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Research Article

Parentage Confirmation of Korean Bred Pear Cultivars by Simple Sequence Repeat SSR Genotyping and S-Genotypes Analysis

Hoy-Taek Kim, Arif Hasan Khan Robin, Ill-Sup Nou,*
Plant Breeding and Biotechnology 2016;4(2):198-211.
Published online: May 31, 2016

Department of Horticulture, Sunchon National University, Suncheon 57922, Korea

*Corresponding author: Ill-Sup Nou, nis@sunchon.ac.kr, Tel: +82-61-750-3249, Fax: +82-61-750-5389
• Received: May 13, 2016   • Revised: May 18, 2016   • Accepted: May 19, 2016

Copyright © 2016 The Korean Society of Breeding Science

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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  • Identification and authentication of parentage are important for effective pear breeding. Within Korean pear cultivars discrepancies are often reported between parents and offspring in skin color of fruits and also in S-genotypes suggesting that reported parentage was often inappropriate. In Korea, the parentage of the most of pear cultivars was never confirmed at the molecular level. Simple sequence repeat (SSR) genotyping and S-genotype analysis are considered effective in identifying parents. In this study, parentage of nine Korean bred cultivars was confirmed using SSR genotyping and S-genotype analysis. A total of 53 SSR markers were used. Six different haplotype-specific endonucleases were used for restriction cleavage of S-genotypes. Most of the Korean bred cultivars had six comparatively shorter S-RNase, S1, S3, S4, S5, S6, or S7 of 450 bp in length whereas the Japanese control cultivars had four other comparatively longer S-RNase. Out of nine pear cultivars only ‘Chuwhangbae’ and ‘Whangkeumbae’ had identical SSR genotypes and S-genotype with previously reported parents. For another cultivar, ‘Sujeonbae’, the parents were the mutants of reported parent, ‘Niitaka’. For four other cultivars, SSR and S-genotypes of offspring matched with only one reported parent ‘Niitaka’ but those of another parent did not match. For the two other pear cultivars ‘Soowhangbae’ and ‘Sooyoung’ none of reported parents were confirmed by SSR genotyping and S-genotype analysis. Historically, the parent ‘Niitaka’ was predominant in the Korean pear breeding programs because of its high yield potential and quality. The methods have been used in this study could be used to identify pear cultivars with diverse S-genotypes to eliminate any existing obscure parent-offspring relations.
  • Key words: Pears, SSR genotype, S-genotype, S-RNase
Pear (Pyrus spp.) is one of the important fruit in the world that is cultivated in more than 50 countries. In Korea, some local pear cultivars such as, ‘Whangsilri’, ‘Cheongsilri’ (Pyrus ussuriensis var. ovoidea Rehder), ‘Cheongdangrori’, ‘Habsilri’ (P. ussuriensis var. viridis T.B. Lee) were being cultivated until the beginning of 19th century. Breeding of Korean pear cultivars (P. pyrifolia Nakai) was started in the late 1920s at the National Institute of Horticultural and Herbal Science (NIHHS) of Rural Development Administration (RDA) in South Korea. The breeding goals at that time were increasing fruit size and improving fruit quality that includes desirable pH, sugar content, flesh firmness and core ratio and also development of disease and pest resistance such as, black spot, scab and mite resistance (Shin et al. 2002). Besides those, utilization of self-compatibility phenomenon was an additional breeding objective aimed to develop labor-saving varieties (Shin et al. 2002). As a part of that extensive pear breeding efforts throughout the 19th century a total of 27 pear cultivars were released by NIHHS between 1969 and 2009 (Cho et al. 2012). A notable number of varieties including ‘Chuwhangbae’, ‘Whangkeumbae’, ‘Hanareum’, ‘Shincheon’, ‘Soowhangbae’, ‘Josengwhangkeum’, ‘Sunhwang’ and ‘Sooyoung’ were bred by using ‘Niitaka’ as one of the parent in those breeding programs. But the same parent ‘Niitaka’ was not used for some other cultivars such as ‘Chuwhangbae’ and ‘Soowhangbae’ (Kim et al. 1986; Hwang et al. 2002; 2005a; 2005b; Shin et al. 2007). Simple sequence repeat (SSR) genotyping in a few notable studies also confirmed that ‘Niitaka’ was not the parent of some pear cultivars as previously reported (Sawamura et al. 2008; Kim and Nou 2016). Other than variation in SSR genotyping of some pear cultivars, such as, ‘Housui’ (Machida et al. 1982; Ishimizu et al. 1998), ‘Kisui’ (Hiratsuka et al. 1998), ‘Tanzawa’ (Castillo et al. 2001), ‘Niitaka’ (Takasaki et al. 2004) and ‘Oharabeni’ (Kim et al. 2007) some of them had discrepancies from their reported parents in terms of skin type and S-genotypes. The registrant parents ‘Ri-14’ (S1S2) and ‘Yakumo’ (S1S4 and/or S2S4) of ‘Housui’ had smooth skin and a different genetic makeup for self-incompatibility compared to their offspring ‘Housui’ (Machida et al. 1982; Ishimizu et al. 1998). Kimura et al. (2003) analyzed the parentage of 14 pear cultivars by using 20 SSR markers and confirmed that ‘Ri-14’ and ‘Yakumo’ were not the parents of ‘Housui’. The parents of ‘Housui’ were ‘Kousui’ (female parent) and ‘Hiratsuka 1 gou’ (synonym ‘I-33’, male parent) as reported by Sawamura et al. (2004) after SSR genotyping. Furthermore, in a separate study parentage of 55 Japanese pear cultivars was identified by using S-RNase allele and 18 SSR markers (Sawamura et al. 2008). The study by Sawamura et al. (2008) thus identified discrepancy of SSR-genotypes between 10 hybrid cultivars (‘Kisui’, ‘Tanzawa’, ‘Niitaka’, ‘Seiryu’, ‘Akemizu’, ‘Atago’, ‘Echigonishiki’, ‘Ishiiwase’, ‘Shusui’, and ‘Yachiyo’) and their previously reported parents and suggested that these hybrid cultivars have new candidate parents. However, identifying the parent-offspring relationships of pear cultivars is very important to improve breeding efficiencies.
Polymorphism exists in S-genotypes at the S-RNase locus that controls self-incompatibility was previously utilized for the identification of Japanese and Korean bred pear cultivars (Ishimizu et al. 1999; Kim et al. 2002; 2007). In addition, DNA marker based profiling techniques could be also utilized for identifying the parents of pear cultivars. Teng et al. (2002) used random amplified polymorphic DNA markers to classify 118 Asian pear cultivars. Monte-Corvo et al. (2001) reported that inter-simple sequence repeat was effective for identifying parents of P. communis L. cultivars of European origin. Kim et al. (2012) analyzed 80 pear cultivars among them 64 were Japanese (P. pyrifolia), 10 were Chinese (P. ussuriensis) and six were European in origin based on their BRIP markers associated DNA profiling. The authors were able to differentiate cultivar ‘Housui’ from the other Japanese pear cultivars. A large number of SSR markers have been developed in the last two decades from genomic DNAs and ESTs in Japanese and European pears (Yamamoto et al. 2002; 2004; Fernandez-Fernandez et al. 2006; Nishitani et al. 2009). The use of these SSR markers has allowed DNA profiling, parentage analysis, and evaluation of genetic diversity in pear cultivars. To discern the real parent-offspring relationship, some apple cultivars were investigated with S-RNase analysis and SSR markers and revealed their true parentage (Kitahara et al. 2005; Moriya et al. 2011)
In Korea, Cho et al. (2012) used 19 sequence-characterized amplified region (SCAR) markers and nine SCAR markers to distinguish 39 pear cultivars (25 Korean pear cultivars and 14 Japanese pear cultivars). Recently, the SNPs, InDels, and SSRs detected between two cultivars ‘Whangkeumbae’ and ‘Minibae’ by using NGS data have been mapped to the reference genome of the Chinese pear ‘Suli’ (P. bretschneideri) (Oh et al. 2015). The number of total SSRs for ‘Whangkeumbae’ and ‘Minibae’ was 75,000 among them 1,200 were found polymorphic. Despite availability of sufficient techniques and markers, to date the parent-offspring relationship of Korean bred pear has not been analyzed. In this study, the nine Korean bred pear cultivars were analyzed using the S-genotypes with S-RNase analysis and SSR genotypes with 53 SSR markers to confirm their parent-offspring relationship.
Plant materials, candidate parent selection and isolation of DNA
The nine Korean bred pear cultivars were collected at the NIHHS (Cho et al. 2012; Table 1). SSR genotyping data of 98 pear cultivars were obtained from the literature (Yamamoto et al. 2002; 2004; 2006; 2007; Kimura et al. 2003; Sawamura et al. 2004; Sawamura et al. 2008; submitted manuscript). Candidate parents were selected using MARCO software with 53 SSR markers information. All candidate parents were of Japanese origin. Twelve candidate parent-pear cultivars were collected at the National Institute of Fruit Tree Science (Ibaraki, Japan) (Sawamura et al. 2008; Table 1). Genomic DNA was extracted from young leaves by using a Genomic tip 20/G (Qiagen, Germany) using the method previously followed by Yamamoto et al. (2006). The extracted genomic DNA was used for SSR analysis and polymerase chain reaction (PCR)-cleaved amplified polymorphic sequences analysis of S-RNases.
Data analysis and SSR genotyping by SSR markers
A total of 53 SSR markers were selected from 96 SSR markers developed for apple and pear (Yamamoto et al. 2002; 2004; 2006; 2007). PCR amplification was performed according Yamamoto et al. (2002) except that the forward primers labeled with a fluorescent dye. The PCR products were separated by electrophoresis on a POP-4 polymer and detected using a Genetic Analyzer 3100 (PE Applied Biosystems, DriveFoster City, CA, USA). The size of amplified bands was scored using an internal DNA standard (GeneScan-400HD ROX; PE Applied Biosystems) with GeneScan software (PE Applied Biosystems). The parent-offspring relationships of Korean bred pear cultivars were analyzed by comparing the SSR alleles in each cultivars with registrant parents using the MARCO software (Fujii et al. unpublished as cited by Shoda et al. 2012). Furthermore, to identify minimal number of marker subsets, MinimalMarker software (Fujii et al. 2007) was used because that was necessary to distinguish all of the cultivars to find out identical genotypes of the 21 cultivars generated by the 53 SSR markers.
S-RNase genotyping by PCR-restriction fragment length polymorphism (RFLP) analysis
PCR amplification was performed using the S-RNase- specific primers, FTQQYQ (TTTACGCAGCAATAT-CAG) and PSprI (DKWCSCRCAGGWGCCATGTTT), which were designed from S-RNase high homology region of pear and amplified S1 to S9-RNase and Sk-RNase, as described by Kim et al. (2007). The amplified S-RNase fragments were checked and digested with the haplotype-specific restriction enzymes SfcI (S1), PpuMI (S3 and S5), NdeI (S4), AlwNI (S5), and BstBI (S9) to determine their size after agarose gel electrophoresis as described by Kim et al. (2002).
Determination of candidate parent of Korean pear cultivars by using SSR genotyping
SSR genotyping based on 53 SSR markers revealed the parentage of nine Korean bred pear cultivars (Table 2). The SSR genotypes of ‘Chuwhangbae’ (‘Imamuraaki’× ‘Nijiiseiiki’) and ‘Whangkeumbae’ (‘Nijiiseiki’×’Niitaka’) were confirmed and matched with the registrant parents SSR genotypes by all SSR markers (Table 2). We confirmed that one SSR allele each from ‘Hannareum’, ‘Shincheon’, ‘Josaengwhangkum’ and ‘Sunhwang’ was inherited from registrant parent ‘Niitaka’, i.e., those 4 pear cultivars had one identical SSR allele of ‘Niitaka’ (Table 2). But they did not have identical SSR alleles with another registrant parents. In addition, two cultivars ‘Soowhangbae’ and ‘Sooyoung’ had different SSR alleles that were not matched with parents (Table 2). Therefore, we concluded that two pear cultivars ‘Chuwhangbae’ and ‘Whangkeumbae’ were bred from a breeding program between registrant parent, but other six pear cultivars were bred from a cross between other non-reported parents. Also, the SSR genotype of ‘Sujeongbae’ being a mutant of ‘Niitaka’ was identical with ‘Niitaka’ (data not shown).
The 53 SSR alleles of five pear cultivars were inherited from SSR alleles of each parent. The candidate parents of ‘Hannareum’ were ‘Niitaka’ and ‘Tama’; those of ‘Shincheon’ were ‘Niitaka’ and ‘Chouju’; those of ‘Sunhwang’ were ‘Niitaka’ and ‘Shinsui’, and those of ‘Soowhangbae’ were ‘Niitaka’ and ‘Nijisseiki’ (Table 3). The cultivar ‘Josaengwhangkum’ was the offspring of ‘Niitaka’ and ‘Nijisseiki’ similar to ‘Whangkeumbae’ although ‘Shinko’ was the reported parent instead of ‘Nijisseiki’ (Table 3). Therefore we suggested that the pear cultivars developed between 1966 and 1986, ‘Soowhangbae’, ‘Josaengwhangkum’ and ‘Whangkeumbae’ were the selected offspring of a cross between ‘Niitaka’ and ‘Nijisseiki’. The cultivar ‘Okusankichi’ was identified as one candidate parent of ‘Sooyoung’ (Table 3). The cultivar ‘Niitaka’ was another reported parent of ‘Sooyoung’ (Table 3). However out 53 SSR alleles not even one allele of ‘Sooyoung’ matched to ‘Niitaka’. Thus the second parent of cultivar ‘Sooyoung’ remain obscure.
S-genotyping by S-RNase PCR-RFLP analysis
The S-genotypes of following five Korean pear cultivars: ‘Sujeongbae’, ‘Hannareum’, ‘Shincheon’, ‘Sooyoung’ and ‘Josaengwhangkum’ were identified by S-RNase PCR- RFLP analysis in this study. The S-genotypes of remaining four cultivars in Table 1 were studied by Kim et al. (2002). The S-RNase PCR analysis amplified S-locus of 11 pear cultivars including six control pear cultivars of Japanese origin and five Korean cultivars. S-genotyping identified nine different types of S-locus from S1 to S9 and Sk-RNase (Fig. 1). S1, S3, S4, S5, S5 or S7 -RNase were about 450 bp in length, S8-RNase was 500 bp in length, Sk-RNase was 1,065 bp length and S2 and S9-RNase were 1,414 bp and 1,374 bp in length respectively. The Japanese control pear cultivars had all S-RNase whereas four Korean cultivars (except ‘Sujeongbae’) had only the shortest S1, S3, S4, S5, S5, or S7-RNase of 450 bp length. The cultivar ‘Sujeongbae’ had S9-RNase in addition to other six types of S-RNase present in four other Korean cultivars (Fig. 1). For the determination of S-genotype, the S-RNase PCR fragments of 5 Korean pear cultivars were digested with S-allele specific enzymes (PpuMI; S3- and S5-allele specific, AlwNI; S5-allele specific, BstBI; S9-allele specific, NdeI; S4-allele specific and ScfI; S1-allele specific) (Fig. 2). The S-RNase PCR fragments of ‘Sujeongbae’ were digested with PpuMI (S3- and S5-allele specific) and BstBI (S9-allele specific), but was not digested with AlwNI (S5-allele specific) (Fig. 2A). Thus, the S-genotype of ‘Sujeongbae’ was determined as S3S9. The S-genotype of ‘Sujeongbae’ corresponded with the S-genotype of ‘Niitkata’ (S3S9) because the ‘Sujeongbae’ is a mutant of ‘Niitkata’ (Fig. 2). The S-RNase PCR fragments of ‘Hannareum’ and ‘Josaengwhangkum’ were digested with S3- and S4-allele specific-enzymes (Fig. 2B, C). The S-genotypes of ‘Hannareum’ and ‘Josaengwhangkum’ were identical, S3S4 (Fig. 2). The S-RNase PCR fragments of ‘Shincheon’ were digested with S1- and S3-allele specific endonucleases. The S5-allele specific endonuclease was unable to digest the S-RNase PCR fragments of ‘Shincheon’ (Fig. 2D). Thus, the S-genotype of ‘Shincheon’ was determined as S1S3 that was not corresponded with the S-genotype of registrant parents ‘Niitaka’ (S3S9) and ‘Chuwhangbae’ (S4S5). The digested S-RNase fragments with PpuMI and AlwNI of ‘Sooyoung’ were identical and that was only S5-RNase (Fig. 2). Thus, the only one S-RNase PCR product of ‘Sooyoung’ was identified; the other S-RNase PCR product was not amplified. Therefore the S-genotype of ‘Sooyoung’ was S5(S5S?). The predicted S-genotype of ‘Sooyoung’ matched neither with registrant parent ‘Niitaka’ (S3S9) nor with ‘Soowhangbae’ (S3S4).
In this study, we confirmed the parents of nine Korean pear cultivars by using the 53 SSR markers and S-RNase based PCR-RFLP analysis. The SSR and S-genotypes of ‘Chuwhangbae’, ‘Whangkeumbae’ and ‘Sujeongbae’ matched with registrant parents; ‘Imamuraaki’×’Nijisseiiki’, ‘Nijisseiki’×’Niitaka’ and mutant of ‘Niitaka’, respectively (Table 4). However, the SSR genotypes of ‘Hannareum’ (S3S4) and ‘Josaengwhangkum’ (S3S4) did not matched with the SSR genotypes of registrant parents, but those matched with SSR genotypes of the new candidate parents (‘Niitaka’(S3S9)×’Tama’(S4S5) for ‘Hannareum’ and ‘Niitaka’ (S3S9)×’Nijisseiki’ (S2S4) for ‘Josaengwhangkum’. Thus our results confirmed that at least one parent of those two pear cultivars was wrongly reported earlier (Table 4).
The S-genotypes of ‘Soowhangbae’ and ‘Sunhwang’ were determined as S3S4 and S3S5 respectively by Kim et al. (2002). However, the authors were unable to confirm the parentage of these two Korean pear cultivars at that time. In this study, the SSR genotypes of two pear cultivars and their registrant parents were found different. Our results suggested that ‘Nijiiseiki’×’Niitaka’ and ‘Niitaka’×’Shinsui’ were the candidate parents of ‘Soowhangbae’ and ‘Sunhwang’ respectively (Table 4). The S3S4 genotype of ‘Soowhangbae’ could not be obtained from registrant parent ‘Chojuro’ (S2S3)×’Kimitsukawase’ (S1S5), but that could be obtained from the new candidate parents ‘Nijisseiki’ (S2S4)×’Niitaka’ (S3S9) (Table 4). ‘Shincheon’ and ‘Sooyoung’ were also different from their registrant parents by their SSR genotyping and S-genotyping. ‘Shincheon’ (S1S3) might be originated from the following candidate parent combination: ‘Niitaka’ (S3S9)×’Chouju’ (S1S5) but the candidate parent of ‘Sooyoung’ was not possible to determine by comparing SSR genotypes of 96 Japanese pear cultivars. Therefore, it could be suggested that ‘Sooyoung’ was possibly a bred of a Korean local cultivars and was not probably a bred of any Japanese pear cultivars (Table 4).
The three Korean pear cultivars namely, ‘Whangkeumbae’, ‘Soowhangbae’ and ‘Josaengwhangkum’ were bred by crossing between ‘Niitaka’×’Nijiiseiki’ as these three cultivars had identical (S3S4) S-genotypes even though fruit characters of those three were different (http://www.nihhs.go.kr/search/search.asp). Seven out of nine Korean bred pear cultivars namely ‘Whangkeumbae’, ‘Hanareum’, ‘Shincheon’, ‘Soowhangbae’, ‘Josengwhangkeum’ and ‘Sunhwang’ were bred using ‘Niitaka’ as a parent probably because ‘Niitaka’ had very high yield potential, producing large fruit with an attractive appearance and good storability (Saito 2016).
In conclusion, we have used 53 reliable SSR markers this study, which were found substantial to determine pear parentage, and the use of S-RNase genes associated PCR-RFLP systems led us towards a reliable determination of S-genotypes. This methods and approaches have been used in this study could be successfully utilized in identifying cultivars with highly diverse S-genotypes and also in identifying obscure relationships between parents and progenies of pear and apple.
We thank Yoon-Kyeong Kim in Pear Research Station, National Institute of Horticultural & Herbal Science for plant materials of Korean bred pear cultivars. This research was supported by Golden Seed Project (Center for Horticultural Seed Development, No. 213003-04-4-SB110) Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), RDA and Korea Forest Service (KFS).
Fig. 1
S-RNase polymerase chain reaction analysis of 6 Japanese pear cultivars of known S-genotypes and 5 Korean bred pear cultivars by using the FTQQYQ-Fam and PsprI primers. Lane 1: Ichiharawase (S1S8), lane 2: Nijisseiki (S2S4), lane 3: Niitaka (S1S9), lane 4: Okusankichi (S5S7), lane 5: Imamuraaki (S1S6), lane 6: Kinchaku (S4Sk), lane 7: Sujeongbae, lane 8: Hannareum, lane 9: Shincheon, lane 10: Sooyoung, lane 11: Josaengwhangkum, and M: 100 bp DNA Ladder.
pbb-4-198f1.jpg
Fig. 2
S-genotypes analysis of five Korean bred pear cultivars by polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis. The S-RNase PCR f[ragments were digested with S-allele-specific restriction enzymes; a: PpuMI (S3 and S5), b: AlwNI (S5), c: BstBI (S9), d: NdeI (S4), e: SfcI (S1). The digested fragments are indicated by arrows.
pbb-4-198f2.jpg
Table 1
The 9 Korean bred pear cultivars and 12 Japanese candidate pear parent cultivars used in this experiment.
Table 1
Cultivar (synonym) Registrant parents Origin
Chuwhangbae Imamuraaki (S1S6)×Nijisseiki (S2S4) Korea
Whangkeumbae Niitaka (S3S9)×Nijisseiki (S2S4) Korea
Hanareum Niitaka (S3S9)×Chuwhangbae (S3S4) Korea
Shincheon Niitaka (S3S9)×Chuwhangbae (S3S4) Korea
Soohwangbae Chojuro (S2S3)×Kimitsukawase (S1S5) Korea
Josaenghwangkeum Niitaka (S3S9)×Shinko (S4S9) Korea
Sunhwang Niitaka (S3S9)×Okusankichi (S5S7) Korea
Sooyoung Niitaka (S3S9)×Soohwangbae (S3S4) Korea
Sujeongbae Mutant of Niitaka (S3S9) Korea
Imamuraaki Breeding process is unknown Japan
Nijisseiki Discovered in 1888, named in 1904 Japan
Niitaka Amanogawa (S1S9)×Chojuro (S2S3) Japan
Chojuro Sown in 1889, fruited in 1893 Japan
Kimitsukawase Shinkozo×Doitsu (S1S2) Japan
Okusankichi Sown in 1840–1850 Japan
Tama Gion (S2S4)×Kosui (S4S5) Japan
Chouju Asahi (S4S5)×Kimitsukawase (S1S5) Japan
Shinsui Kikusui (S4S4)×Kimitsukawase (S1S5) Japan
Shinko Nijisseiki (S2S4)×Amanokawa (S1S9) Japan
Ichiharawase Discovered in 1892 or 1893 Japan
Kinchaku Breeding process is unknown, local cultivar Japan
Table 2
SSR genotyping analysis of registrant parent and nine Korean bred pear cultivars by the 53 SSR markers and the MARCO software.
Table 2
Errorsz) Parent/Offspring Cultivar SSR markersy)
TsuENH003 CN444636 TsuENH045 CH02b10 NH023a NB113a TsuENH074 BGA35 NH011b CH02h11a CH02c02b CH03a09 NB103a
0 Parent Imamuraaki FF BG BD DF BC DH AB EE FG AC BI AC DD
0 Parent Nijiiseiki GG AE DD DF CJ CC CC EE DE BE BF AC BB
0 Offspring Chuwhangbae FG BE BD DF CC CD AC EE DF AE BB AA BD
0 Parent Nijiiseiki GG AE DD DF CJ CC CC EE DE BE BF AC BB
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
0 Offspring Whangkeumbae GG AE DE AD GJ CD AC EE EE BB BB BC BB
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
10 Parent Chuwhangbae FG BE BD DF CC CD AC EE DF AE BB AA BD
11 Offspring Hanareum GG BE BD DD CC CD AC EE EF AD BG BC BD
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
12 Parent Chuwhangbae FG BE BD DF CC CD AC EE DF AE BB AA BD
22 Offspring Shincheon FG AE EE AF CG CE CD EE EF BB BB AA BF
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
17 Parent Shinko FG BE DD DF CC CD AC EE DF AE BG AC BD
20 Offspring Josaengwhangkum GG AE DE DD CG CE CD EE EE BB FG AA BB
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
20 Parent Okusankichi EF BE DD DF CC DE AE AE FF AC BF CC DE
28 Offspring Sunhwang GG BC BE DF GG CE CD AE EE BB BB AA DF
10 Parent Chojuro BC AD BD AA AD CC CD AB BC BE AA AB AC
18 Parent Kimitsukawase CC CD BD AD AC CD CD BB CC AB AA AC BE
34 Offspring Soowhangbae BC AB BC CD BB AC CD BB BD AE AA AC AC
12 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
13 Parent Soowhangbae FG AB BD DF CC CE CD EE DF AE BB AC BD
29 Offspring Sooyoung EF BB AD CF BC DE AD EE AF AA BB AC DD
Parent/Offspring Cultivar SSR markersy)
CH01b11 TsuENH046 TsuENH006 CH04e05 NB114a IPPN13 NH029a TsuENH008 CH05a03 NH039a NH017a EMPc105 CH01f07a
Parent Imamuraaki AA BB BC CG CD AF BB BG BC CE DE CH FG
Parent Nijiiseiki AC AB BC GH AC AE BB JJ BD BB EF AB BF
Offspring Chuwhangbae AC AB BC GH CD AA BB BJ CD BE DF AC FF
Parent Nijiiseiki AC AB BC GH AC AE BB JJ BD BB EF AB BF
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Offspring Whangkeumbae AA BB CC CH CD AC BC CJ BB BE DE BH EF
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Parent Chuwhangbae AC AB BC GH CD AA BB BJ CD BE DF AC FF
Offspring Hanareum AA BB BC CG DD EG BB JJ BD BE DF EH EF
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Parent Chuwhangbae AC AB BC GH CD AA BB BJ CD BE DF AC FF
Offspring Shincheon AA BB AB EG CD CG BC CJ FG BE DE EG FH
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Parent Shinko AC AB BC CG AC CE BC CJ DD BE DE BH EF
Offspring Josaengwhangkum AA AB AB CG CC EG BB JJ DF BB FH BE FF
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Parent Okusankichi AA BB CC DG CE AG AC CJ GI BB CF AI BE
Offspring Sunhwang AA BB AC CE DD CG BC CJ AB BE DF GH EH
Parent Chojuro AA BB AA DH BC AE BB AE EF AA DE DE DF
Parent Kimitsukawase AA BB AC BH BC EE AA DE EF AA CD BE BG
Offspring Soowhangbae AB BB AC DF AB AB BC BE BE AC BD AF AC
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Parent Soowhangbae AC BB AC EG AC AC BC CJ BF BE DF AH BE
Offspring Sooyoung AA AB AC DF CE AG AB CJ FG BB FH AE BF
Parent/Offspring Cultivar SSR markersy)
CH04h02 TsuENH083 NB105a CH04d08 NH207a CH04g04 CH05d11 NB104a CH04d02 NH009b NB120a NH004a CH04c07 TsuENH032
Parent Imamuraaki AB AA DH AA AB BG DE CE DI AC GK AJ BD AG
Parent Nijiiseiki CD BC BB AC BB BB DD EE DD EE AJ EI AB AG
Offspring Chuwhangbae BD AC BD AA AB BG DE CE DI AE JK EJ BB GG
Parent Nijiiseiki CD BC BB AC BB BB DD EE DD EE AJ EI AB AG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Offspring Whangkeumbae DD CC BD AC BB BB DD CE DI EE JK EI AD AA
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Parent Chuwhangbae BD AC BD AA AB BG DE CE DI AE JK EJ BB GG
Offspring Hanareum DD AC DF AD BD BC CD CD FI CE AB EI DG AG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Parent Chuwhangbae BD AC BD AA AB BG DE CE DI AE JK EJ BB GG
Offspring Shincheon CD AC BD AC CD BC CD CD FI AE AB AI DF AE
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Parent Shinko AD AC BD AA AB BG DE CE DI DE AK II BE GH
Offspring Josaengwhangkum CD CC BF AD BD BC DD DE DF EE BJ EE AD AA
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Parent Okusankichi BC AA BE AC BD BC DI AE DF AD AB GI AB FG
Offspring Sunhwang CD AC BF CD BC BB DD CD FI CE BJ AE DD AB
Parent Chojuro DE AC BE BC AB AE BC BB FF DD AG BC AC AB
Parent Kimitsukawase DE AA BB BB AC AE BC BB FF AD GG AA BC BE
Offspring Soowhangbae CD AC BC AC BD AB AB CD CD BD BF DD BC AE
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Parent Soowhangbae CD AC BD AD BD BC CD DE DF CE BJ II BD AG
Offspring Sooyoung BD AA AE AA CD CE DD AA BG AE BC GG AA AG
Parent/Offspring Cultivar SSR markersy)
CH05d03 TsuENH093 CH02e12 NH204a IPPN17 NH025a CH02c09 TsuENH035 NH007b CH05a04 TsuENH033 NB125a NH008b
Parent Imamuraaki CC BC DE CD BE GG BE DG BB CD BC BC BD
Parent Nijiiseiki CE AA FF CE CF BI DE DE BG DD BG BH CG
Offspring Chuwhangbae CC AC DF CC EF GI DE EG BG CD BC BC CD
Parent Nijiiseiki CE AA FF CE CF BI DE DE BG DD BG BH CG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Offspring Whangkeumbae CE AB EF CE BF EI AD DE FG AD BB BB EG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Parent Chuwhangbae CC AC DF CC EF GI DE EG BG CD BC BC CD
Offspring Hanareum CC AA FF DE BD BE AA EE BB AD BB BB EE
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Parent Chuwhangbae CC AC DF CC EF GI DE EG BG CD BC BC CD
Offspring Shincheon CD AB EF CD DE GH BE DE EF AC AB AB EG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Parent Shinko CG AB EF CC EF GI EE EE BG CD BG BH BG
Offspring Josaengwhangkum CE AB EF CE BC BE AD DE BF CD BG BH EG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Parent Okusankichi BC AC CF CD DE GH DE DE FG CD AD AD BC
Offspring Sunhwang CE AA FF DE BD EI BD DD EF AC BE BF EE
Parent Chojuro CE AA EE BC AC BD AB CD AD AC EF FG EE
Parent Kimitsukawase CE AA EE BB CC AA BC CC BD AC AB AB CF
Offspring Soowhangbae CC AA EE CC AB AB AD CC AD AC BB BG BF
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Parent Soowhangbae CC AA FF EE BC BE AE EE BG AD BB BH BG
Offspring Sooyoung AC BC AC CC BE GH AE CE BF AC AD AD AC

z)Numbers of the not matched simple sequence repeat (SSR) alleles among the parent and offspring by the MARCO software. Letters A to J was generated by the MARCO software correspond to each SSR fragment.

y)Different SSR alleles among the parent and offspring were indicated by shaded box.

Table 3
SSR genotyping analysis of candidate parents and 7 Korean bred pear cultivars by the 53 SSR markers and the MARCO software.
Table 3
Errorsz) Parent/Offspring Cultivar SSR markersy)
TsuENH003 CN444636 TsuENH045 CH02b10 NH023a NB113a TsuENH074 BGA35 NH011b CH02h11a CH02c02b CH03a09 NB103a
0 Parent Tama GG EE DD DD CJ CC CC EE DE BD BF AC BB
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
0 Offspring Hanareum GG BE BD DD CC CD AC EE EF AD BG BC BD
0 Parent Chouju GG EE BE AF BG CE CD EE DE BD BB AC BF
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
0 Offspring Shincheon FG AE EE AF CG CE CD EE EF BB BB AA BF
0 Parent Nijisseiki GG AE DD DF CJ CC CC EE DE BE BF AC BB
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
0 Offspring Soowhangbae FG AB BD DF CC CE CD EE DF AE BB AC BD
0 Parent Nijisseiki GG AE DD DF CJ CC CC EE DE BE BF AC BB
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
0 Offspring Josaengwhangkum GG AE DE DD CG CE CD EE EE BB FG AA BB
0 Parent Shinsui GG CE DE DF GG CH CC AE EE BB BF AA BF
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
0 Offspring Sunhwang GG BC BE DF GG CE CD AE EE BB BB AA DF
1 Parent Okusankichi EF BE DD DF CC DE AE AE FF AC BF CC DE
12 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
20 Offspring Sooyoung EF BB AD CF BC DE AD EE AF AA BB AC DD
Parent/Offspring Cultivar SSR Markers
CH01b11 TsuENH046 TsuENH006 CH04e05 NB114a IPPN13 NH029a TsuENH008 CH05a03 NH039a NH017a EMPc105 CH01f07a
Parent Tama AC AB AB EG DD AE BB JJ DG BB FF AE BF
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Offspring Hanareum AA BB BC CG DD EG BB JJ BD BE DF EH EF
Parent Chouju AA BB BC GI CC GG AB HJ GG BB EH EG FH
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Offspring Shincheon AA BB AB EG CD CG BC CJ FG BE DE EG FH
Parent Nijisseiki AC AB BC GH AC AE BB JJ BD BB EF AB BF
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Offspring Soowhangbae AC BB AC EG AC AC BC CJ BF BE DF AH BE
Parent Nijisseiki AC AB BC GH AC AE BB JJ BD BB EF AB BF
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Offspring Josaengwhangkum AA AB AB CG CC EG BB JJ DF BB FH BE FF
Parent Shinsui AA BB BC CG AD EG AB HJ AG BB FF AG BH
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Offspring Sunhwang AA BB AC CE DD CG BC CJ AB BE DF GH EH
Parent Okusankichi AA BB CC DG CE AG AC CJ GI BB CF AI BE
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Offspring Sooyoung AA AB AC DF CE AG AB CJ FG BB FH AE BF
Parent/Offspring Cultivar SSR markersy)
CH04h02 TsuENH083 NB105a CH04d08 NH207a CH04g04 CH05d11 NB104a CH04d02 NH009b NB120a NH004a CH04c07 TsuENH032
Parent Tama DD AC BF CD BB BB DD CE DI EE AF EE BG AG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Offspring Hanareum DD AC DF AD BD BC CD CD FI CE AB EI DG AG
Parent Chouju DD AC BB AC BC BB DD CE DI AE AK AE BF EG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Offspring Shincheon CD AC BD AC CD BC CD CD FI AE AB AI DF AE
Parent Nijisseiki CD BC BB AC BB BB DD EE DD EE AJ EI AB AG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Offspring Soowhangbae CD AC BD AD BD BC CD DE DF CE BJ II BD AG
Parent Nijisseiki CD BC BB AC BB BB DD EE DD EE AJ EI AB AG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Offspring Josaengwhangkum CD CC BF AD BD BC DD DE DF EE BJ EE AD AA
Parent Shinsui DE AC BB CC BC BB DD CE DI AE JK AA BD BG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Offspring Sunhwang CD AC BF CD BC BB DD CD FI CE BJ AE DD AB
Parent Okusankichi BC AA BE AC BD BC DI AE DF AD AB GI AB FG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Offspring Sooyoung BD AA AE AA CD CE DD AA BG AE BC GG AA AG
Parent/Offspring Cultivar SSR Markers
CH05d03 TsuENH093 CH02e12 NH204a IPPN17 NH025a CH02c09 TsuENH035 NH007b CH05a04 TsuENH033 NB125a NH008b
Parent Tama CH AA FF DE CD BB AA EE BG DD BB BB EG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Offspring Hanareum CC AA FF DE BD BE AA EE BB AD BB BB EE
Parent Chouju CD AA FF DD DD BH BE EE BE AA AE AF EG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Offspring Shincheon CD AB EF CD DE GH BE DE EF AC AB AB EG
Parent Nijisseiki CE AA FF CE CF BI DE DE BG DD BG BH CG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Offspring Soowhangbae CC AA FF EE BC BE AE EE BG AD BB BH BG
Parent Nijisseiki CE AA FF CE CF BI DE DE BG DD BG BH CG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Offspring Josaengwhangkum CE AB EF CE BC BE AD DE BF CD BG BH EG
Parent Shinsui CE AA FF CD DF BI BD DE BE AD BB BB CE
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Offspring Sunhwang CE AA FF DE BD EI BD DD EF AC BE BF EE
Parent Okusankichi BC AC CF CD DE GH DE DE FG CD AD AD BC
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Offspring Sooyoung AC BC AC CC BE GH AE CE BF AC AD AD AC

z)Numbers of the not matched simple sequence repeat (SSR) alleles among the parent and offspring by the MARCO software. Letters A to J was generated by the MARCO software correspond to each SSR fragment.

y)Different SSR alleles among the parent and offspring were indicated by shaded box.

Table 4
S-genotypes relationship among the 9 Korean pear cultivars and their parents.
Table 4
Cultivars Registrant parents SSR genotypingz) Candidate parents S-genotype
Sujeongbae Mutant of Niitaka (S3S9) O S3S9
Chuwhangbaey) Imamuaraki (S1S6)×Nijisseiki (S2S4) O S4S6
Whangkeumbaey) Niitaka (S3S9)×Nijisseiki (S2S4) O S3S4
Hanareum Niitaka (S3S9)×Chuwhangbae (S4S6) X Niitaka (S3S9)×Tama (S4S5) S3S4
Shincheon Niitaka (S3S9)×Chuwhangbae (S4S6) X Niitaka (S3S9)×Chouju (S1S5) S1S3
Soowhangbaey) Chojuro (S2S3)×Kimitsukawase (S1S5) X Niitaka (S3S9)×Nijisseiki (S2S4) S3S4
Josaengwhangkum Niitaka (S3S9)×Shinko (S4S9) X Niitaka (S3S9)×Nijisseiki (S2S4) S3S4
Sunhwangy) Niitaka (S3S9)×Okusankichi (S5S7) X Niitaka (S3S9)×Shinsui (S4S5) S3S5
Sooyoung Niitaka (S3S9)×Soowhangbae (S3S4) X ?×Okusankichi (S5S7) S5S?

z)O is matched the simple sequence repeat (SSR) genotypes among the registrant parents and cultivar, X is not matched the SSR genotypes among the registrant parents and cultivar.

y)S-genotypes were previously determined by Kim et al. (2002).

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Parentage Confirmation of Korean Bred Pear Cultivars by Simple Sequence Repeat SSR Genotyping and S-Genotypes Analysis
Plant Breed. Biotech.. 2016;4(2):198-211.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.198
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Parentage Confirmation of Korean Bred Pear Cultivars by Simple Sequence Repeat SSR Genotyping and S-Genotypes Analysis
Plant Breed. Biotech.. 2016;4(2):198-211.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.198
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Parentage Confirmation of Korean Bred Pear Cultivars by Simple Sequence Repeat SSR Genotyping and S-Genotypes Analysis
Image Image
Fig. 1 S-RNase polymerase chain reaction analysis of 6 Japanese pear cultivars of known S-genotypes and 5 Korean bred pear cultivars by using the FTQQYQ-Fam and PsprI primers. Lane 1: Ichiharawase (S1S8), lane 2: Nijisseiki (S2S4), lane 3: Niitaka (S1S9), lane 4: Okusankichi (S5S7), lane 5: Imamuraaki (S1S6), lane 6: Kinchaku (S4Sk), lane 7: Sujeongbae, lane 8: Hannareum, lane 9: Shincheon, lane 10: Sooyoung, lane 11: Josaengwhangkum, and M: 100 bp DNA Ladder.
Fig. 2 S-genotypes analysis of five Korean bred pear cultivars by polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis. The S-RNase PCR f[ragments were digested with S-allele-specific restriction enzymes; a: PpuMI (S3 and S5), b: AlwNI (S5), c: BstBI (S9), d: NdeI (S4), e: SfcI (S1). The digested fragments are indicated by arrows.

Fig. 1

Fig. 2

Parentage Confirmation of Korean Bred Pear Cultivars by Simple Sequence Repeat SSR Genotyping and S-Genotypes Analysis

The 9 Korean bred pear cultivars and 12 Japanese candidate pear parent cultivars used in this experiment.

Cultivar (synonym) Registrant parents Origin
Chuwhangbae Imamuraaki (S1S6)×Nijisseiki (S2S4) Korea
Whangkeumbae Niitaka (S3S9)×Nijisseiki (S2S4) Korea
Hanareum Niitaka (S3S9)×Chuwhangbae (S3S4) Korea
Shincheon Niitaka (S3S9)×Chuwhangbae (S3S4) Korea
Soohwangbae Chojuro (S2S3)×Kimitsukawase (S1S5) Korea
Josaenghwangkeum Niitaka (S3S9)×Shinko (S4S9) Korea
Sunhwang Niitaka (S3S9)×Okusankichi (S5S7) Korea
Sooyoung Niitaka (S3S9)×Soohwangbae (S3S4) Korea
Sujeongbae Mutant of Niitaka (S3S9) Korea
Imamuraaki Breeding process is unknown Japan
Nijisseiki Discovered in 1888, named in 1904 Japan
Niitaka Amanogawa (S1S9)×Chojuro (S2S3) Japan
Chojuro Sown in 1889, fruited in 1893 Japan
Kimitsukawase Shinkozo×Doitsu (S1S2) Japan
Okusankichi Sown in 1840–1850 Japan
Tama Gion (S2S4)×Kosui (S4S5) Japan
Chouju Asahi (S4S5)×Kimitsukawase (S1S5) Japan
Shinsui Kikusui (S4S4)×Kimitsukawase (S1S5) Japan
Shinko Nijisseiki (S2S4)×Amanokawa (S1S9) Japan
Ichiharawase Discovered in 1892 or 1893 Japan
Kinchaku Breeding process is unknown, local cultivar Japan

SSR genotyping analysis of registrant parent and nine Korean bred pear cultivars by the 53 SSR markers and the MARCO software.

Errorsz) Parent/Offspring Cultivar SSR markersy)
TsuENH003 CN444636 TsuENH045 CH02b10 NH023a NB113a TsuENH074 BGA35 NH011b CH02h11a CH02c02b CH03a09 NB103a
0 Parent Imamuraaki FF BG BD DF BC DH AB EE FG AC BI AC DD
0 Parent Nijiiseiki GG AE DD DF CJ CC CC EE DE BE BF AC BB
0 Offspring Chuwhangbae FG BE BD DF CC CD AC EE DF AE BB AA BD
0 Parent Nijiiseiki GG AE DD DF CJ CC CC EE DE BE BF AC BB
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
0 Offspring Whangkeumbae GG AE DE AD GJ CD AC EE EE BB BB BC BB
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
10 Parent Chuwhangbae FG BE BD DF CC CD AC EE DF AE BB AA BD
11 Offspring Hanareum GG BE BD DD CC CD AC EE EF AD BG BC BD
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
12 Parent Chuwhangbae FG BE BD DF CC CD AC EE DF AE BB AA BD
22 Offspring Shincheon FG AE EE AF CG CE CD EE EF BB BB AA BF
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
17 Parent Shinko FG BE DD DF CC CD AC EE DF AE BG AC BD
20 Offspring Josaengwhangkum GG AE DE DD CG CE CD EE EE BB FG AA BB
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
20 Parent Okusankichi EF BE DD DF CC DE AE AE FF AC BF CC DE
28 Offspring Sunhwang GG BC BE DF GG CE CD AE EE BB BB AA DF
10 Parent Chojuro BC AD BD AA AD CC CD AB BC BE AA AB AC
18 Parent Kimitsukawase CC CD BD AD AC CD CD BB CC AB AA AC BE
34 Offspring Soowhangbae BC AB BC CD BB AC CD BB BD AE AA AC AC
12 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
13 Parent Soowhangbae FG AB BD DF CC CE CD EE DF AE BB AC BD
29 Offspring Sooyoung EF BB AD CF BC DE AD EE AF AA BB AC DD
Parent/Offspring Cultivar SSR markersy)
CH01b11 TsuENH046 TsuENH006 CH04e05 NB114a IPPN13 NH029a TsuENH008 CH05a03 NH039a NH017a EMPc105 CH01f07a
Parent Imamuraaki AA BB BC CG CD AF BB BG BC CE DE CH FG
Parent Nijiiseiki AC AB BC GH AC AE BB JJ BD BB EF AB BF
Offspring Chuwhangbae AC AB BC GH CD AA BB BJ CD BE DF AC FF
Parent Nijiiseiki AC AB BC GH AC AE BB JJ BD BB EF AB BF
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Offspring Whangkeumbae AA BB CC CH CD AC BC CJ BB BE DE BH EF
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Parent Chuwhangbae AC AB BC GH CD AA BB BJ CD BE DF AC FF
Offspring Hanareum AA BB BC CG DD EG BB JJ BD BE DF EH EF
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Parent Chuwhangbae AC AB BC GH CD AA BB BJ CD BE DF AC FF
Offspring Shincheon AA BB AB EG CD CG BC CJ FG BE DE EG FH
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Parent Shinko AC AB BC CG AC CE BC CJ DD BE DE BH EF
Offspring Josaengwhangkum AA AB AB CG CC EG BB JJ DF BB FH BE FF
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Parent Okusankichi AA BB CC DG CE AG AC CJ GI BB CF AI BE
Offspring Sunhwang AA BB AC CE DD CG BC CJ AB BE DF GH EH
Parent Chojuro AA BB AA DH BC AE BB AE EF AA DE DE DF
Parent Kimitsukawase AA BB AC BH BC EE AA DE EF AA CD BE BG
Offspring Soowhangbae AB BB AC DF AB AB BC BE BE AC BD AF AC
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Parent Soowhangbae AC BB AC EG AC AC BC CJ BF BE DF AH BE
Offspring Sooyoung AA AB AC DF CE AG AB CJ FG BB FH AE BF
Parent/Offspring Cultivar SSR markersy)
CH04h02 TsuENH083 NB105a CH04d08 NH207a CH04g04 CH05d11 NB104a CH04d02 NH009b NB120a NH004a CH04c07 TsuENH032
Parent Imamuraaki AB AA DH AA AB BG DE CE DI AC GK AJ BD AG
Parent Nijiiseiki CD BC BB AC BB BB DD EE DD EE AJ EI AB AG
Offspring Chuwhangbae BD AC BD AA AB BG DE CE DI AE JK EJ BB GG
Parent Nijiiseiki CD BC BB AC BB BB DD EE DD EE AJ EI AB AG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Offspring Whangkeumbae DD CC BD AC BB BB DD CE DI EE JK EI AD AA
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Parent Chuwhangbae BD AC BD AA AB BG DE CE DI AE JK EJ BB GG
Offspring Hanareum DD AC DF AD BD BC CD CD FI CE AB EI DG AG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Parent Chuwhangbae BD AC BD AA AB BG DE CE DI AE JK EJ BB GG
Offspring Shincheon CD AC BD AC CD BC CD CD FI AE AB AI DF AE
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Parent Shinko AD AC BD AA AB BG DE CE DI DE AK II BE GH
Offspring Josaengwhangkum CD CC BF AD BD BC DD DE DF EE BJ EE AD AA
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Parent Okusankichi BC AA BE AC BD BC DI AE DF AD AB GI AB FG
Offspring Sunhwang CD AC BF CD BC BB DD CD FI CE BJ AE DD AB
Parent Chojuro DE AC BE BC AB AE BC BB FF DD AG BC AC AB
Parent Kimitsukawase DE AA BB BB AC AE BC BB FF AD GG AA BC BE
Offspring Soowhangbae CD AC BC AC BD AB AB CD CD BD BF DD BC AE
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Parent Soowhangbae CD AC BD AD BD BC CD DE DF CE BJ II BD AG
Offspring Sooyoung BD AA AE AA CD CE DD AA BG AE BC GG AA AG
Parent/Offspring Cultivar SSR markersy)
CH05d03 TsuENH093 CH02e12 NH204a IPPN17 NH025a CH02c09 TsuENH035 NH007b CH05a04 TsuENH033 NB125a NH008b
Parent Imamuraaki CC BC DE CD BE GG BE DG BB CD BC BC BD
Parent Nijiiseiki CE AA FF CE CF BI DE DE BG DD BG BH CG
Offspring Chuwhangbae CC AC DF CC EF GI DE EG BG CD BC BC CD
Parent Nijiiseiki CE AA FF CE CF BI DE DE BG DD BG BH CG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Offspring Whangkeumbae CE AB EF CE BF EI AD DE FG AD BB BB EG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Parent Chuwhangbae CC AC DF CC EF GI DE EG BG CD BC BC CD
Offspring Hanareum CC AA FF DE BD BE AA EE BB AD BB BB EE
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Parent Chuwhangbae CC AC DF CC EF GI DE EG BG CD BC BC CD
Offspring Shincheon CD AB EF CD DE GH BE DE EF AC AB AB EG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Parent Shinko CG AB EF CC EF GI EE EE BG CD BG BH BG
Offspring Josaengwhangkum CE AB EF CE BC BE AD DE BF CD BG BH EG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Parent Okusankichi BC AC CF CD DE GH DE DE FG CD AD AD BC
Offspring Sunhwang CE AA FF DE BD EI BD DD EF AC BE BF EE
Parent Chojuro CE AA EE BC AC BD AB CD AD AC EF FG EE
Parent Kimitsukawase CE AA EE BB CC AA BC CC BD AC AB AB CF
Offspring Soowhangbae CC AA EE CC AB AB AD CC AD AC BB BG BF
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Parent Soowhangbae CC AA FF EE BC BE AE EE BG AD BB BH BG
Offspring Sooyoung AC BC AC CC BE GH AE CE BF AC AD AD AC

z)Numbers of the not matched simple sequence repeat (SSR) alleles among the parent and offspring by the MARCO software. Letters A to J was generated by the MARCO software correspond to each SSR fragment.

y)Different SSR alleles among the parent and offspring were indicated by shaded box.

SSR genotyping analysis of candidate parents and 7 Korean bred pear cultivars by the 53 SSR markers and the MARCO software.

Errorsz) Parent/Offspring Cultivar SSR markersy)
TsuENH003 CN444636 TsuENH045 CH02b10 NH023a NB113a TsuENH074 BGA35 NH011b CH02h11a CH02c02b CH03a09 NB103a
0 Parent Tama GG EE DD DD CJ CC CC EE DE BD BF AC BB
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
0 Offspring Hanareum GG BE BD DD CC CD AC EE EF AD BG BC BD
0 Parent Chouju GG EE BE AF BG CE CD EE DE BD BB AC BF
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
0 Offspring Shincheon FG AE EE AF CG CE CD EE EF BB BB AA BF
0 Parent Nijisseiki GG AE DD DF CJ CC CC EE DE BE BF AC BB
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
0 Offspring Soowhangbae FG AB BD DF CC CE CD EE DF AE BB AC BD
0 Parent Nijisseiki GG AE DD DF CJ CC CC EE DE BE BF AC BB
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
0 Offspring Josaengwhangkum GG AE DE DD CG CE CD EE EE BB FG AA BB
0 Parent Shinsui GG CE DE DF GG CH CC AE EE BB BF AA BF
0 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
0 Offspring Sunhwang GG BC BE DF GG CE CD AE EE BB BB AA DF
1 Parent Okusankichi EF BE DD DF CC DE AE AE FF AC BF CC DE
12 Parent Niitaka FG AB BE AD CG DE AD EE EF AB BG AB BD
20 Offspring Sooyoung EF BB AD CF BC DE AD EE AF AA BB AC DD
Parent/Offspring Cultivar SSR Markers
CH01b11 TsuENH046 TsuENH006 CH04e05 NB114a IPPN13 NH029a TsuENH008 CH05a03 NH039a NH017a EMPc105 CH01f07a
Parent Tama AC AB AB EG DD AE BB JJ DG BB FF AE BF
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Offspring Hanareum AA BB BC CG DD EG BB JJ BD BE DF EH EF
Parent Chouju AA BB BC GI CC GG AB HJ GG BB EH EG FH
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Offspring Shincheon AA BB AB EG CD CG BC CJ FG BE DE EG FH
Parent Nijisseiki AC AB BC GH AC AE BB JJ BD BB EF AB BF
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Offspring Soowhangbae AC BB AC EG AC AC BC CJ BF BE DF AH BE
Parent Nijisseiki AC AB BC GH AC AE BB JJ BD BB EF AB BF
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Offspring Josaengwhangkum AA AB AB CG CC EG BB JJ DF BB FH BE FF
Parent Shinsui AA BB BC CG AD EG AB HJ AG BB FF AG BH
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Offspring Sunhwang AA BB AC CE DD CG BC CJ AB BE DF GH EH
Parent Okusankichi AA BB CC DG CE AG AC CJ GI BB CF AI BE
Parent Niitaka AA BB AC CE CD CG BC CJ BF BE DH EH EF
Offspring Sooyoung AA AB AC DF CE AG AB CJ FG BB FH AE BF
Parent/Offspring Cultivar SSR markersy)
CH04h02 TsuENH083 NB105a CH04d08 NH207a CH04g04 CH05d11 NB104a CH04d02 NH009b NB120a NH004a CH04c07 TsuENH032
Parent Tama DD AC BF CD BB BB DD CE DI EE AF EE BG AG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Offspring Hanareum DD AC DF AD BD BC CD CD FI CE AB EI DG AG
Parent Chouju DD AC BB AC BC BB DD CE DI AE AK AE BF EG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Offspring Shincheon CD AC BD AC CD BC CD CD FI AE AB AI DF AE
Parent Nijisseiki CD BC BB AC BB BB DD EE DD EE AJ EI AB AG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Offspring Soowhangbae CD AC BD AD BD BC CD DE DF CE BJ II BD AG
Parent Nijisseiki CD BC BB AC BB BB DD EE DD EE AJ EI AB AG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Offspring Josaengwhangkum CD CC BF AD BD BC DD DE DF EE BJ EE AD AA
Parent Shinsui DE AC BB CC BC BB DD CE DI AE JK AA BD BG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Offspring Sunhwang CD AC BF CD BC BB DD CD FI CE BJ AE DD AB
Parent Okusankichi BC AA BE AC BD BC DI AE DF AD AB GI AB FG
Parent Niitaka CD AC DF AD BD BC CD CD FI CE BK EI DE AH
Offspring Sooyoung BD AA AE AA CD CE DD AA BG AE BC GG AA AG
Parent/Offspring Cultivar SSR Markers
CH05d03 TsuENH093 CH02e12 NH204a IPPN17 NH025a CH02c09 TsuENH035 NH007b CH05a04 TsuENH033 NB125a NH008b
Parent Tama CH AA FF DE CD BB AA EE BG DD BB BB EG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Offspring Hanareum CC AA FF DE BD BE AA EE BB AD BB BB EE
Parent Chouju CD AA FF DD DD BH BE EE BE AA AE AF EG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Offspring Shincheon CD AB EF CD DE GH BE DE EF AC AB AB EG
Parent Nijisseiki CE AA FF CE CF BI DE DE BG DD BG BH CG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Offspring Soowhangbae CC AA FF EE BC BE AE EE BG AD BB BH BG
Parent Nijisseiki CE AA FF CE CF BI DE DE BG DD BG BH CG
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Offspring Josaengwhangkum CE AB EF CE BC BE AD DE BF CD BG BH EG
Parent Shinsui CE AA FF CD DF BI BD DE BE AD BB BB CE
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Offspring Sunhwang CE AA FF DE BD EI BD DD EF AC BE BF EE
Parent Okusankichi BC AC CF CD DE GH DE DE FG CD AD AD BC
Parent Niitaka CG AB EF CE BE EG AB DE BF AC BE BF BE
Offspring Sooyoung AC BC AC CC BE GH AE CE BF AC AD AD AC

z)Numbers of the not matched simple sequence repeat (SSR) alleles among the parent and offspring by the MARCO software. Letters A to J was generated by the MARCO software correspond to each SSR fragment.

y)Different SSR alleles among the parent and offspring were indicated by shaded box.

S-genotypes relationship among the 9 Korean pear cultivars and their parents.

Cultivars Registrant parents SSR genotypingz) Candidate parents S-genotype
Sujeongbae Mutant of Niitaka (S3S9) O S3S9
Chuwhangbaey) Imamuaraki (S1S6)×Nijisseiki (S2S4) O S4S6
Whangkeumbaey) Niitaka (S3S9)×Nijisseiki (S2S4) O S3S4
Hanareum Niitaka (S3S9)×Chuwhangbae (S4S6) X Niitaka (S3S9)×Tama (S4S5) S3S4
Shincheon Niitaka (S3S9)×Chuwhangbae (S4S6) X Niitaka (S3S9)×Chouju (S1S5) S1S3
Soowhangbaey) Chojuro (S2S3)×Kimitsukawase (S1S5) X Niitaka (S3S9)×Nijisseiki (S2S4) S3S4
Josaengwhangkum Niitaka (S3S9)×Shinko (S4S9) X Niitaka (S3S9)×Nijisseiki (S2S4) S3S4
Sunhwangy) Niitaka (S3S9)×Okusankichi (S5S7) X Niitaka (S3S9)×Shinsui (S4S5) S3S5
Sooyoung Niitaka (S3S9)×Soowhangbae (S3S4) X ?×Okusankichi (S5S7) S5S?

z)O is matched the simple sequence repeat (SSR) genotypes among the registrant parents and cultivar, X is not matched the SSR genotypes among the registrant parents and cultivar.

y)S-genotypes were previously determined by Kim et al. (2002).

Table 1 The 9 Korean bred pear cultivars and 12 Japanese candidate pear parent cultivars used in this experiment.
Table 2 SSR genotyping analysis of registrant parent and nine Korean bred pear cultivars by the 53 SSR markers and the MARCO software.

Numbers of the not matched simple sequence repeat (SSR) alleles among the parent and offspring by the MARCO software. Letters A to J was generated by the MARCO software correspond to each SSR fragment.

Different SSR alleles among the parent and offspring were indicated by shaded box.

Table 3 SSR genotyping analysis of candidate parents and 7 Korean bred pear cultivars by the 53 SSR markers and the MARCO software.

Numbers of the not matched simple sequence repeat (SSR) alleles among the parent and offspring by the MARCO software. Letters A to J was generated by the MARCO software correspond to each SSR fragment.

Different SSR alleles among the parent and offspring were indicated by shaded box.

Table 4 S-genotypes relationship among the 9 Korean pear cultivars and their parents.

O is matched the simple sequence repeat (SSR) genotypes among the registrant parents and cultivar, X is not matched the SSR genotypes among the registrant parents and cultivar.

S-genotypes were previously determined by Kim et al. (2002).

Table 1

Table 2

Table 3

Table 4

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