Breeding Science 62: 248–255 (2012) doi:10.1270/jsbbs.62.248 Clone identification in Japanese flowering cherry (Prunus subgenus Cerasus) cultivars using nuclear SSR markers Shuri Kato*1), Asako Matsumoto1), Kensuke Yoshimura1), Toshio Katsuki2), Kojiro Iwamoto2), Yoshiaki Tsuda3), Shogo Ishio4), Kentaro Nakamura4), Kazuo Moriwaki5), Toshihiko Shiroishi6), Takashi Gojobori6) and Hiroshi Yoshimaru2) 1) Department of Forest Genetics, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan 2) Tama Forest Science Garden, Forestry and Forest Products Research Institute, 1833-81 Todorimachi, Hachioji, Tokyo 193-0843, Japan 3) Department of Evolutionary Functional Genomics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden 4) Tsukuba Research Institute, Sumitomo Forestry Co., Ltd., 3-2, Midorigahara, Tsukuba, Ibaraki 300-2646, Japan 5) RIKEN BioResource Center, 3-1-1 Koyadai,Tsukuba, Ibaraki 305-0074, Japan 6) National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan Numerous cultivars of Japanese flowering cherry (Prunus subgenus Cerasus) are recognized, but in many cases they are difficult to distinguish morphologically. Therefore, we evaluated the clonal status of 215 des- ignated cultivars using 17 SSR markers. More than half the cultivars were morphologically distinct and had unique genotypes. However, 22 cultivars were found to consist of multiple clones, which probably originate from the chance seedlings, suggesting that their unique characteristics have not been maintained through propagation by grafting alone. We also identified 23 groups consisting of two or more cultivars with identical genotypes. Most members of these groups were putatively synonymously related and morphologically iden- tical. However, some of them were probably derived from bud sport mutants and had distinct morphologies. SSR marker analysis provided useful insights into the clonal status of the examined Japanese flowering cher- ry cultivars and proved to be a useful tool for cultivar characterization. Key Words: Cerasus, clone identification, cultivars, Prunus, SSR, microsatellite, taxonomy. Introduction Arakawa-zutsumi (Koidzumi 1913, Miyoshi 1916, Wilson 1916). Later works established a taxonomy for the cultivars Flowering cherries (members of Prunus subgenus Cerasus, (Flower Association of Japan 1982, Kawasaki 1993) that is Rosaceae) are the most popular ornamental trees in Japan, now widely accepted (Ohba et al. 2007). However, it is dif- and have been cultivated for more than 1,000 years (Flower ficult to classify the cultivars’ morphological characteristics, Association of Japan 1982, Kuitert 1999). There are more which can vary with weather and nutrient conditions and are than 200 traditional cultivars in Japan (Kobayashi 1992), sometimes affected by their rootstocks. Consequently, which mainly differ in flower color, form, size and number seemingly different cultivars may really be different clones of petals. Some have been exported widely and are grown of the same cultivar, i.e. synonymous cultivars (Ohba et al. world-wide. Most cultivars have been clonally propagated to 2007). Such incorrect classification may also arise from avoid the dilution or loss of their unique characteristics and management errors such as mislabeling and/or mistrans- many are believed to have originated from native Japanese planting. Consequently, morphology-based classification of taxa (Kawasaki 1993, Koidzumi 1913, Kuitert 1999, cultivars is complicated and needs to be reviewed thorough- Miyoshi 1916). Some are considered to be related with ly. While many taxonomists are primarily interested in the P. campanulata, which is endemic to Taiwan, southern origin and pedigree of the cultivars, which are reflected in China and neighboring countries and P. pseudo-cerasus, a their morphological traits and were the primary focus of pre- native of China (Kawasaki 1993). The first morphological vious studies, the key objective in contemporary research is studies on Japanese flowering cherry cultivars were con- to determine the trees’ clonal status. ducted in the early 20th century, focusing on the cultivars in Molecular genetics provides powerful tools for identify- ing clones in plant cultivars. In particular, nuclear simple se- Communicated by T. Yamamoto quence repeat (SSR) markers have proven to be extremely Received December 26, 2011. Accepted May 5, 2012. useful for characterizing cultivars. The key advantages of *Corresponding author (e-mail: [email protected]) SSR markers are their codominant mode of inheritance and Clone identification in flowering cherry cultivars 249 hypervariability, which make them ideal for diverse applica- NIG or SGNS, as appropriate. The nominal designation for tions (Goldstein and Schlötterer 1999). They have therefore each tree was the cultivar name recorded in the archives; found widespread use for identifying clones within cultivars many of these cultivar names were published in one of 10 of many fruit tree species that are closely related to the scientific papers (Asari 1995, Hayashi 1985, Kawasaki Japanese flowering cherry. These include sweet cherry, 1959, 1993, Kimura 1982, Kubota 1982, Ministry of Agri- Prunus avium (Wünsch and Hormaza 2002); peach, Prunus culture, Forestry and Fisheries 1981, Ohwi 1973, Tamura persica (Aranzana et al. 2003, Yamamoto et al. 2003) and and Iyama 1989 and a chapter written by Tanaka, H. in Ohba the apricot species, Prunus armeniaca and Prunus mume 2007). We observed flower characteristics especially calyx (Maghuly et al. 2005 and Hayashi et al. 2008, respectively). tube and calyx lobe according to the description of Molecular genetics techniques have not been applied exten- Kawasaki (1993). When the nominal designation and ob- sively to Japanese flowering cherry cultivars. Hattori et al. served characteristics of sampled tree matched with the (2002) analyzed several cultivars and identified two pairs of names and morphological characteristics described in these putative synonymous cultivars, each of which has identical papers, we identified it as a cultivar. However, some trees genotypes, and the clonal status of P. ×yedoensis could not be confirmed only from their morphological char- ‘Yedoensis’ (Somei-yoshino), the most common cultivar in acteristics. The notation of the scientific name in this paper Japan, has been confirmed by molecular genetic approaches followed that of Kawasaki (1993), but the cultivar epithets (Iketani et al. 2007, Innan et al. 1995). However, the clonal of Kawasaki (1993) were described using “cv.”. The usage status of many other cultivars remains unclear (Ohba et al. of “cv.” is not permitted in the current international code of 2007). nomenclature for cultivated plants (Brickell et al. 2009). The objective of the study reported here was to investi- Therefore, cultivar epithets were corrected by enclosing gate the clonal status of selected Japanese flowering cherry them within single quotation marks. The scientific name that cultivars using SSR markers. We increased the reliability of should be revised elsewhere exists, but is regarded as a fu- the gathered data by performing comparative analyses of ture issue. cultivars growing at multiple locations. Trees grown at the sampling sites were separated into distinct cultivated lines, DNA analysis for each of which archived records detailing its supplier and DNA was isolated from leaves of each sampled tree fol- nominal designation were available. We therefore began by lowing Murray and Thompson (1980). Genotypes of the checking the accuracy of the records for each cultivated line, samples were scored using three genomic SSRs (Ishio et al. then genotyped the lines and compared the genotypic and patent pending) and 14 SSRs in expressed sequence tags nominal classifications. (ESTs), i.e. EST-SSRs (Tabe 1). Eleven of the EST-SSRs were previously reported by Tsuda et al. (2009) and one by Materials and Methods Xu et al. (2004). The other two were developed in the course of this study, according to the procedure of Tsuda et al. Sample collection and archival records (2009); their designations and the corresponding primers are Samples were obtained from the collections of cultivated DN556408 (forward primer, 5′-attcttcttccgccacttctgaat-3′; taxa maintained in the Tama Forest Science Garden (TFSG; reverse primer, 5′-gtttagatcacagcacgcgaaaatg-3′) and Hachioji, Tokyo, Japan) of the Forestry and Forest Products DW358868 (forward primer, 5′-attgatttcggacccataaaaccc-3′; Research Institute (FFPRI), National Institute of Genetics reverse primer, 5′-gtttacaacatcacgtacgggcctc-3′). PCR am- (NIG; Mishima, Shizuoka, Japan) and Shinjuku Gyoen plification was performed in 2 μl reaction mixtures contain- National Garden (SGNG; Shinjuku, Tokyo, Japan). A total ing 5 ng of template DNA, 1× Qiagen multiplex PCR master of 1986 trees were sampled—1567 from the TFSG, 331 mix and the appropriate primers. Multiplex PCR was per- from the NIG and 88 from the SGNG. The morphological formed using conditions recommended by Qiagen. PCR traits of the sampled trees growing in the field were recorded products were separated using an ABI 3100 Avant Genetic and sampled leaves were frozen immediately then stored Analyzer with the GeneScan software system or an ABI frozen until DNA extraction. We also prepared the flower 3130 Genetic Analyzer (Applied biosystems, USA). To specimens of almost sampled trees and deposited in the avoid the electrophoresis results possibly