped with three different chloroplast cleaved amplified polymorphic sequence (CAPS) markers to detect species-specific chloroplast haplotypes (McCleary et al 2009). CAPS products were visualized using electrophoresis in 1.5 per cent agarose gels.…”

“…To investigate the possibility of genetic invasion, we developed a set of nuclear microsatellite markers ( Hoban et al 2008) and a set of chloroplast markers (McCleary et al 2009) to reliably identify the parent species and hybrids. As no definitive silvic characters distinguish hybrids from J. cinerea (Ross-Davis et al 2008), identification using DNA markers is essential.…”