All Issue

2015 Vol.33, Issue 5 Preview Page
Use of Microsatellite Markers Derived from Genomic and Expressed Sequence Tag (EST) Data to Identify Commercial Watermelon Cultivars

수박 시판 품종의 식별을 위한 Genomic과 Expressed Sequence Tag (EST)에서 유래된 Microsatellite Marker의 이용

Yong-Sham Kwon1*
,
Jee-Hwa Hong2
,
Du-Hyun Kim1
,
Do-Hoon Kim1
권 용삼1*
,
홍 지화2
,
김 두현1
,
김 도훈1
1Department of Genetic Engineering, College of Natural Resources & Life Science, Dong-A University
2Seed Test & Research Center, Korea Seed & Variety Service, Ministry for Agriculture, Food & Rural Affairs
1동아대학교 생명자원과학대학 유전공학과
2농림축산식품부 국립종자원 종자검정연구센터
*교신저자. *Corresponding Author. 
31 October 2015. pp. 737-750
PDF XML Citation
Abstract

This study was carried out to construct a DNA profile database for 102 watermelon cultivars through the comparison of polymorphism level and genetic relatedness using genomic microsatellite (gMS) and expressed sequence tag (EST)-microsatellite (eMS) markers. Sixteen gMS and 10 eMS primers showed hyper-variability and were able to represent the genetic variation within 102 watermelon cultivars. With gMS markers, an average of 3.63 alleles per marker were detected with a polymorphism information content (PIC) value of 0.479, whereas with eMS markers, the average number of alleles per marker was 2.50 and the PIC value was 0.425, indicating that eMS detects a lower polymorphism level compared to gMS. Cluster analysis and Jaccard’s genetic distance coefficients using the unweighted pair group method with arithmetic average (UPGMA) based on the gMS, eMS, and combined data sets showed that 102 commercial watermelon cultivars could be categorized into 6 to 8 major groups corresponding to phenotypic traits. Moreover, this method was sufficient to identify 78 out of 102 cultivars. Correlation analysis with Mantel tests for those clusters using 3 data sets showed high correlation (r ≥ 0.80). Therefore, the microsatellite markers used in this study may serve as a useful tool for germplasm evaluation, genetic purity assessment, and fingerprinting of watermelon cultivars.

Keywords
Citrullus lanatus
genetic relationship
molecular marker
plant variety protection
variety fingerprinting

국내에서 시판되고 있는 수박 102 품종에 대한 DNA 프로파일 데이터베이스를 구축하기 위하여 genomic microsatellite (gMS)와 expressed sequence tag(EST) microsatellite(eMS) 마커의 다형성 정도의 비교와 유전적 연관성 분석을 통한 품종식별력 검정 등에 대한 일련의 연구를 수행하였다. 수박 gMS 마커를 이용하여 국내에서 시판되고 있는 수박 102 품종을 검정하였을 때 마커당 3.63개의 평균 대립유전자가 검출되었으며, 평균 PIC 값은 0.479로 나타났다. 이에 반해 eMS 마커는 평균 대립유전자의 수가 2.50개, PIC 값이 0.425로 나타나 gMS 마커보다 다형성 정도가 낮게 나타났다. gMS와 eMS 및 이들 두 종류의 마커를 병합하여 작성된 계통도는 microsatellite 마커의 다형성에 따라 수박 102개 품종을 6-8개의 그룹으로 구분하였고 대부분의 품종의 식별이 가능하였다. 3가지 마커 유형에 따라 작성된 계통도를 Mantel test에 의해 상관 정도를 분석하였을 때 높은 상관(r ≥ 0.80)을 나타내었다. 따라서 본 연구에 활용된 microsatellite마커는 수박 유전자원의 특성평가, 순도검정 및 품종의 지문화 작업의 수단으로 유용하게 활용될 수 있을 것이다.

키워드
수박
유전적 유연관계
분자마커
식물품종보호
품종지문화
References
1
Anderson, J.A., G.A. Churchill, J.E. Autrigue, and S.D. Tanksley. 1993. Optimizing parental selection for genetic linkage maps. Genome 36:181-186.
2
Bae, K.M., S.C. Sim, J.H. Hong, K.J. Choi, D.H. Kim, and Y.S. Kwon. 2015. Development of genomic SSR markers and genetic diversity analysis in cultivated radish (Raphanus sativus L.). Hortic. Environ. Biotechnol. 56:216-224.
3
Bate, D.M., and R. Robinson. 1995. Cucumber, melons, and watermelon: Cucumis and Citrullus (Cucurbitaceae), p. 89-96. In: J. Smartt and N.W. Simmonds (eds). Evolution of Crop Plants. Longman, London, UK.
4
Bredemeijer, G.M.M, R.J. Cooke, M.W. Ganal, R. Peeters, P. Isaac, Y. Noordijk, S. Rendell, J. Jackson, M.S. Röder, K. Wendehake, M. Dijcks, M. Amelaine, V. Wickaert, L. Bertrand, and B. Vosman. 2002. Construction and testing of a microsatellite database containing more than 500 tomato varieties. Theor. Appl. Genet. 105:1019-1026.
5
Che, K.P., C.Y. Liang, Y.G. Wang, D.M. Jin, and B. Wang. 2003. Genetic assessment of watermelon germplasm using the AFLP technique. HortScience 38:81-84.
6
Gadaleta, A., A. Giancaspro, S. Zacheo, D. Nigro, S.L. Giove, P. Colasuonno, and A. Blanco. 2011. Comparison of genomic and EST-derived SSR markers in phylogenetic analysis of wheat. Plant Genet. Resour. 9:243-246.
7
Guerra-Sanz, J.M. 2002. Citrullus simple sequence repeats markers from sequence databases. Mol. Ecol. Notes 2:223-225.
8
Hong, J.H., K.J. Choi, and Y.S. Kwon. 2014. Construction of DNA profile data base of strawberry cultivars using microsatellite markers. Kor. J. Hort. Sci. Technol. 32: 856-863.
9
Hong, J.H., Y.S. Kwon, R.K. Mishra, and D.H. Kim. 2015. Construction of EST-SSR databases for effective cultivar identification and their applicability to complement for lettuce (Lactuca sativa L.) distinctness test. Am. J. Plant Sci. 6:113-125
10
Hu, J., L. Wang, and J. Li. 2011. Comparison of genomic SSR and EST-SSR markers for estimating genetic diversity in cucumber. Biol. Plant. 55:577-580.
11
International Union for the Protection of New Varieties of Plants (UPOV). 2010. Guideline for DNA-profiling: Molecular marker selection and database construction (BMT Guideline). UPOV, Geneva. UPOV/INF/17/1.
12
Jaccard, P. 1908. Nouvelles recherché sur la distribution florale. Bulletin de la Sociétévaudoise des sciences naturelles 44:223-270.
13
Jarret, R.L., L.C. Merrick, T. Holms, J. Evans, and M.K. Aradhya. 1996. Simple sequence repeats in watermelon (Citrullus lanatus (Thunb) Matsum. & Nakai). Genome 40:433-441.
14
Joobeur, T., G. Gusmini, X. Zhang, A. Levi, Y. Xu, T.C. Wehner, M. Oliver, and R.A. Dean. 2006. Construction of a watermelon BAC library and identification of SSRs anchored to melon or Arabidopsis genomes. Theor. Appl. Genet. 112:1553-1562.
15
Kalia, R.J., M.K. Rai, S. Kalia, R. Singh, and A. K. Dhawan. 2011. Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309-334.
16
Kim, Y.H., H.M. Park, T.Y. Hwang, S.K. Lee, M.S. Choi, S.W. Jho, S.W. Hwang, H.M. Kim, B.C. Kim, C.P. Hong, Y.S. Cho, H.M. Kim, K.H. Jeong, M.J. Seo, H.T. Yun, S.L. Kim, Y.U. Kwon, W.H. Kim, H.K. Chun, S.J. Lim, I.Y Choi, Y.S. Kim, H.S. Yoon, S.H. Lee, and S.H. Lee. 2014. Variation block-based genomics methods for crop plants. BMC Genomics 15:477.
17
Kwon, Y.S. 2013. Use of EST-SSR markers for genetic characterisation of commercial watermelon cultivars and hybrid seed purity testing. Seed Sci. Technol. 41:245-256.
18
Kwon, Y.S., and K.J. Choi. 2013. Construction of a DNA profile database for commercial cucumber (Cucumis sativus L.) cultivars using microsatellite markers. Kor. J. Hort. Sci. Technol. 31: 344-351.
19
Kwon, Y.S., and J. H. Hong. 2014. Use of microsatellite markers to identify commercial melon cultivars and for hybrid seed purity testing. Korean J. Hortic. Sci. Technol. 32:525-534.
20
Kwon, Y.S., Y.H. Oh, S.I. Yi, H.Y. Kim, J.M. An, S.G. Yang, S.H. Ok, and J.S. Shin. 2010. Informative SSR markers for commercial variety discrimination in watermelon (Citrullus lanatus). Genes Genom. 32:115-122.
21
Kwon, Y.S., E.K. Park, W.S. Lee, S.I. Yi, K.M. Bae, J.S. An, and H.Y. Kim. 2007. Genetic assessment of watermelon (Citrullus lanatus) varieties using SSR markers developed from Cucurbit species. Korean J. Genetics 29:137-146.
22
Lee, S.J., J.S. Shin, K.W. Park, and Y.P. Hong. 1996. Detection of genetic diversity using RAPD-PCR and sugar analysis in watermelon [Citrullus lanatus (Thunb.) Mansf.] germplasm. Theor. Appl. Genet. 92:719-725.
23
Mantel, N. 1967. The detection of disease clustering and generalized repression approach. Cancer Res. 27:209-220.
24
Mujaju, C., J. Sehic, G. Werlemark, L. Garkava-gustavsson, M. Fatih, and H. Nybom. 2010. Genetic diversity in watermelon (Citrullus lanatus) landraces from Zimbabwe revealed by RAPD and SSR markers. Hereditas 147:142-153.
25
Reid, A., L. Hof, G. Felix, B. Rücker, S. Tams, E. Milczynska, D. Esselink, G. Uenk, B. Vosman, and A. Weitz. 2011. Construction of an integrated microsatellite and key morphological characteristic database of potato varieties on the EU common catalogue. Euphytica 182:239-249.
26
Ren, Y., H. Zhao, Q. Kou, J. Jiang, S. Guo, H. Zhang, W. Hou, X. Zou, H. Sun, G. Gong, A. Levi, and Y. Xu. 2012. A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome. PLoS One 7:e29453.
27
Rohlf, F.J. 2000. NTSYSpc: Numerical taxonomy and multivariate analysis system, ver. 2.10b. Applied Biostatistics Inc., New York.
28
Sneath, P.H.A. and R.R. Sokal. 1973. Numerical taxonomy: The principles and practice of numerical classification, Freeman W.H., San Francisco.
29
Tabbasam, N., Y. Zafar., and M. Rahman. 2014. Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium. Plant Syst. Evol. 300:559-575
30
Varshney, R.K., A. Garner, and M.E. Sorells. 2005. Genic micro-satellite markers in plants: features and applications. Trends Biotechnol. 23:48-63.
31
Wang, F.G., H.L. Tian, J.R. Zhao, H.M. Yi, L. Wang, and W. Song. 2011. Development and characterization of a core set of SSR markers for fingerprinting analysis of Chinese maize varieties. Maydica 56:7-18.
32
Zhang, H., H. Wang, S. Guo, Y. Ren, G. Gong, Y. Weng, and Y. Xu. 2012. Identification and validation of a core set of microsatellite markers for genetic diversity analysis in watermelon, Citrullus lanatus Thunb. Matsum. & Nakai. Euphytica 186:329-342.
Information
  • Publisher :KOREAN SOCIETY FOR HORTICULTURAL SCIENCE
  • Publisher(Ko) :한국원예학회
  • Journal Title :Horticultural Science and Technology
  • Journal Title(Ko) :원예과학기술지
  • Volume : 33
  • No :5
  • Pages :737-750
  • Received Date : 2015-03-10
  • Revised Date : 2015-06-08
  • Accepted Date : 2015-06-12
  • DOI :https://doi.org/10.7235/hort.2015.15045
Journal Informaiton Horticultural Science and Technology Horticultural Science and Technology
Online Submission
  • scopus
  • NRF
  • KOFST
  • crossref crossmark
  • crossref cited-by
  • crosscheck
  • orcid
  • open access
  • ccl
Journal Informaiton Journal Informaiton - close