Identification and Parentage Analysis of Citrus Cultivars Developed in Japan by CAPS Markers

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Identification and Parentage Analysis of Citrus Cultivars Developed in Japan by CAPS Markers The Horticulture Journal 86 (2): 208–221. 2017. e Japanese Society for doi: 10.2503/hortj.OKD-026 JSHS Horticultural Science http://www.jshs.jp/ Identification and Parentage Analysis of Citrus Cultivars Developed in Japan by CAPS Markers Keisuke Nonaka1*, Hiroshi Fujii1, Masayuki Kita2, Takehiko Shimada1, Tomoko Endo1, Terutaka Yoshioka1 and Mitsuo Omura3 1NARO Institute of Fruit Tree and Tea Science, Shizuoka 424-0292, Japan 2NARO Western Region Agricultural Research Center, Zentsuji 765-8508, Japan 3Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan To protect the rights of breeders of the major citrus cultivars developed under breeding programs by the national institute of Japan, we developed a method of cultivar identification based on cleaved amplified polymorphic sequence (CAPS) markers, and used it to evaluate their identity and parentage. We selected 19 CAPS markers that had a single-locus origin and moderate polymorphism, and used them to construct genotyping data for 59 citrus cultivars (including American accessions), local varieties, and selections. Of the 19 CAPS markers, 8 were sufficient to discriminate among all accessions except ‘Mato’ buntan (Citrus grandis Osbeck) and ‘Hirado’ buntan (Citrus grandis Osbeck). Among the 33 Japanese cultivars, the parentage of 30 agreed with that reported, but ‘Setoka’, ‘Southern Red’, and ‘Reikou’ had discrepancies at one or more loci. Using 15 to 18 CAPS markers to validate the putative parentage revealed that the seed parent of ‘Setoka’ was ‘KyEn No. 4’, not ‘Tsunonozomi’, and the pollen parent of ‘Southern Red’ was ‘Osceola’, not ponkan (C. reticulate Blanco). The seed parent of ‘Reikou’ remains unknown. Key Words: breeder rights, genotype, ‘Reikou’, ‘Setoka’, ‘Southern Red’. simultaneously consider how to protect the rights of Introduction farmers and plant breeders from unwarranted damage Citrus is one of the most important genera of fruit concerning the outflow of a new cultivar overseas and trees that are adapted to temperate and subtropical areas the inflow of such products back to the host country. of Japan. The citrus cross-breeding program in Japan Therefore, it has become necessary to develop cultivar began in 1937 at the National Horticulture Research identification techniques (Kunihisa et al., 2003; Station of the Ministry of Agriculture and Forestry, now Ninomiya et al., 2015). The rights of plant breeders are the Okitsu Citrus Research Station of the National of increasing interest worldwide. The International Agriculture and Food Research Organization Institute Union for the Protection of New Varieties of Plants of Fruit Tree Science (NIFTS). The program has con- (UPOV; http://www.upov.int/index_en.html, June 14, tinued since 1964 at the NIFTS Okitsu and Kuchinotsu 2016) has provided and promoted effective systems of Citrus Research Stations. It is focused mainly on im- plant variety protection. For example, UPOV’s working proving fruit quality, with the goals of a high sugar con- group on Biochemical and Molecular Techniques, and tent, excellent flavor, seedlessness, ease of peeling, and DNA-profiling in particular (BMT), has encouraged the presence of a thin locular membrane, which are charac- use of DNA profiling techniques to protect the rights of teristics specific to mandarins. The program released 41 plant breeders (Shoda et al., 2012). new citrus cultivars by means of controlled cross- To help identify citrus cultivars developed in Japan breeding between 1963 and 2014. by using DNA-profiling techniques, several research When we develop a new plant cultivar, we must groups have reported the development of DNA markers (Matsuyama et al., 1992; Omura et al., 2004; Ueda et al., 2003). However, information on these markers, Received; June 14, 2016. Accepted; August 17, 2016. First Published Online in J-STAGE on October 4, 2016. their polymorphisms and their application to important * Corresponding author (E-mail: [email protected]). commercial cultivars has not been made fully available © 2017 The Japanese Society for Horticultural Science (JSHS), All rights reserved. Hort. J. 86 (2): 208–221. 2017. 209 to the public. Recently, Ninomiya et al. (2015) reported et al., 1999d; Moriya et al., 2011; Ninomiya et al., that 33 citrus cultivars or accessions, including 7 local 2015; Sawamura et al., 2004, 2008; Yamamoto et al., varieties and 11 cultivars collected from abroad, could 2003). However, citrus cultivars developed in the be identified from polymorphisms at 11 cleaved ampli- NIFTS breeding program have generally not been in- fied polymorphic sequence (CAPS) markers. However, vestigated to confirm their parent–offspring relation- this information was not sufficient because the acces- ships, even though they have frequently been used as sions they examined included only 8 of 41 cultivars de- parents in other breeding programs. veloped by NIFTS that are commercially produced and Here, we aimed at establishing a method for identifi- frequently used as parents in citrus breeding programs cation of the citrus cultivars developed by the citrus in Japan. breeding program in Japan by using a subset of the In Citrus, a variety of DNA marker types have been CAPS markers developed by Shimada et al. (2014). We developed. These include random amplified polymor- also aimed at confirming the parent–offspring relation- phic DNA (RAPD), restriction-fragment-length poly- ships of these cultivars by adding related cultivars and morphism (RFLP), amplified-fragment-length selections in the analysis to increase the reliability of polymorphism (AFLP), CAPS, and simple sequence re- the identification. Using the results of this analysis, we peat (SSR) markers (Cai et al., 1994; Chen et al., 2008; investigated candidate parents of the cultivars that had Jarrell et al., 1992; Ollitrault et al., 2010; Omura et al., discrepancies in the parent–offspring relationships. 2003; Ruiz and Asins, 2003; Shimada et al., 2014). Materials and Methods CAPS markers utilize amplified DNA fragments di- gested with a restriction endonuclease to reveal Plant material and DNA preparation restriction-site polymorphisms (Konieczny and We selected 59 citrus cultivars, local varieties and se- Ausubel, 1993). CAPS markers have several advan- lections that were developed or used as parents in the tages for the identification of cultivars and for parent- NIFTS citrus breeding program (Table 1), for use in the age analysis. They are more applicable to a wide range CAPS analysis. ‘Okitsu-wase’, ‘Trovita’, and ‘Yoshida’ of cultivars and selections than is the case for RAPD were chosen for the analysis as representative mutants and RFLP molecular-marker systems. In addition, they of satsuma mandarin (Citrus unshiu Marc.), sweet are easy to assay, require only a few nanograms of orange (C. sinensis (L.) Osbeck), and ponkan DNA for the PCR amplification, and are mainly in- (C. reticulata Blanco), respectively. All plant materials herited in a codominant manner. CAPS markers are ro- were obtained from the NIFTS collections at bust because an amplified product is always obtained, Kuchinotsu Citrus Research Station (Nagasaki, Japan) whereas RAPD and AFLP markers have inherently null and Okitsu Citrus Research Station (Shizuoka, Japan). alleles (Iwata et al., 2001). Shimada et al. (2014) devel- Total DNA was isolated from fully expanded fresh oped 708 CAPS markers from sequenced-tagged-site leaves by using the Qiagen DNeasy Plant Mini Kit (STS) primers with designs based on cDNA (i.e., ex- (Qiagen, Hilden, Germany), following the manufactur- pressed sequence tags; ESTs) and used them to con- er’s instructions. struct a linkage map for citrus. Pedigree information is also important for traditional CAPS analysis fruit tree breeding to estimate the values of various pa- The CAPS genotypes were identified by using 37 of rameters for genetic analysis or to predict the target trait the citrus CAPS markers developed by Shimada et al. characteristics of the offspring (Sato et al., 2006; (2014) that showed high versatility in the cultivars and Yamada et al., 1994, 1995b, 1997). As high-throughput selections used in this study (Table 2). Each CAPS am- single nucleotide polymorphism (SNP) genotyping plification was conducted in 12.5 μL of 10 mM technologies have developed rapidly, a genotyping Tris·HCl (pH 8.3), 50 mM KCl, 2.5 mM MgCl2, method for SNPs based on the GoldenGate assay 0.16 mM each dNTP, 10 pM each forward and reverse (Illumina, San Diego, California, USA) has been devel- primers, 10 ng of genomic DNA, 1.25 units of oped for citrus (Fujii et al., 2013b). Unfortunately, mis- AmpliTaq Gold DNA polymerase (Roche, Branchburg, genotyping often occurs in high-throughput genotyping NJ, USA), and the manufacturer’s PCR buffer for the (Close et al., 2009). Fujii et al. (2013b) showed that polymerase. After 10 min of denaturation at 94.5°C, parentage information could be used to detect mis- amplification was performed using 35 cycles of 1 min genotyping. Therefore, it is also important to confirm denaturation at 94°C, 1 min annealing at 52 to 64°C parent–offspring relationships for cultivars by using tra- (Table 2), and a 2 min extension at 70°C, followed by a ditional molecular markers and to provide the correct 10-min final extension at 70°C. The PCR products were pedigree information for use in fruit tree breeding pro- checked using a 200-bp ladder marker using 1.5% aga- grams. In perennial fruit tree species, discrepancies in rose gel electrophoresis. parent–offspring relationships of some cultivars have The PCR products were digested with restriction en- been found and corrected by using molecular markers zymes (Takara Bio Inc., Shiga, Japan) (Table 2) under (Kimura et al., 2003; Kitahara et al., 2005; Matsumoto the following conditions. We mixed 4 μL of the PCR Table210 1. Citrus cultivars, local varieties,K. Nonaka, and other H. Fujii, selections M. Kita, used T. inShimada, the present T. Endo, study. T. Cultivars Yoshioka 1 andto 33 M. were Omura developed by the citrus breeding pro- gram at the national institute of Japan and were used for parentage analysis.
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