AJPS  Vol.6 No.1 , January 2015
Construction of EST-SSR Databases for Effective Cultivar Identification and Their Applicability to Complement for Lettuce (Lactuca sativa L.) Distinctness Test
Abstract: The objectives of this study were to construct a database of expressed sequence tag (EST)-simple sequence repeat (SSR) markers to identify lettuce cultivars. A set of 370 EST-SSR primer pairs were applied for fingerprinting the lettuce cultivars. Fifty-eight EST-SSR markers showed hy-per-variability and were able to differentiate 92 cultivars. A total of 176 polymorphic amplified fragments were obtained by the 58 markers, and two to eight SSR alleles were detected for each l°Cus with an average of three alleles per locus. Average polymorphism information content (PIC) was 0.425, ranging from 0.022 to 0.743. Cluster analysis was based on Jaccard’s distance coefficients using the method of unweighted pair group. In this method we used arithmetical averages (UPGMA) algorithm categorized 4 major groups, which were in accordance to morphological traits. The eight cultivars of three groups with 100% genetic similarity through SSR analysis were investigated by phenotypic traits. These cultivars including these pairs are very similar in 27 morphological characteristics. Therefore, these EST-SSR markers could be used to select similar cultivars through management of reference collection to complement distinctiveness test of lettuce cultivars.
Cite this paper: Hong, J. , Kwon, Y. , Mishra, R. and Kim, D. (2015) Construction of EST-SSR Databases for Effective Cultivar Identification and Their Applicability to Complement for Lettuce (Lactuca sativa L.) Distinctness Test. American Journal of Plant Sciences, 6, 113-125. doi: 10.4236/ajps.2015.61013.

[1]   Still, D.W. (2007) Genome Mapping and Molecular Breeding in Plants. In: Kole, C., Ed., Vegetables, Vol. 5, 127-128.

[2]   Bredemeijer, G.M.M., Cooke, R.J., Ganal, M.W., Peeters, R., Isaac, P., Noordijk, Y., Rendell, S., Jackson, J., Röder, M.S., Wendehake, K., Dijcks, M., Amelaine, M., Wickaert, V., Bertrand, L. and Vosman, B. (2002) Construction and Testing of a Microsatellite Database Containing More than 500 Tomato Varieties. Theoretical and Applied Genetics, 105, 1019-1026.

[3]   Reid, A., Hof, L., Felix, G., Rücker, B., Tams, S., Milczynska, E., Esselink, D., Uenk, G., Vosman, B. and Weitz, A. (2011) Construction of an Integrated Microsatellite and Key Morphological Characteristic Database of Potato Varieties on the EU Common Catalogue. Euphytica, 182, 239-249.

[4]   Wang, F.G., Tian, H.L., Zhao, J.R., Yi, H.M., Wang, L. and Song, W. (2011) Development and Characterization of a Core Set of SSR Markers for Fingerprinting Analysis of Chinese Maize Varieties. Maydica, 56, 7-18.

[5]   UPOV/INF/17/1 (2010) Guideline for DNA-Profiling: Molecular Marker Selection and Database Construction (“BMT Guideline”). Geneva.

[6]   Kalia, R.K., Rai, M.K., Kalia, S., Singh, R. and Dhawan, A.K. (2011) Microsatellite Markers: An Overview of the Recent Progress in Plants. Euphytica, 177, 309-334.

[7]   Varshney, R.K., Graner, A. and Sorrells, M.E. (2005) Genic Microsatellite Markers in Plants: Features and Application. Trends in Biotechnology, 23, 48-55.

[8]   Scott, K.D., Eggler, P., Seaton, G., Rosetto, M., Ablett, E.M., Lee, L.S. and Henry, R.J. (2000) Analysis of SSRs Derived from Grape ESTs. Theoretical and Applied Genetics, 100, 723-726.

[9]   Jeuken, M.J.W., Pelgrom, K., Stam, P. and Lindhout, P. (2008) Efficient QTL Detection for Nonhost Resistance in Wild Lettuce: Backcross Inbred Lines versus F2 Population. Theoretical and Applied Genetics, 116, 845-857.

[10]   Simko, I. (2009) Development of EST-SSR Markers for the Study of Population Structure in Lettuce (Lactuca sativa L.). Journal of Heredity, 100, 256-262.

[11]   Hong, J.H., Kwon, Y.S., Choi, K.J., Mishra, R.K. and Kim, D.H. (2013) Identification of Lettuce Germplasms and Commercial Cultivars Using SSR Markers Developed from EST. Korean Journal of Horticultural Science & Technology, 31, 772-781.

[12]   Huang, X. and Madan, A. (1999) CAP3: A DNA Sequence Assembly Program. Genome Research, 9, 868-877.

[13]   Rozen, S. and Skaletsky, H.J. (2000) Primer3 on the WWW for General Users and for Biologist Programmers. Methods in Molecular Biology, 132, 365-386.

[14]   Anderson, J.A., Churchill, G.A., Autrigue, J.E. and Tanksley, S.D. (1993) Optimizing Parental Selection for Genetic Linkage Maps. Genome, 36, 181-186.

[15]   Sneath, P.H.A. and Sokal, R.R. (1973) Numerical Taxonomy: The Principles and Practice of Numerical Classification. Freeman, San Francisco.

[16]   Rohlf, F.J. (2000) NTSYSpc: Numerical Taxonomy and Multivariate Analysis System. Version 2.10b.

[17]   Mantel, N. (1967) The Detection of Disease Clustering and a Generalized Regression Approach. Cancer Research, 27, 209-220.

[18]   Ge, H., Li, H., Liu, Y., Li, X. and Chen, H. (2011) Characterization of Novel Developed Expressed Sequence Tag (EST)-Derived Simple Sequence Repeat (SSR) Markers and Their Application in Diversity Analysis of Eggplant. African Journal of Biotechnology, 10, 9023-9031.

[19]   Van de Wiel, C., Arens, P. and Vosman, B. (1999) Microsatellite Retrieval in Lettuce. Genome, 42, 139-149.

[20]   Rauscher, G. and Simko, I. (2013) Development of Genomic SSR Markers for Fingerprinting Lettuce (Lactuca sativa L.) Cultivars and Mapping Genes. BMC Plant Biology, 13, 11.

[21]   Hibrand-Saint Oyant, L., Crespel, L., Rajapakse, S., Zhang, L. and Foucher, F. (2008) Genetic Linkage Maps of Rose Constructed with New Microsatellite Markers and Locating QTL Controlling Flowering Traits. Tree Genet Genomes, 4, 11-23.

[22]   UPOV/INF/18/1 (2011) Possible Use of Molecular Markers in the Test of Distinctness, Uniformity, and Stability (DUS). Geneva.