Assessing Genetic Structure and Relatedness of Jerusalem Artichoke (<i>Helianthus tuberosus</i> L.) Germplasm with RAPD, ISSR and SRAP Markers — Oak Academic Publishing
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Assessing Genetic Structure and Relatedness of Jerusalem Artichoke (<i>Helianthus tuberosus</i> L.) Germplasm with RAPD, ISSR and SRAP Markers
Jerusalem artichoke (<i>Helianthus tuberosus</i> L.) is an old tuber crop with a recently renewed interest in multipurpose improvement, but little effort has been made to characterize its genetic resources. A study was conducted to assess genetic structure and genetic relatedness of 47 diverse Jerusalem artichoke accessions using RAPD, ISSR and SRAP markers. A total of 296 (87.1%) polymorphic bands were detected from 13 RAPD markers; 92 (80%) from six ISSR primers; and 194 (88.6%) for nine combinations of SRAP primers. Five optimal clusters were inferred by the STRUCTURE program from the RAPD or ISSR data, while six optimal clusters were found from the SRAP data or combined marker data. Significant linear relationships between the distance matrices for all pairs of individual accessions were detected for all marker pairs and the estimated correlation coefficient was 0.40 for RAPD-ISSR, 0.53 for RAPD-SRAP, and 0.43 for ISSR-SRAP. Based on the combined data, the neighbor-joining clustering of the 47 accessions matched closely with those inferred from the STRUCTURE program. Three ancestral groups were observed for the Canadian germplasm. Most diverse germplasm harbored in the USA collection. These findings not only reveal the compatible patterns of genetic structure and relatedness inferred with three marker types, but also are useful for managing Jerusalem artichoke germplasm and utilizing diverse germplasm for genetic improvement.
N. Liu, L. Chen, S. Wang, C. Oh and H. Zhao, “Comparison of Single Nucleotide Polymorphism and Microsatellites in Inference of Population Structure,” BMC Genetics, Vol. 6, Supplement 1, 2005, p. S26. doi:10.1371/journal.pone.0001367
M. T. Hamblin, M. L. Warburton and E. S. Buckler, “Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphism in Assessment of Maize Diversity and Relatedness,” PLOS One, Vol. 2, No. 12, 2007, p. e1367.
P. K. Ingvarsson and N. R. Street, “Association Genetics of Complex Traits in Plants,” New Phytologist, Vol. 189, No. 4, 2011, pp. 909-922. doi:10.1111/j.1469-8137.2010.03593.x
A. Karp, “The New Genetic Era: Will It Help Us in Managing Genetic Diversity?” In: J. M. M. Engels, V. R. Rao, A. H. D. Brown and M. T. Jackson, Eds., Managing Plant Genetic Diversity, International Plant Genetic Resources Institute, Rome, 2002, pp. 43-56.
Y. B. Fu, G. W. Peterson, K. W. Richards, T. R. Tarn and J. E. Percy, “Genetic Diversity of Canadian and Exotic Potato Germplasm Revealed by Simple Sequence Repeat Markers,” American Journal of Potato Research, Vol. 86, No. 1, 2009, pp. 38-48. doi:10.1007/s12230-008-9059-6
A. H. D. Brown, “Core Collection: A Practical Approach to Genetic Resources Management,” Genome, Vol. 31, No. 2, 1989, pp. 818-824. doi:10.1139/g89-144
J. Yu, G. Pressoir, W. H. Briggs, I. V. Bi, M. Yamasaki, J. F. Doebley, M. D. McMullen, B. S. Gaut, D. M. Nielsen, J. B. Holland, S. Kresovich and E. S. Buckler, “A Unified Mixed-Model Method for Association Mapping that Accounts for Multiple Levels of Relatedness,” Nature Genetics, Vol. 38, 2006, pp. 203-208. doi:10.1038/ng1702
H. Nybom, “Comparison of Different Nuclear DNA Markers for Estimating Intraspecific Genetic Diversity in Plants,” Molecular Ecology, Vol. 13, No. 15, 2004, pp. 1143-1155. doi:10.1111/j.1365-294X.2004.02141.x
S. J. Kays and S. F. Nottingham, “Chapter 8 Genetic Resources, Breeding and Cultivars,” In: Biology and Biochemistry of Jerusalem Artichoke, Taylor and Francis, CRC Press, Boca-Raton, 2008, pp. 149-240.
E. A. Zaky, “Physiological Response to Diets Fortified with Jerusalem Artichoke Tubers (Helianthus tuberosus L.) Powder by Diabetic Rats,” American-Eurasian Journal of Agricultural & Environmental Sciences, Vol. 5, No. 5, 2009, pp. 682-688.
G. J. Seiler, “The Potential of Wild Sunflower Species for Industrial Uses,” Helia, Vol. 30, No. 46, 2007, pp. 175-198.
H. Serieys, I. Souyris, A. Gil, B. Poinso and A. Berville, “Diversity of Jerusalem Artichoke Clones (Helianthus tuberosus L.) from the INRA-Montpellier Collection,” Genetic Resources and Crop Evolution, Vol. 57, No. 8, 2010, pp. 1207-1215. doi:10.1007/s10722-010-9560-x
R. Sennoi, S. Jogloy, W. Saksirirat and A. Patanothai, “Pathogeneicity Test of Sclerotium rolfsii, a Causal Agent of Jerusalem Artichoke (Helianthus tuberosus L.) Stem rot,” Asian Journal of Plant Sciences, Vol. 9, No. 5, 2010, pp. 281-284. doi:10.3923/ajps.2010.281.284
C. Breton, H. Serieys and A. Bervill, “Gene Transfer from Wild Helianthus to Sunflower: Topicalities and Limits,” Oleagineux Corps Gras Lipides, Vol. 17, No. 2, 2010, pp. 104-114.
J. R. Mandel, J. M. Dechaine, L. F. Marek and J. M. Burke, “Genetic Diversity and Population Structure in Cultivated Sunflower and a Comparison to Its Wild Progenitor, Helianthus annuus L,” Theoretical and Applied Genetics, Vol. 123, No. 5, 2011, pp. 693-704. doi:10.1007/s00122-011-1619-3
L. J. M. van Soest, H. D. Mastebroek and E. P. M. de Meijer, “Genetic Resources and Breeding: A Necessity for the Success of Industrial Crops,” Industrial Crops and Products, Vol. 1, 1993, pp. 283-288. doi:10.1016/0926-6690(92)90029-U
G. M. Volk and K. Richards, “Preservation Methods for Jerusalem Artichoke Cultivars,” HortScience, Vol. 41, No. 1, 2006, pp. 80-83.
S. Schittenhelm, “Inheritance of Agronomical Important Traits in Jerusalem Artichoke (Helianthus tuberosus L.),” Vortr?ge für Pflanzenz?chtung, 1990, pp. 15-16.
S. J. Kays and F. Kultur, “Genetic Variation in Jerusalem Artichoke (Helianthus tuberosus L.) Flowering Date and Duration,” HortScience, Vol. 40, No. 6, 2005, pp. 1675-1678.
R. Puttha, S. Jogloy, P. P. Wangsomnuk, S. Srijaranai, T. Kesmala and A. Patanothai, “Genotypic Variability and Genotype by Environment Interactions for Inulin Content of Jerusalem Artichoke Germplasm,” Euphytica, Vol. 183, No. 1, pp. 119-131. doi:10.1007/s10681-011-0520-0
I. A. Arif, M. A. Bakir, H. A. Khan, A. H. A. Farhan, A. A. A. Homaidan, A. H. Bahkali, M. A. Sadoon and M. Shobrak, “A Brief Review of Molecular Techniques to Assess Plant Diversity,” International Journal of Molecular Sciences, Vol. 11, No. 5, 2010, pp. 2079-2096. doi:10.3390/ijms11052079
J. G. K. Williams, A. R. Kubelik, K. J. Livak, J. A. Rafalski and S. V. Tingey, “DNA Polymorphisms Amplified by Arbitrary Primers Are Useful as Genetic Markers,” Nucleic Acids Research, Vol. 18, No. 22, 1990, pp. 6531-6535. doi:10.1093/nar/18.22.6531
E. Zietkiewicz, A. Rafalski and D. Labuda, “Genome Fingerprinting by Simple Sequence Repeats (SSR)-Anchored PCR Amplification,” Genomics, Vol. 20, No. 2, 1994, pp. 176-183. doi:10.1006/geno.1994.1151
W. J. M. Koopman, “Phylogenetic Signal in AFLP Data sets,” Systems Biology, Vol. 54, No. 2, 2005, pp. 197-217. doi:10.1080/10635150590924181
G. Li and C. F. Quiros, “Sequence-Related Amplified Polymorphism (SRAP), a New Marker System Based on a Simple PCR Reaction: Its Application to Mapping and Gene tagging in Brassica,” Theoretical and Applied Genetics, Vol. 103, 2001, pp. 455-461. doi:10.1007/s001220100570
M. Ferriol, B. Pico and F. Nuez, “Genetic Diversity of Some Accessions of Cucurbita maxima from Spain Using RAPD and SRAP Markers,” Genetic Resources and Crop Evolution, Vol. 50, 2003, pp. 227-238. doi:10.1023/A:1023502925766
H. Budak, R. C. Shearman, I. Parmaksiz and I. Dweikat, “Comparative Analysis of Seeded and Vegetative Biotype Buffalograsses Based on Phylogenetic Relationship Using ISSRs, SSRs, RAPDs and SRAPs,” Theoretical and Applied Genetics, Vol.109, No. 2, 2004, pp. 280-288. doi:10.1007/s00122-004-1630-z
B. Dozet, R. Marinkovi?, D. Vasi? and A. Marjanovi?, “Genetic Similarity of the Jerusalem Artichoke Populations (Helianthus tuberosus L.) Collected in Montenegro,” Helia, Vol. 16, No. 18, 1993, pp. 41-48.
P. P. Wangsomnuk, S. Khampa, S. Jogloy, P. Wangsomnuk and Y. Kitijataropas, “Assessment of Genome and Genetic Diversity in Jerusalem Artichoke (Helianthus tuberosus L.) with ISSR Markers,” Khon Kaen Agriculture Journal, Vol. 34, No. 2, 2006, pp. 124-138.
S. A. El Gengaihi, A. M. Aboul Enein, F. M. Abou Elalla and D. H. Abou Baker, “Molecular Characterizations and Antimicrobial Activities of Chicory and Jerusalem Artichoke Plants,” International Journal of Academic Research, Vol. 1, No. 2, 2009, pp. 66-71.
T. H. Tai and S. D. Tanksley, “A Rapid and Inexpensive Method for Isolation of Total DNA from Dehydrated Plant Tissue,” Plant Molecular Biology Reporter, Vol. 8, No. 4, 1990, pp. 297-303. doi:10.1007/BF02668766
T. Mornkham, P. P. Wangsomnuk, S. Jogloy, P. Wangsomnuk, A. Patanothai and Y. B. Fu, “An Assessment of Five DNA Extraction Methods for Molecular Analyses of Jerusalem Artichoke (Helianthus tuberosus L.),” Genetics and Molecular Research, in press.
J. R. Russell, F. Hosein, E. Johnson, R. Waugh and W. Powell, “Genetic Differentiation of Cocoa (Theobroma cacao L.) Populations Revealed by RAPD Analysis,” Molecular Ecology, Vol. 2, No. 2, 1993, pp. 89-97. doi:10.1111/j.1365-294X.1993.tb00003.x
M. H. Reyes-Valdes and C. G. Williams, “An EntropyBased Measure of Founder Informativeness,” Genetics Research, Vol. 85, 2005, pp. 81-88. doi:10.1017/S0016672305007354
SAS Institute Inc, “The SAS System for Windows V9.2,” SAS Institute Incorporated, Cary, 2008.
J. Pritchard, M. Stephens and P. Donnelly, “Inference of Population Structure Using Multilocus Genotype Data,” Genetics, Vol. 155, No. 2, 2000, pp. 945-959.
D. Falush, M. Stephens and J. K. Pritchard, “Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies,” Genetics, Vol. 164, No. 4, 2003, pp. 1567-1587.
D. Falush, M. Stephens and J. K. Pritchard, “Inference of Population Structure Using Multilocus Genotype Data: Dominant Markers and Null Alleles,” Molecular Ecology Notes, Vol. 7, No. 4, 2007, pp. 574-578. doi:10.1111/j.1471-8286.2007.01758.x
G. Evanno, S. Regnaut and J. Goudet, “Detecting the Number of Clusters of Individuals Using the Software STRUCTURE: A Simulation Study,” Molecular Ecology, Vol. 14, No. 8, 2005, pp. 2611-2620. doi:10.1111/j.1365-294X.2005.02553.x
R. Peakall and P. E. Smouse, “GenAlEx 6: Genetic Analysis in Excel. Population Genetic Software for Teaching and Research,” The Australian National University, Canberra, 2005. http://www.anu.edu.au/BoZo/GenAlEx/
N. Mantel, “The Detection of Disease Clustering and a Generalized Regression Approach,” Cancer Research, Vol. 27, No. 2, 1967, pp. 209-220.
D. L. Swofford, “PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4,” Sinauer Associates, Sunderland, 1998.
S. Kumar, K. Tamura and M. Nei, “MEGA3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment,” Briefings in Bioinformatics, Vol. 5, No. 2, 2004, pp. 150-163. doi:10.1093/bib/5.2.150
C. J. Swanton, P. B. Cavers, D. R. Clements and M. J. Moore, “The Biology of Canadian Weeds. 101. Helianthus tuberosus L.,” Canadian Journal of Plant Science, Vol. 72, No. 4, 1992, pp. 1367-1382. doi:10.4141/cjps92-169
J. L. Hamrick and M. J. W. Godt, “Allozyme Diversity in Plant Species,” In A. H. D. Brown, M. T. Clegg, A. L. Kahler and B. S. Weir, Eds., Plant Population Genetics, Breeding and Gentic Resources, Sinauer Associates, Sunderland, 1989, pp. 43-63.
W.R. Lawson, R. J. Henry, J. K. Kochman and G. A. Kong, “Genetic Diversity in Sunflower (Helianthus annuus L.) as Revealed by Random Amplified Polymorphic DNA Analysis,” Australian Journal of Agricultural Research, Vol. 45, No. 7, 1994, pp. 1319-1327. doi:10.1071/AR9941319
G. Quagliaro, M. Vischi, M. Tyrka and A. M. Olivieri, “Identification of Wild and Cultivated Sunflower for Breeding Purposes by AFLP Markers,” Journal of Heredity, Vol. 92, 2001, pp. 38-42. doi:10.1093/jhered/92.1.38
L. Liu, L. Zhao, Y. Gong, M. Wang, L. Chen, J. Yang, Y. Wang, F. Yu and L. Wang, “DNA Fingerprinting and Genetic Diversity Analysis of Late-Bolting Radish Cultivars with RAPD, ISSR and SRAP Markers,” Scientia Horticulturae, Vol. 116, 2008, pp. 240-247. doi:10.1016/j.scienta.2007.12.011
P. Kumar, M. A. Alam, H. Singh, V. Goyal, S. Parida, S. Kalia and T. Mohapatra, “Assessment of Genetic Diversity through RAPD, ISSR and AFLP Markers in Podophyllum hexandrum: A Medicinal Herb from the Northwestern Himalayan Region,” Physiology and Molecular Biology of Plants, Vol. 16, No. 2, 2010, pp. 135-148. doi:10.1007/s12298-010-0015-9