Horticultural Science & Technology (원예과학기술지)

Korean Society of Horticultural Science (한국원예학회)
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Development of Sequence Characterized Amplified Region Markers for Cultivar Identification in Persimmon

감 품종 판별용 SCAR 마커 개발

  • Cho, Kang Hee (Fruit Research Division, National Institute of Horticultural & Herbal Science) ;
  • Cho, Kwang-Sik (Pear Experiment Station, National Institute of Horticultural & Herbal Science) ;
  • Han, Jeom Hwa (Fruit Research Division, National Institute of Horticultural & Herbal Science) ;
  • Kim, Hyun Ran (Fruit Research Division, National Institute of Horticultural & Herbal Science) ;
  • Shin, Il Sheob (Fruit Research Division, National Institute of Horticultural & Herbal Science) ;
  • Kim, Se Hee (Fruit Research Division, National Institute of Horticultural & Herbal Science) ;
  • Chun, Jae An (Fruit Research Division, National Institute of Horticultural & Herbal Science) ;
  • Hwang, Hae-Sung (Fruit Research Division, National Institute of Horticultural & Herbal Science)
  • 조강희 (국립원예특작과학원 과수과) ;
  • 조광식 (국립원예특작과학원 배시험장) ;
  • 한점화 (국립원예특작과학원 과수과) ;
  • 김현란 (국립원예특작과학원 과수과) ;
  • 신일섭 (국립원예특작과학원 과수과) ;
  • 김세희 (국립원예특작과학원 과수과) ;
  • 천재안 (국립원예특작과학원 과수과) ;
  • 황해성 (국립원예특작과학원 과수과)
  • Received : 2013.04.22
  • Accepted : 2013.10.01
  • Published : 2013.12.31
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Abstract

Precise, fast, and cost-effective identification of crop cultivars is essential for plant breeder's rights. Traditional methods for identification of persimmon cultivars are based on the evaluation of sets of morphological characteristics. However, it is difficult to distinguish closely related cultivars using only morphological traits. This study was conducted to develop DNA markers for identification of the 32 persimmon cultivars in Korea and Japan. A total of 309 randomly amplified polymorphic DNA (RAPD) markers were identified using 40 different random primers. Various number of polymorphic bands ranged from 4 (OPP-08) to 14 (UBC159) were detected with an average of 7.7. Resulting 57 RAPD fragments were selected, and their sequences were determined for developing sequence characterized amplified region (SCAR) markers. As a result, 15 of 57 RAPD fragments were successfully converted to SCAR markers. Single polymorphic bands of the same size as or smaller than the RAPD fragments were amplified depending on SCAR markers. Among these markers, a combination of eight SCAR markers (PS225_200, PSN05_420, PSF13_523, PSN11_540, PS372_567, PS485_569, PSP08_635, and PS631_735) provided sufficient polymorphisms to identify 32 persimmon cultivars. These newly developed markers will be a fast and reliable tool to identify persimmon cultivars.

중요 작물의 신속 정확하고 비용 면에서 효율적인 품종 판별은 실용적인 육종과 육종가의 권리 보호를 위해 필수적이다. 감 품종을 구분하는 전통적인 방법은 형태적인 특성 평가를 근거로 하지만 유전적으로 밀접하게 연관되어 있는 품종들은 형태적 형질에 의해 품종을 구별하기는 어렵다. 본 연구는 국내와 일본 감 32 품종을 판별할 수 있는 신뢰성 있는 DNA 마커를 개발하고자 수행하였다. 40종의 임의 프라이머를 이용한 RAPD 분석을 통해 품종 간 다형성을 나타내는 밴드 309종을 획득하였다. 프라이머에 따라 얻은 다형성 밴드 수는 4(OPP-08)-14(UBC159)개로 평균 7.7개였다. SCAR 마커로 전환하기 위해 57종의 RAPD 단편들을 선발하여 염기서열을 분석하였고 그 중 15종이 SCAR 마커로 전환되었다. 개발된 15종의 SCAR마커는 프라이머 조합에 따라 RAPD 단편과 동일한 크기나 작은 크기의 단일 밴드가 증폭되었다. 이들 마커 중 8종(PS225_200, PSN05_420, PSF13_523, PSN11_540, PS372_567, PS485_569, PSP08_635, PS631_735)의 조합을 적용하여 증폭산물의 수와 크기에 따라 감 32품종의 판별이 가능하였다. 새로 개발된 마커들은 감 품종 판별을 위해 신뢰성 있는 수단으로서 효과적으로 이용될 수 있을 것으로 판단된다.

Keywords

References

  1. Badenes, M., A. Garces, C. Romero, M. Romero, J. Clave, M. Rovira, and G. Llacer. 2003. Genetic diversity of introduced and local Spanish persimmon cultivars revealed by RAPD markers. Genet. Resour. Crop Evol. 50:579-585. https://doi.org/10.1023/A:1024474719036
  2. Bernet, G.P., S. Bramardi, D. Calvache, E.A. Carbonell, and M.J. Asins. 2003. Applicability of molecular markers in the context of protection of new varieties of cucumber. Plant Breed. 122:146-152. https://doi.org/10.1046/j.1439-0523.2003.00838.x
  3. Cho, D.H., I.J. Chun, S.T. Kwon, Y.S. Song, and Y.D. Chou. 2007. Genetic relationships of Korean astringent persimmon varieties using AFLP analysis. Kor. J. Hort. Sci. Technol. 25:114-118.
  4. Cho, K.H., I.S. Shin, S.H. Kim, J.H. Kim, D.H. Kim, Y.K. Shin, and H.S. Hwang. 2012. Identification of Korean pear cultivars using combinations of SCAR markers. Hort. Environ. Biotechnol. 53:228-236. https://doi.org/10.1007/s13580-012-0082-7
  5. Cho, K.H., S. Heo, H.Y. Kim, J.H. Kim, I.S. Shin, S.E. Han, S.H. Kim, and D.H. Kim. 2010. Discrimination of Korean apple cultivars using combination of RAPD-SCAR markers. Kor. J. Hort. Sci. Technol. 28:825-835.
  6. Du, X.Y., Q.L. Zhang, and Z.R. Luo. 2009. Comparison of four molecular markers for genetic analysis in Diospyros L. (Ebenaceae). Plant Syst. Evol. 281:171-181. https://doi.org/10.1007/s00606-009-0199-z
  7. Food and Agriculture Organization of the United Nations (FAO). 2011. FAOSTAT database. http://faostat.fao.org/
  8. Gallego, F.J. and I. Martinez. 1997. Method to improve reliability of random amplified polymorphic DNA markers. BioTechniques 23:663-664.
  9. Goulao, L., L. Cabrita, C.M. Oliveira, and J.M. Leitao. 2001. Comparing RAPD and $AFLP^{TM}$ analysis in discrimination and estimation of genetic similarities among apple (Malus domestica Borkh.) cultivars. Euphytica 119:259-270. https://doi.org/10.1023/A:1017519920447
  10. Guo, D.L. and Z.R. Luo. 2006. Genetic relationships of some PCNA persimmons (Diospyros kaki Thunb.) from China and Japan revealed by SRAP analysis. Genet. Resour. Crop Evol. 53:1597-1603. https://doi.org/10.1007/s10722-005-8717-5
  11. Hwang, J.H., Y.O. Park, S.C. Kim, Y.J. Lee, J.S. Kang, Y.W. Choi, B.G. Son, and Y.H. Park. 2010. Evaluation of genetic diversity among persimmon cultivars (Diospyros kaki Thunb.) using microsatellite markers. J. Life Sci. 20:632-638. https://doi.org/10.5352/JLS.2010.20.4.632
  12. Je, H.J., Y.O. Park, S.C. Kim, J.H. Hwang, Y.J. Lee, B.G. Son, and Y.H. Park. 2009. Evaluation of genetic relationships among persimmon cultivars introduced and indigenous in Korea using RAPD. Kor. J. Hort. Sci. Technol. 27:448-455.
  13. Kanzaki, S., K. Yonemori, and A. Sugiura. 2001. Identification of molecular markers linked to the trait of natural astringency loss of Japanese persimmon (Diospyros kaki) fruit. J. Amer. Soc. Hort. Sci. 126:51-55.
  14. Kim, S.H., J.W. Chung, J.K. Moon, S.H. Woo, Y.G. Cho, S.K. Jong, and H.S. Kim. 2006. Discrimination of Korean soybean cultivars by SSR markers. Kor. J. Crop Sci. 51:658-668.
  15. Lin, J., X.C. Wang, Y.H. Chang, and J.G. Fang. 2011. Development of a novel and efficient strategy for practical identification of Pyrus spp (Rosaceae) cultivars using RAPD fingerprints. Genet. Mol. Res. 10:932-942. https://doi.org/10.4238/vol10-2gmr1097
  16. Luo, Z.R., K. Yonemori, and A. Sugiura. 1995. Evaluation of RAPD analysis for cultivar identification of persimmons. J. Jpn. Soc. Hortic. Sci. 64:535-541. https://doi.org/10.2503/jjshs.64.535
  17. Maki, S., K. Oyama, T. Kurahashi, T. Nakahira, T. Kawabata, and T. Yamada. 2001. RFLP analysis for cultivar identification of persimmons. Sci. Hortic. 91:407-412. https://doi.org/10.1016/S0304-4238(01)00254-0
  18. Nakamura, Y. and S. Kobayashi. 1994. DNA restriction fragment length variability in Diospyros kaki and related Diospyros species. HortScience 29:809-811.
  19. Naval, M. del M., E. Zuriaga, S. Pecchioli, G. Llacer, E. Giordani, and M.L. Badenes. 2010. Analysis of genetic diversity among persimmon cultivars using microsatellite markers. Tree Genet. Genom. 6:677-687. https://doi.org/10.1007/s11295-010-0283-0
  20. Park, Y.O., D.S. Park, J.Y. Son, S.T. Choi, S.C. Kim, G.P. Hong, and Y.H. Park. 2012. Evaluation of genetic diversity among persimmon (Diospyros kaki Thunb.) collection lines and cultivars using simple sequence repeat markers. Kor. J. Breed. Sci. 44:127-135.
  21. Paran, I. and R.W. Michelmore. 1993. Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor. Appl. Genet. 85:985-993.
  22. Soriano, J.M., S. Pecchioli, C. Romero, S. Vilanova, G. Llacer, E. Giordani, and M.L. Badenes. 2006. Development of microsatellite markers in polyploidy persimmon (Diospyros kaki Lf.) from an enriched genomic library. Mol. Ecol. Notes 6:368-370. https://doi.org/10.1111/j.1471-8286.2006.01236.x
  23. This, P., C. Cuisset, and J.M. Boursiquot. 1997. Development of stable RAPD markers for the identification of grapevine rootstocks and the analysis of genetic relationships. Am. J. Enol. Vitic. 48:492-501.
  24. Vidal, J.R., P. Delavault, M. Coarer, and A. Defontaine. 2000. Design of grapevine (Vitis vinifera L.) cultivar-specific SCAR primers for PCR fingerprinting. Theor. Appl. Genet. 101:1194-1201. https://doi.org/10.1007/s001220051597
  25. Xu, H., D.J. Wilson, S. Arulsekar, and A.T. Bakalinsky. 1995. Sequence-specific polymerase chain-reaction markers derived from randomly amplified polymorphic DNA markers for fingerprinting grape (Vitis) rootstocks. J. Amer. Soc. Hort. Sci. 120:714-720.
  26. Yamagishi, M., S. Matsumoto, A. Nakatsuka, and H. Itamura. 2005. Identification of persimmon (Diospyros kaki) cultivars and phenetic relationships between Diospyros species by more effective RAPD analysis. Sci. Hortic. 105:283-290. https://doi.org/10.1016/j.scienta.2005.01.020
  27. Yonemori, K., A. Sugiura, and M. Yamada. 2000. Persimmon genetics and breeding. Plant Breed. Rev. 19:191-225.
  28. Yonemori, K., C. Honsho, A. Kitajima, M. Aradhya, E. Giordani, E. Bellini, and D.E. Parfitt. 2008. Relationship of European persimmon (Diospyros kaki Thunb.) cultivars to Asian cultivars, characterized using AFLPs. Genet. Resour. Crop Evol. 55:81-89. https://doi.org/10.1007/s10722-007-9216-7
  29. Yu, M.L., W.Y. Wang, R.J. Ma, Z.J. Shen, and J.G. Fang. 2012. An improved strategy based on RAPD markers efficiently identified 95 peach cultivars. Genet. Mol. Res. 11:1158-1168. https://doi.org/10.4238/2012.May.7.1
  30. Zhuang, D.H., A. Kitajima, M. Ishida, and Y. Sobajima. 1990. Chromosome numbers of Diospyros kaki cultivars. J. Jpn. Soc. Hortic. Sci. 59:289-297. https://doi.org/10.2503/jjshs.59.289

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