AJPS  Vol.5 No.11 , May 2014
In Silico Mining of EST-SSRs in Jatropha curcas L. towards Assessing Genetic Polymorphism and Marker Development for Selection of High Oil Yielding Clones
Abstract: In recent years, Jatropha curcas L. has gained popularity as a potential biodiesel plant. The varying oil content, reported between accessions belonging to different agroclimatic zones, has necessitated the assessment of the existing genetic variability to generate reliable molecular markers for selection of high oil yielding variety. EST derived SSR markers are more useful than genomic markers as they represent the transcriptome, thus, directly linked to functional genes. The present report describes the in silico mining of the microsatellites (SSRs) using J. curcas ESTs from various tissues viz. embryo, root, leaf and seed available in the public domain of NCBI. A total of 13,513 ESTs were downloaded. From these ESTs, 7552 unigenes were obtained and 395 SSRs were generated from 377 SSR-ESTs. These EST-SSRs can be used as potential microsatellite markers for diversity analysis, MAS etc. Since the Jatropha genes carrying SSRs have been identified in this study, thus, EST-SSRs directly linked to genes will be useful for developing trait linked markers.
Cite this paper: Jain, N. , Patil, G. , Bhargava, P. and Nadgauda, R. (2014) In Silico Mining of EST-SSRs in Jatropha curcas L. towards Assessing Genetic Polymorphism and Marker Development for Selection of High Oil Yielding Clones. American Journal of Plant Sciences, 5, 1521-1541. doi: 10.4236/ajps.2014.511167.

[1]   Ginwal, H.S., Rawat, P.S. and Srivastava, R.L. (2004) Seed Source Variation in Growth Performance and Oil Yield of Jatropha curcas Linn. in Central India. Silvae Genetics, 53, 186-192.

[2]   Ikbal, K., Boora, S. and Dhillon, R.S. (2010) Evaluation of Genetic Diversity in Jatropha curcas L. Using RAPD Markers. Indian Journal of Biotechnology, 9, 50-57.

[3]   Tatikonda, L., Wani, S.P., Kannan, S., Beerelli, N., Sreedevi, T.K., Hoisington, D.A., Devi P. and Varshney, R.K. (2009) AFLP-Based Molecular Characterization of an Elite Germplasm Collection of Jatropha curcas L., a Biofuel Plant. Plant Science, 176, 505-513.

[4]   Jubera, M.A., Janagoudar, B.S., Biradar, D.P., Ravikumar, R.L., Koti, R.V. and Patil, S.J. (2009) Genetic Diversity Analysis of Elite Jatropha curcas (L.) Genotypes Using Randomly Amplified Polymorphic DNA Markers. Karnataka. Journal of Agricultural Sciences, 22, 293-295.

[5]   Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A. and Tingey, S.V. (1990) DNA Polymorphisms Amplified by Arbitrary Primers Are Useful as Genetic Markers. Nucleic Acids Research, 18, 6531-6535.

[6]   Alhani, M.C. and Wilkinson, M.J. (1998) Inter Simple Sequence Repeat Polymerase Chain Reaction for the Detection of Somaclonal Variation. Plant Breeding, 117, 573-575.

[7]   Blair, M.W., Panaud, O. and McCouch, S.R. (1999) Inter-Simple Sequence Repeat (ISSR) Amplification for Analysis of Microsatellite Motif Frequency and Fingerprinting in Rice (Oryza sativa L.). Theoretical and Applied Genetics, 98, 780-792.

[8]   Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Zabeau, M. and Kuiper, M. (1995) AFLP: A New Technique for DNA Fingerprinting. Nucleic Acids Research, 23, 4407-4414.

[9]   Zhu, J., Gale, M.D., Quarrie, S., Jackson, M.T. and Bryan, G.J. (1998) AFLP Markers for the Study of Rice Biodiversity. Theoretical and Applied Genetics, 96, 602-611.

[10]   Basha, S.D., Francis, G., Makkar, H.P.S., Becker, K. and Sujatha, M. (2009) A Comparative Study of Biochemical Traits and Molecular Markers for Assessment of Genetic Relationships between Jatropha curcas L. Germplasm from Different Countries. Plant Science, 176, 812-823.

[11]   Basha, S.D. and Sujatha, M. (2007) Inter and Intra-Population Variability of Jatropha curcas L. Characterized by RAPD and ISSR Markers and Development of Population-Specific SCAR Markers. Euphytica, 156, 375-386.

[12]   Sujatha, M., Reddy, T.P. and Mahasi, M.J. (2008) Role of Biotechnological Interventions in the Improvement of Castor (Ricinus communis L.) and Jatropha curcas L. Biotechnology Advances, 26, 424-435.

[13]   Vieux, E.F., Kwok, P.Y. and Miller, R.D. (2002) Primer Design for PCR and Sequencing in High-Throughput Analysis of SNPs. BioTechniques, 32, S28-S32.

[14]   Levinson, G. and Gutman, G.A. (1987) Slipped-Strand Mispairing: A Major Mechanism for DNA Sequence Evolution. Molecular Biology and Evolution, 4, 203-221.

[15]   Chakravarthi, B.K. and Naravaneni, R. (2006) SSR Marker Based DNA Fingerprinting and Diversity Study in Rice (Oryza sativa. L.). African Journal of Biotechnology, 5, 684-688.

[16]   Tripathi, K.P., Roy, S., Khan, F., Shasany, A.K., Sharma, A. and Khanuja, S.P.S. (2008) Identification of SSR-ESTs Corresponding to Alkaloid, Phenylpropanoid and Terpenoid Biosynthesis in MAPs. Online Journal of Bioinformatics, 9, 78-91.

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

[18]   Raji, A.A.J., Anderson, J.V., Kolade, O.A., Ugwu, C.D., Dixon, A.G.O. and Ingelbrecht, I.L. (2009) Gene-Based Microsatellites for Cassava (Manihot esculenta Crantz): Prevalence, Polymorphisms, and Cross-Taxa Utility. BMC Plant Biology, 9, 1471-1429.

[19]   Wang, Y.H., Liu, S.J., Ji, S.L., Zhang, W.W., Wang, C.M., Jiang, L. and Wan, J.M. (2005) Fine Mapping and Marker-Assisted Selection (MAS) of a Low Glutelin Content Gene in Rice. Cell Research, 15, 622-630.

[20]   Carneiro, F.F., Santos, J.B. and Leite, M.E. (2010) Marker-Assisted Backcrossing Using Microsatellites and Validation of SCAR Phs Marker for Resistance to White Mold in Common Bean. Electronic Journal of Biotechnology, 13, Online Version.

[21]   Gupta, S. and Prasad, M. (2009) Development and Characterization of Genic SSR Markers in Medicago truncatula and Their Transferability in Leguminous and Non-Leguminous Species. Genome, 52, 761-771.

[22]   Wen, M., Wang, H., Xia, Z., Zou, M., Lu, C. and Wang, W. (2010) Development of EST-SSR and Genomic-SSR Markers to Assess Genetic Diversity in Jatropha curcas L. BMC Resarch Notes, 3, 42.

[23]   Morgante, M., Hanafey, M. and Powell, W. (2002) Microsatellites Are Preferentially Associated with Nonrepetitive DNA in Plant Genomes. Nature Genetics, 30, 194-200.

[24]   Riju, A, Chandrasekar, A. and Arunachalam, V. (2007) Mining for Single Nucleotide Polymorphisms and Insertions / Deletions in Expressed Sequence Tag Libraries of Oil Palm. Bioinformation, 2, 128-131.

[25]   Kumpatla, S.P. and Mukhopadhyay, S. (2005) Mining and Survey of Simple Sequence Repeats in Expressed Sequence Tags of Dicotyledonous Species. Genome, 48, 985-998.

[26]   Garcia, R.A.V., Rangel, P.N., Brondani, C., Martins, W.S., Melo, L.C., Carneiro, M.S., Borba, T.C. and Brondani, R.P. (2011) The Characterization of a New Set of EST-Derived Simple Sequence Repeat (SSR) Markers as a Resource for the Genetic Analysis of Phaseolus vulgaris. BMC Genetic, 12, 41-54.

[27]   Ceresini, P.C., Silva, C.L.S.P., Missio, R.F., Souza, E.C., Fischer, C.N., Guillherme, I.R., Gregorio, I., Da Silva, E.H.T., Cicarelli, R.M.B., Silva, M.T.A., Garcia, J.F., Avelar, G.A., Porto Neto, L.R., Marcon, A.R., Bacci Jr., M. and Marini, D.C. (2005) Satellyptus: Analysis and Database of Microsatellites from ESTs of Eucalyptus. Genetics and Molecular Biology, 28, 589-600.

[28]   Pinto, L.R., Oliveira, K.M., Ulian, E.C., Garcia, A.A.F. and De Souza, A.P. (2004) Survey in the Sugarcane Expressed Sequence Tag Database (SUCEST) for Simple Sequence Repeats. Genome, 47, 795-804.

[29]   Eujayl, I., Sledge, M.K., Wang, L., May, G.D., Chekhovskiy, K., Zwonitzer, J.C. and Mian, M.A.R. (2004) Medicago truncatula EST-SSRs Reveal Cross-Species Genetic Markers for Medicago spp. Theoretical and Applied Genetics, 108, 414-422.

[30]   Fraser, L.G., Harvey, C.F., Crowhurst, R.N. and Silva, H.N. (2003) EST-Derived Microsatellites from Actinidia Species and Their Potential for Mapping. Theoretical and Applied Genetics, 108, 1010-1016.

[31]   Ellis, J.R. and Burke, J.M. (2007) EST-SSRs as a Resource for Population Genetic Analyses. Heredity, 99, 125-132.

[32]   Sato, K., Nankaku, N. and Takeda, K. (2009) A high-Density Transcript Linkage Map of Barley Derived from a Single Population. Heredity, 103, 110-117.

[33]   Shirasawa, K., Oyama, M., Hirakawa, H., Sato, S., Tabata, S., Fujioka, T., et al. (2011) An EST-SSR Linkage Map of Raphanus sativus and Comparative Genomics of the Brassicaceae. DNA Research, 18, 221-232.

[34]   Varshney, R.K., Mahendar, T., Aggarwal, R.K. and Börner, A. (2007) Genetic Molecular Markers in Plants: Development and Applications. In: Varshney, R.K. and Tuberosa, R., Eds., Genomics-Assisted Crop Improvement: 1: Genomics Approaches and Platforms, Springer, Berlin, 13-29.

[35]   Wang, C.M., Liu, P., Yi, C., Gu, K., Sun, F., Li, L., Lo, L.C., Liu, X., Feng, F., Lin, G., Cao, S., Hong, Y., Yi, Z. and Yue, G.H. (2011) A First Generation Microsatellite and SNP-based Linkage Map of Jatropha. PLoS ONE, 6, e23632.

[36]   NCBI’s dbEST Database.

[37]   EGassembler.

[38]   SSRlocator Version 1. [Standalone software]

[39]   TAIR. [online]

[40]   Locus Identifiers at Bulk Data Retrieval System of TAIR.

[41]   Carvalho, C.R., Clarindo, W.R., Praca, M.M., Araújo, F.S. and Carels, N. (2008) Genome Size, Base Composition and Karyotype of Jatropha curcas L., an Important Biofuel Plant. Plant Science, 174, 613-617.

[42]   Raju, N.L., Gnanesh, B.N., Lekha, P., Jayashree, B., Pande, S., Hiremath, P.J., Byregowda, M., Singh, N.K. and Varshney, R.K. (2010) The First Set of EST Resource for Gene Discovery and Marker Development in Pigeon Pea (Cajanus cajan L.). BMC Plant Biology, 10, 45.

[43]   Varshney, R.K., Thiel, T., Stein, N., Langridge, P. and Graner, A. (2002) In Silico Analysis on Frequency and Distribution of Microsatellites in ESTs of Some Cereal Species. Cell and Molecular Biology Letters, 7, 537-546.

[44]   Cardle, L., Ramsay, L., Milbourne, D., Macaulay, M., Marshall, D. and Waug, R. (2000) Computational and Experimental Characterization of Physically Clustered Simple Sequence Repeats in Plants. Genetics, 156, 847-854.

[45]   Metzgar, D., Bytof, J. and Wills, C. (2000) Selection against Frameshift Mutations Limits Microsatellite Expansion in Coding DNA. Genome Research, 10, 72-80.

[46]   Morgante, M. and Olivieri, A.M. (1993) PCR-Amplified Microsatellites as Markers in Plant Genetics. The Plant Journal, 3, 175-182.

[47]   Cho, Y.G., Ishii, T., Temnykh, S., Chen, X., Lipovich, L., McCouch, S.R., Park, W.D., Ayres, N. and Cartinhour, S. (2000) Diversity of Microsatellites Derived from Genomic Libraries and GenBank Sequences in Rice (Oryza sativa L.). Theoretical Applied Genetics, 100, 713-722.

[48]   La Rota, M., Kantety, R.V., Yu, J.K. and Sorrells, M.E. (2005) Nonrandom Distribution and Frequencies of Genomic and EST-Derived Microsatellite Markers in Rice, Wheat, and Barley. BMC Genomics, 6, 23.

[49]   Temnykh, S., DeClerck, G., Lukashova, A., Lipovich, L., Cartinhour, S. and McCouch, S. (2001) Computational and Experimental Analysis of Microsatellites in Rice (Oryza sativa L.): Frequency, Length Variation, Transposon Associations, and Genetic Marker Potential. Genome Research, 11, 1441-1452.

[50]   Powell, W., Morgante, M., McDevitt, R., Vendramin, G.G. and Rafalski, J.A. (1995) Polymorphic Simple Sequence Repeat Regions in Chloroplast Genomes: Applications to the Population Genetics of Pines. Proceedings of National Academy of Sciences of the United States of America, 92, 7759-7763.