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2016
T. Mornkham, Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., Kurzweil, H., Mornkham, T., Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., Kurzweil, H., Mornkham, T., Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., Kurzweil, H., Mornkham, T., Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., and Kurzweil, H., Development and characterization of novel EST-SSR markers and their application for genetic diversity analysis of Jerusalem artichoke (Helianthus tuberosus L.), vol. 15, no. 4, p. -, 2016.
Conflicts of interest The authors declare no conflict of interest. ACKNOWLEDGEMENTS The Higher Education Research Promotion, the National Research University Project of Thailand, the Office of the Higher Education Commission through the Food and Functional Food Research Cluster of Khon Kaen University (F-2553-Ph.d-02 and FC1.1.5 PhD), and research funding from Khon Kaen University to the corresponding author are acknowledged for financially support. We thank Assistant Professor Dr. Tawan Remsungnen for his assistance on the preliminary analysis of SSRs, and the journal reviewers for their valuable comments on this manuscript. REFERENCES Adawy SS, Mokhtar MM, Alsamman MA and Sakr MM (2015). Development of EST-SSR annotated database in olive (Oleaeuropaea). IJSR09. Alla NA, Domokos-Szabolcsy É, El-Ramady H, Hodossi S, et al (2014). Jerusalem artichoke (Helianthus tuberosus L.): A review of in vivo and in vitro propagation. Int. J. Hortic. Sci. 20: 131-136. Andersen JR, Lübberstedt T, et al (2003). Functional markers in plants. Trends Plant Sci. 8: 554-560. http://dx.doi.org/10.1016/j.tplants.2003.09.010 Bassam BJ, Caetano-Anollés G, Gresshoff PM, et al (1991). Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. 196: 80-83. http://dx.doi.org/10.1016/0003-2697(91)90120-I Bock DG, Kane NC, Ebert DP, Rieseberg LH, et al (2014). Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke. New Phytol. 201: 1021-1030. http://dx.doi.org/10.1111/nph.12560 Botstein D, White RL, Skolnick M, Davis RW, et al (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32: 314-331. Chen H, Liu L, Wang L, Wang S, et al (2015). Development and validation of EST-SSR markers from the transcriptome of Adzuki bean (Vigna angularis). PLoS One 10: e0131939. http://dx.doi.org/10.1371/journal.pone.0131939 Debnath SC, et al (2014). Structured diversity using EST-PCR and EST-SSR markers in a set of wild blueberry clones and cultivars. Biochem. Syst. Ecol. 54: 337-347. http://dx.doi.org/10.1016/j.bse.2014.03.018 Excoffier L, Smouse PE, Quattro JM, et al (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491. Gadaleta A, Giancaspro A, Zacheo S, Nigro D, et al (2011). Comparison of genomic and EST-derived SSR markers in phylogenetic analysis of wheat. Plant Genet. Resour. 9: 243-246. http://dx.doi.org/10.1017/S147926211100030X Garcia RAV, Rangel PN, Brondani C, Martins WS, et al (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 Genet. 12: 41-54. http://dx.doi.org/10.1186/1471-2156-12-41 Gupta SK, Gopalakrishna T, et al (2010). Development of unigene-derived SSR markers in cowpea (Vigna unguiculata) and their transferability to other Vigna species. Genome 53: 508-523. http://dx.doi.org/10.1139/G10-028 Hartl DL and Clark AG (1997). Principle of Population Genetics. 1997. Sinauer Associates, Inc. Hildebrand CE, Torney DC, Wagner RP, et al (1992). Informativeness of polymorphic DNA markers. Los Alamos Sci. 20: 100-102. Huang X, Madan A, et al (1999). CAP3: A DNA sequence assembly program. Genome Res. 9: 868-877. http://dx.doi.org/10.1101/gr.9.9.868 Johansson E, Prade T, Angelidaki I, Svensson SE, et al (2015). Economically viable components from Jerusalem artichoke (Helianthus tuberosus L.) in a biorefinery concept. Int. J. Mol. Sci. 16: 8997-9016. http://dx.doi.org/10.3390/ijms16048997 Ju MM, Ma HC, Xin PY, Zhou ZL, et al (2015). Development and characterization of EST-SSR markers in Bombax ceiba (Malvaceae). Appl. Plant Sci. 3: 1500001. http://dx.doi.org/10.3732/apps.1500001 Jung WY, Lee SS, Kim CW, Kim H-S, et al (2014). RNA-seq analysis and de novo transcriptome assembly of Jerusalem artichoke (Helianthus tuberosus Linne). PLoS One 9: e111982. http://dx.doi.org/10.1371/journal.pone.0111982 Kays SJ and Nottingham SF (2008). Genetic resources, breeding and cultivars. In: Biology and Biochemistry of Jerusalem Artichoke (Taylor and Francis eds.). CRC Press, 149-240. Kiru S, Nasenko I, et al (2010). Use of genetic resources from Jerusalem artichoke collection of N. Vavilov Institute in breeding for bioenergy and health. Agron. Res. 8: 625-632. Kou YX, Zeng J, Liu JQ, Kou YX, et al (2014). Germplasm diversity and differentiation of Helianthus tuberosus L. revealed by AFLP marker and phenotypic traits. J. Agric. Sci. 152: 779-789. http://dx.doi.org/10.1017/S0021859613000476 Kumari M, Grover A, Yadav PV, Arif M, et al (2013). Development of EST-SSR markers through data mining and their use for genetic diversity study in Indian accessions of Jatropha curcas L.: a potential energy crop. Genes Genomics 35: 661-670. http://dx.doi.org/10.1007/s13258-013-0118-0 Malfa SL, Currò S, Douglas AB, Brugaletta M, et al (2014). Genetic diversity revealed by EST-SSR markers in carob tree (Ceratonia siliqua L.). Biochem. Syst. Ecol. 55: 205-211. http://dx.doi.org/10.1016/j.bse.2014.03.022 Merritt BJ, Culley TM, Avanesyan A, Stokes R, et al (2015). An empirical review: Characteristics of plant microsatellite markers that confer higher levels of genetic variation. Appl. Plant Sci. 3: 1500025. http://dx.doi.org/10.3732/apps.1500025 Mondini L, Noorani A, Pagnotta MA, et al (2009). Assessing plant genetic diversity by molecular tools. Diversity (Basel) 1: 19-35. http://dx.doi.org/10.3390/d1010019 Moose SP, Mumm RH, et al (2008). Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol. 147: 969-977. http://dx.doi.org/10.1104/pp.108.118232 Mujaju C, Sehic J, Nybom H, et al (2013). Assessment of EST-SSR markers for evaluating genetic diversity in watermelon accessions from Zimbabwe. Am. J. Plant Sci. 4: 1448-1456. http://dx.doi.org/10.4236/ajps.2013.47177 Mullis K, Faloona F, Scharf S, Saiki R, et al (1986). Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb. Symp. Quant. Biol. 51: 263-273. http://dx.doi.org/10.1101/SQB.1986.051.01.032 Park YJ, Lee JK, Kim NS, et al (2009). Simple sequence repeat polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops. Molecules 14: 4546-4569. http://dx.doi.org/10.3390/molecules14114546 Peakall R, Smouse P, et al (2006). GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6: 288-295. http://dx.doi.org/10.1111/j.1471-8286.2005.01155.x Peakall R, Smouse PE, et al (2012). GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. Bioinformatics 28: 2537-2539. http://dx.doi.org/10.1093/bioinformatics/bts460 Poczai P, Varga I, Laos M, Cseh A, et al (2013). Advances in plant gene-targeted and functional markers: a review. Plant Methods 9: 6. http://dx.doi.org/10.1186/1746-4811-9-6 Ramu P, Billot C, Rami JF, Senthilvel S, et al (2013). Assessment of genetic diversity in the sorghum reference set using EST-SSR markers. Theor. Appl. Genet. 126: 2051-2064. http://dx.doi.org/10.1007/s00122-013-2117-6 Şelale H, Çelik I, Gültekin V, Allmer J, et al (2013). Development of EST-SSR markers for diversity and breeding studies in opium poppy. Plant Breed. 132: 344-351. http://dx.doi.org/10.1111/pbr.12059 Sokal RR, Michener CD, et al (1958). A statistical method for evaluating systematic relationships. Univ. Kans. Sci. Bull. 38: 1409-1438. Temnykh S, DeClerck G, Lukashova A, Lipovich L, et al (2001). Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11: 1441-1452. http://dx.doi.org/10.1101/gr.184001 Wangsomnuk PP, Khampa S, Jogloy S, Srivong T, et al (2011a). Assessing genetic structure and relatedness of Jerusalem Artichoke (Helianthus tuberosus L.) germplasm with RAPD, ISSR and SRAP Markers. AJPS 2: 753-764. http://dx.doi.org/10.4236/ajps.2011.26090 Wangsomnuk PP, Khampa S, Wangsomnuk P, Jogloy S, et al (2011b). Genetic diversity of worldwide Jerusalem artichoke (Helianthus tuberosus) germplasm as revealed by RAPD markers. Genet. Mol. Res. 10: 4012-4025. http://dx.doi.org/10.4238/2011.December.12.4 Wangsomnuk PP, Khampa S, Jogloy S, et al (2015). Exogenous supplementation of growth regulators and temperature improves germination of dormant Jerusalem Artichoke (Helianthus tuberosus L.) seeds under in vitro and in vivo conditions. JABS 9: 23-30. Zhang M, Mao W, Zhang G, Wu F, et al (2014). Development and characterization of polymorphic EST-SSR and genomic SSR markers for Tibetan annual wild barley. PLoS One 9: e94881. http://dx.doi.org/10.1371/journal.pone.0094881 Zhou Q, Chen TL, Wang YR, Liu ZP, et al (2014). The development of 204 novel EST-SSRs and their use for genetic diversity analyses in cultivated alfalfa. Biochem. Syst. Ecol. 57: 227-230. http://dx.doi.org/10.1016/j.bse.2014.08.023
T. Mornkham, Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., Kurzweil, H., Mornkham, T., Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., Kurzweil, H., Mornkham, T., Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., Kurzweil, H., Mornkham, T., Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., and Kurzweil, H., Development and characterization of novel EST-SSR markers and their application for genetic diversity analysis of Jerusalem artichoke (Helianthus tuberosus L.), vol. 15, no. 4, p. -, 2016.
Conflicts of interest The authors declare no conflict of interest. ACKNOWLEDGEMENTS The Higher Education Research Promotion, the National Research University Project of Thailand, the Office of the Higher Education Commission through the Food and Functional Food Research Cluster of Khon Kaen University (F-2553-Ph.d-02 and FC1.1.5 PhD), and research funding from Khon Kaen University to the corresponding author are acknowledged for financially support. We thank Assistant Professor Dr. Tawan Remsungnen for his assistance on the preliminary analysis of SSRs, and the journal reviewers for their valuable comments on this manuscript. REFERENCES Adawy SS, Mokhtar MM, Alsamman MA and Sakr MM (2015). Development of EST-SSR annotated database in olive (Oleaeuropaea). IJSR09. Alla NA, Domokos-Szabolcsy É, El-Ramady H, Hodossi S, et al (2014). Jerusalem artichoke (Helianthus tuberosus L.): A review of in vivo and in vitro propagation. Int. J. Hortic. Sci. 20: 131-136. Andersen JR, Lübberstedt T, et al (2003). Functional markers in plants. Trends Plant Sci. 8: 554-560. http://dx.doi.org/10.1016/j.tplants.2003.09.010 Bassam BJ, Caetano-Anollés G, Gresshoff PM, et al (1991). Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. 196: 80-83. http://dx.doi.org/10.1016/0003-2697(91)90120-I Bock DG, Kane NC, Ebert DP, Rieseberg LH, et al (2014). Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke. New Phytol. 201: 1021-1030. http://dx.doi.org/10.1111/nph.12560 Botstein D, White RL, Skolnick M, Davis RW, et al (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32: 314-331. Chen H, Liu L, Wang L, Wang S, et al (2015). Development and validation of EST-SSR markers from the transcriptome of Adzuki bean (Vigna angularis). PLoS One 10: e0131939. http://dx.doi.org/10.1371/journal.pone.0131939 Debnath SC, et al (2014). Structured diversity using EST-PCR and EST-SSR markers in a set of wild blueberry clones and cultivars. Biochem. Syst. Ecol. 54: 337-347. http://dx.doi.org/10.1016/j.bse.2014.03.018 Excoffier L, Smouse PE, Quattro JM, et al (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491. Gadaleta A, Giancaspro A, Zacheo S, Nigro D, et al (2011). Comparison of genomic and EST-derived SSR markers in phylogenetic analysis of wheat. Plant Genet. Resour. 9: 243-246. http://dx.doi.org/10.1017/S147926211100030X Garcia RAV, Rangel PN, Brondani C, Martins WS, et al (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 Genet. 12: 41-54. http://dx.doi.org/10.1186/1471-2156-12-41 Gupta SK, Gopalakrishna T, et al (2010). Development of unigene-derived SSR markers in cowpea (Vigna unguiculata) and their transferability to other Vigna species. Genome 53: 508-523. http://dx.doi.org/10.1139/G10-028 Hartl DL and Clark AG (1997). Principle of Population Genetics. 1997. Sinauer Associates, Inc. Hildebrand CE, Torney DC, Wagner RP, et al (1992). Informativeness of polymorphic DNA markers. Los Alamos Sci. 20: 100-102. Huang X, Madan A, et al (1999). CAP3: A DNA sequence assembly program. Genome Res. 9: 868-877. http://dx.doi.org/10.1101/gr.9.9.868 Johansson E, Prade T, Angelidaki I, Svensson SE, et al (2015). Economically viable components from Jerusalem artichoke (Helianthus tuberosus L.) in a biorefinery concept. Int. J. Mol. Sci. 16: 8997-9016. http://dx.doi.org/10.3390/ijms16048997 Ju MM, Ma HC, Xin PY, Zhou ZL, et al (2015). Development and characterization of EST-SSR markers in Bombax ceiba (Malvaceae). Appl. Plant Sci. 3: 1500001. http://dx.doi.org/10.3732/apps.1500001 Jung WY, Lee SS, Kim CW, Kim H-S, et al (2014). RNA-seq analysis and de novo transcriptome assembly of Jerusalem artichoke (Helianthus tuberosus Linne). PLoS One 9: e111982. http://dx.doi.org/10.1371/journal.pone.0111982 Kays SJ and Nottingham SF (2008). Genetic resources, breeding and cultivars. In: Biology and Biochemistry of Jerusalem Artichoke (Taylor and Francis eds.). CRC Press, 149-240. Kiru S, Nasenko I, et al (2010). Use of genetic resources from Jerusalem artichoke collection of N. Vavilov Institute in breeding for bioenergy and health. Agron. Res. 8: 625-632. Kou YX, Zeng J, Liu JQ, Kou YX, et al (2014). Germplasm diversity and differentiation of Helianthus tuberosus L. revealed by AFLP marker and phenotypic traits. J. Agric. Sci. 152: 779-789. http://dx.doi.org/10.1017/S0021859613000476 Kumari M, Grover A, Yadav PV, Arif M, et al (2013). Development of EST-SSR markers through data mining and their use for genetic diversity study in Indian accessions of Jatropha curcas L.: a potential energy crop. Genes Genomics 35: 661-670. http://dx.doi.org/10.1007/s13258-013-0118-0 Malfa SL, Currò S, Douglas AB, Brugaletta M, et al (2014). Genetic diversity revealed by EST-SSR markers in carob tree (Ceratonia siliqua L.). Biochem. Syst. Ecol. 55: 205-211. http://dx.doi.org/10.1016/j.bse.2014.03.022 Merritt BJ, Culley TM, Avanesyan A, Stokes R, et al (2015). An empirical review: Characteristics of plant microsatellite markers that confer higher levels of genetic variation. Appl. Plant Sci. 3: 1500025. http://dx.doi.org/10.3732/apps.1500025 Mondini L, Noorani A, Pagnotta MA, et al (2009). Assessing plant genetic diversity by molecular tools. Diversity (Basel) 1: 19-35. http://dx.doi.org/10.3390/d1010019 Moose SP, Mumm RH, et al (2008). Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol. 147: 969-977. http://dx.doi.org/10.1104/pp.108.118232 Mujaju C, Sehic J, Nybom H, et al (2013). Assessment of EST-SSR markers for evaluating genetic diversity in watermelon accessions from Zimbabwe. Am. J. Plant Sci. 4: 1448-1456. http://dx.doi.org/10.4236/ajps.2013.47177 Mullis K, Faloona F, Scharf S, Saiki R, et al (1986). Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb. Symp. Quant. Biol. 51: 263-273. http://dx.doi.org/10.1101/SQB.1986.051.01.032 Park YJ, Lee JK, Kim NS, et al (2009). Simple sequence repeat polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops. Molecules 14: 4546-4569. http://dx.doi.org/10.3390/molecules14114546 Peakall R, Smouse P, et al (2006). GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6: 288-295. http://dx.doi.org/10.1111/j.1471-8286.2005.01155.x Peakall R, Smouse PE, et al (2012). GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. Bioinformatics 28: 2537-2539. http://dx.doi.org/10.1093/bioinformatics/bts460 Poczai P, Varga I, Laos M, Cseh A, et al (2013). Advances in plant gene-targeted and functional markers: a review. Plant Methods 9: 6. http://dx.doi.org/10.1186/1746-4811-9-6 Ramu P, Billot C, Rami JF, Senthilvel S, et al (2013). Assessment of genetic diversity in the sorghum reference set using EST-SSR markers. Theor. Appl. Genet. 126: 2051-2064. http://dx.doi.org/10.1007/s00122-013-2117-6 Şelale H, Çelik I, Gültekin V, Allmer J, et al (2013). Development of EST-SSR markers for diversity and breeding studies in opium poppy. Plant Breed. 132: 344-351. http://dx.doi.org/10.1111/pbr.12059 Sokal RR, Michener CD, et al (1958). A statistical method for evaluating systematic relationships. Univ. Kans. Sci. Bull. 38: 1409-1438. Temnykh S, DeClerck G, Lukashova A, Lipovich L, et al (2001). Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11: 1441-1452. http://dx.doi.org/10.1101/gr.184001 Wangsomnuk PP, Khampa S, Jogloy S, Srivong T, et al (2011a). Assessing genetic structure and relatedness of Jerusalem Artichoke (Helianthus tuberosus L.) germplasm with RAPD, ISSR and SRAP Markers. AJPS 2: 753-764. http://dx.doi.org/10.4236/ajps.2011.26090 Wangsomnuk PP, Khampa S, Wangsomnuk P, Jogloy S, et al (2011b). Genetic diversity of worldwide Jerusalem artichoke (Helianthus tuberosus) germplasm as revealed by RAPD markers. Genet. Mol. Res. 10: 4012-4025. http://dx.doi.org/10.4238/2011.December.12.4 Wangsomnuk PP, Khampa S, Jogloy S, et al (2015). Exogenous supplementation of growth regulators and temperature improves germination of dormant Jerusalem Artichoke (Helianthus tuberosus L.) seeds under in vitro and in vivo conditions. JABS 9: 23-30. Zhang M, Mao W, Zhang G, Wu F, et al (2014). Development and characterization of polymorphic EST-SSR and genomic SSR markers for Tibetan annual wild barley. PLoS One 9: e94881. http://dx.doi.org/10.1371/journal.pone.0094881 Zhou Q, Chen TL, Wang YR, Liu ZP, et al (2014). The development of 204 novel EST-SSRs and their use for genetic diversity analyses in cultivated alfalfa. Biochem. Syst. Ecol. 57: 227-230. http://dx.doi.org/10.1016/j.bse.2014.08.023
T. Mornkham, Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., Kurzweil, H., Mornkham, T., Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., Kurzweil, H., Mornkham, T., Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., Kurzweil, H., Mornkham, T., Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., and Kurzweil, H., Development and characterization of novel EST-SSR markers and their application for genetic diversity analysis of Jerusalem artichoke (Helianthus tuberosus L.), vol. 15, no. 4, p. -, 2016.
Conflicts of interest The authors declare no conflict of interest. ACKNOWLEDGEMENTS The Higher Education Research Promotion, the National Research University Project of Thailand, the Office of the Higher Education Commission through the Food and Functional Food Research Cluster of Khon Kaen University (F-2553-Ph.d-02 and FC1.1.5 PhD), and research funding from Khon Kaen University to the corresponding author are acknowledged for financially support. We thank Assistant Professor Dr. Tawan Remsungnen for his assistance on the preliminary analysis of SSRs, and the journal reviewers for their valuable comments on this manuscript. REFERENCES Adawy SS, Mokhtar MM, Alsamman MA and Sakr MM (2015). Development of EST-SSR annotated database in olive (Oleaeuropaea). IJSR09. Alla NA, Domokos-Szabolcsy É, El-Ramady H, Hodossi S, et al (2014). Jerusalem artichoke (Helianthus tuberosus L.): A review of in vivo and in vitro propagation. Int. J. Hortic. Sci. 20: 131-136. Andersen JR, Lübberstedt T, et al (2003). Functional markers in plants. Trends Plant Sci. 8: 554-560. http://dx.doi.org/10.1016/j.tplants.2003.09.010 Bassam BJ, Caetano-Anollés G, Gresshoff PM, et al (1991). Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. 196: 80-83. http://dx.doi.org/10.1016/0003-2697(91)90120-I Bock DG, Kane NC, Ebert DP, Rieseberg LH, et al (2014). Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke. New Phytol. 201: 1021-1030. http://dx.doi.org/10.1111/nph.12560 Botstein D, White RL, Skolnick M, Davis RW, et al (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32: 314-331. Chen H, Liu L, Wang L, Wang S, et al (2015). Development and validation of EST-SSR markers from the transcriptome of Adzuki bean (Vigna angularis). PLoS One 10: e0131939. http://dx.doi.org/10.1371/journal.pone.0131939 Debnath SC, et al (2014). Structured diversity using EST-PCR and EST-SSR markers in a set of wild blueberry clones and cultivars. Biochem. Syst. Ecol. 54: 337-347. http://dx.doi.org/10.1016/j.bse.2014.03.018 Excoffier L, Smouse PE, Quattro JM, et al (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491. Gadaleta A, Giancaspro A, Zacheo S, Nigro D, et al (2011). Comparison of genomic and EST-derived SSR markers in phylogenetic analysis of wheat. Plant Genet. Resour. 9: 243-246. http://dx.doi.org/10.1017/S147926211100030X Garcia RAV, Rangel PN, Brondani C, Martins WS, et al (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 Genet. 12: 41-54. http://dx.doi.org/10.1186/1471-2156-12-41 Gupta SK, Gopalakrishna T, et al (2010). Development of unigene-derived SSR markers in cowpea (Vigna unguiculata) and their transferability to other Vigna species. Genome 53: 508-523. http://dx.doi.org/10.1139/G10-028 Hartl DL and Clark AG (1997). Principle of Population Genetics. 1997. Sinauer Associates, Inc. Hildebrand CE, Torney DC, Wagner RP, et al (1992). Informativeness of polymorphic DNA markers. Los Alamos Sci. 20: 100-102. Huang X, Madan A, et al (1999). CAP3: A DNA sequence assembly program. Genome Res. 9: 868-877. http://dx.doi.org/10.1101/gr.9.9.868 Johansson E, Prade T, Angelidaki I, Svensson SE, et al (2015). Economically viable components from Jerusalem artichoke (Helianthus tuberosus L.) in a biorefinery concept. Int. J. Mol. Sci. 16: 8997-9016. http://dx.doi.org/10.3390/ijms16048997 Ju MM, Ma HC, Xin PY, Zhou ZL, et al (2015). Development and characterization of EST-SSR markers in Bombax ceiba (Malvaceae). Appl. Plant Sci. 3: 1500001. http://dx.doi.org/10.3732/apps.1500001 Jung WY, Lee SS, Kim CW, Kim H-S, et al (2014). RNA-seq analysis and de novo transcriptome assembly of Jerusalem artichoke (Helianthus tuberosus Linne). PLoS One 9: e111982. http://dx.doi.org/10.1371/journal.pone.0111982 Kays SJ and Nottingham SF (2008). Genetic resources, breeding and cultivars. In: Biology and Biochemistry of Jerusalem Artichoke (Taylor and Francis eds.). CRC Press, 149-240. Kiru S, Nasenko I, et al (2010). Use of genetic resources from Jerusalem artichoke collection of N. Vavilov Institute in breeding for bioenergy and health. Agron. Res. 8: 625-632. Kou YX, Zeng J, Liu JQ, Kou YX, et al (2014). Germplasm diversity and differentiation of Helianthus tuberosus L. revealed by AFLP marker and phenotypic traits. J. Agric. Sci. 152: 779-789. http://dx.doi.org/10.1017/S0021859613000476 Kumari M, Grover A, Yadav PV, Arif M, et al (2013). Development of EST-SSR markers through data mining and their use for genetic diversity study in Indian accessions of Jatropha curcas L.: a potential energy crop. Genes Genomics 35: 661-670. http://dx.doi.org/10.1007/s13258-013-0118-0 Malfa SL, Currò S, Douglas AB, Brugaletta M, et al (2014). Genetic diversity revealed by EST-SSR markers in carob tree (Ceratonia siliqua L.). Biochem. Syst. Ecol. 55: 205-211. http://dx.doi.org/10.1016/j.bse.2014.03.022 Merritt BJ, Culley TM, Avanesyan A, Stokes R, et al (2015). An empirical review: Characteristics of plant microsatellite markers that confer higher levels of genetic variation. Appl. Plant Sci. 3: 1500025. http://dx.doi.org/10.3732/apps.1500025 Mondini L, Noorani A, Pagnotta MA, et al (2009). Assessing plant genetic diversity by molecular tools. 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GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6: 288-295. http://dx.doi.org/10.1111/j.1471-8286.2005.01155.x Peakall R, Smouse PE, et al (2012). GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. Bioinformatics 28: 2537-2539. http://dx.doi.org/10.1093/bioinformatics/bts460 Poczai P, Varga I, Laos M, Cseh A, et al (2013). Advances in plant gene-targeted and functional markers: a review. Plant Methods 9: 6. http://dx.doi.org/10.1186/1746-4811-9-6 Ramu P, Billot C, Rami JF, Senthilvel S, et al (2013). Assessment of genetic diversity in the sorghum reference set using EST-SSR markers. Theor. Appl. Genet. 126: 2051-2064. http://dx.doi.org/10.1007/s00122-013-2117-6 Şelale H, Çelik I, Gültekin V, Allmer J, et al (2013). Development of EST-SSR markers for diversity and breeding studies in opium poppy. 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Res. 10: 4012-4025. http://dx.doi.org/10.4238/2011.December.12.4 Wangsomnuk PP, Khampa S, Jogloy S, et al (2015). Exogenous supplementation of growth regulators and temperature improves germination of dormant Jerusalem Artichoke (Helianthus tuberosus L.) seeds under in vitro and in vivo conditions. JABS 9: 23-30. Zhang M, Mao W, Zhang G, Wu F, et al (2014). Development and characterization of polymorphic EST-SSR and genomic SSR markers for Tibetan annual wild barley. PLoS One 9: e94881. http://dx.doi.org/10.1371/journal.pone.0094881 Zhou Q, Chen TL, Wang YR, Liu ZP, et al (2014). The development of 204 novel EST-SSRs and their use for genetic diversity analyses in cultivated alfalfa. Biochem. Syst. Ecol. 57: 227-230. http://dx.doi.org/10.1016/j.bse.2014.08.023
T. Mornkham, Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., Kurzweil, H., Mornkham, T., Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., Kurzweil, H., Mornkham, T., Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., Kurzweil, H., Mornkham, T., Wangsomnuk, P. P., Mo, X. C., Francisco, F. O., Gao, L. Z., and Kurzweil, H., Development and characterization of novel EST-SSR markers and their application for genetic diversity analysis of Jerusalem artichoke (Helianthus tuberosus L.), vol. 15, no. 4, p. -, 2016.
Conflicts of interest The authors declare no conflict of interest. ACKNOWLEDGEMENTS The Higher Education Research Promotion, the National Research University Project of Thailand, the Office of the Higher Education Commission through the Food and Functional Food Research Cluster of Khon Kaen University (F-2553-Ph.d-02 and FC1.1.5 PhD), and research funding from Khon Kaen University to the corresponding author are acknowledged for financially support. We thank Assistant Professor Dr. Tawan Remsungnen for his assistance on the preliminary analysis of SSRs, and the journal reviewers for their valuable comments on this manuscript. REFERENCES Adawy SS, Mokhtar MM, Alsamman MA and Sakr MM (2015). Development of EST-SSR annotated database in olive (Oleaeuropaea). IJSR09. Alla NA, Domokos-Szabolcsy É, El-Ramady H, Hodossi S, et al (2014). Jerusalem artichoke (Helianthus tuberosus L.): A review of in vivo and in vitro propagation. Int. J. Hortic. Sci. 20: 131-136. 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