GENETIC DIVERSITY ANALYSIS OF RIPENING SPECIFIC GENOTYPES USING POTENTIAL PUBLIC DOMAIN SSR MARKERS IN TOMATO (SOLANUM LYCOPERSICUM)

Pavan K. Velpula, Dwarkesh S. Parihar, Rajasekhar Pinnamaneni

Abstract


Tomato (Solanum lycopersicum) is one of the most important vegetable crops belongs to the family Solanaceae and acts as a model system for genetic and genomic studies. It is highly monomorphic at molecular level due to intensive selection during domestication. However, introgressions from wild species for potential traits led to increased diversity in the present day cultivars.  Eventually, it resulted in difficulty in identifying potential breeding material for crop improvement. In the present study, molecular genetic diversity analysis of 29 inbred lines and 3 natural mutant lines, with respect to fruit ripening, was carried out using 245 microsatellite markers derived from sol genomics network database. A UPGMA based genetic tree was constructed using 68 polymoprhic loci, which differentiated the genotypes into two main branches.  PCA also supported the UPGMA based genetic diversity analysis with minor exceptions.


Keywords


Tomato; Ripening; Genetic diversity; SSR

Full Text:

PDF XPS

References


Aflitos, S., Schijlen, E., Jong, H., Ridder, D., Smit, S., Finkers, R., ... & Bakker, F. 2014. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole‐genome sequencing. The Plant Journal, 80(1), 136-148.

Barchi, L., Lanteri, S., Portis, E., Acquadro, A., Valè, G., Toppino, L., Rotino, G.L. 2011. Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics 12.

Benor, S., Zhang, M., Wang, Z., Zhang, H. 2008. Assessment of genetic variation in tomato (Solanum lycopersicum L.) inbred lines using SSR molecular markers. Journal of Genetics and Genomics 35, 373-379.

Benor, S., Zhang, M., Wang, Z., Zhang, H. 2008. Assessment of genetic variation in tomato (Solanum lycopersicum L.) inbred lines using SSR molecular markers. Journal of Genetics and Genomics 35, 373-379.

Bolger, A., Scossa, F., Bolger, M.E., Lanz, C., Maumus, F., Tohge, T., Quesneville, H., Alseekh, S., Sørensen, I., Lichtenstein, G., Fich, E.A., Conte, M., Keller, H., Schneeberger, K., Schwacke, R., Ofner, I., Vrebalov, J., Xu, Y., Osorio, S., Aflitos, S.A., Schijlen, E., Jiménez-Goméz, J.M., Ryngajllo, M., Kimura, S., Kumar, R., Koenig, D., Headland, L.R., Maloof, J.N., Sinha, N., van Ham, R.C.H.J., Lankhorst, R.K., Mao, L., Vogel, A., Arsova, B., Panstruga, R., Fei, Z., Rose, J.K.C., Zamir, D., Carrari, F., Giovannoni, J.J., Weigel, D., Usadel, B., Fernie, A.R. 2014. The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Genetics 46, 1034-1038.

Bousquet, J., Simon, L., Lalonde, M. 1990. DNA amplification from vegetative and sexual tissues of trees using polymerase chain reaction. Canadian Journal of Forest Research 20, 254-257.

Bredemeijer, G., Cooke, R., Ganal, M., Peeters, R., Isaac, P., Noordijk, Y., ... & Dijcks, M. 2002. Construction and testing of a microsatellite database containing more than 500 tomato varieties. TAG Theoretical and Applied Genetics, 105(6), 1019-1026.

Doganlar, S., Tanksley, S.D., Mutschler, M.A. 2000. Identification and molecular mapping of loci controlling fruit ripening time in tomato. TAG Theoretical and Applied Genetics 100, 249-255.

He, C., Poysa, V., Yu, K. 2003. Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars. Theoretical and Applied Genetics 106, 363-373.

Ichihashi, Y., Sinha, N.R. 2014. From genome to phenome and back in tomato. Current Opinion in Plant Biology 18, 9-15.

Korir, N.K., Diao, W., Tao, R., Li, X., Kayesh, E., Li, A., Zhen, W., Wang, S. 2014. Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers. Genetics and Molecular Research 13, 43-53.

Korir, N.K., Han, J., Shangguan, L., Wang, C., Kayesh, E., Zhang, Y., Fang, J. 2012. Plant variety and cultivar identification: advances and prospects. Critical Reviews in Biotechnology 33, 111-125.

Labate, J.A., Robertson, L.D. 2012. Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles. BMC Plant Biology 12, 133.

Liu, K., Muse, S.V. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21, 2128-2129.

Murray, M.G., Thompson, W.F. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research 8, 4321-4326.

Olmstead, R. G., Bohs, L., Migid, H. A., Santiago-Valentin, E., Garcia, V. F., & Collier, S. M. 2008. A molecular phylogeny of the Solanaceae. Taxon, 57(4), 1159-1181.

Peakall, R., Smouse, P.E. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. Bioinformatics 28, 2537-2539.

Shirasawa, K., Asamizu, E., Fukuoka, H., Ohyama, A., Sato, S., Nakamura, Y., Tabata, S., Sasamoto, S., Wada, T., Kishida, Y., Tsuruoka, H., Fujishiro, T., Yamada, M., Isobe, S. 2010. An interspecific linkage map of SSR and intronic polymorphism markers in tomato. Theoretical and Applied Genetics 121, 731-739.

Shirasawa, K., Ishii, K., Kim, C., Ban, T., Suzuki, M., Ito, T., Muranaka, T., Kobayashi, M., Nagata, N., Isobe, S., Tabata, S. 2012. Development of Capsicum EST–SSR markers for species identification and in silico mapping onto the tomato genome sequence. Molecular Breeding 31, 101-110.

Sim, S. C., Van Deynze, A., Stoffel, K., Douches, D. S., Zarka, D., Ganal, M. W., ... & Panthee, D. R. 2012. High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding. PloS one, 7(9), e45520.

Tam, S.M., Mhiri, C., Vogelaar, A., Kerkveld, M., Pearce, S.R., Grandbastien, M.-A. 2005. Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theoretical and Applied Genetics 110, 819-831.

Tomato Consortium. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–41.

Varshney, R.K., Sigmund, R., Börner, A., Korzun, V., Stein, N., Sorrells, M.E., Langridge, P., Graner, A. 2005. Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Science 168, 195-202.

Zhao, M. Z., Zhang, Y. P., Wu, W. M., Wang, C., Qian, Y. M., Yang, G., & Fang, J. G. 2011. A new strategy for complete identification of 69 grapevine cultivars using random amplified polymorphic DNA (RAPD) markers. African Journal of Plant Science, 5(4), 273-280.


Refbacks

  • There are currently no refbacks.


Bookmark and Share


Copyright (c) 2017 Pavan K. Velpula, Dwarkesh S. Parihar, Rajasekhar Pinnamaneni

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

Journal of Plant Breeding and Genetics
ISSN: 2305-297X (Online), 2308-121X (Print)
© EScience Press. All Rights Reserved.