Assessment of Genetic Variation in Soybean (<i>Glycine max</i>) Accessions from International Gene Pools Using RAPD Markers: Comparison with the ISSR System — Oak Academic Publishing
Research ArticleOpen AccessGoogle Scholar indexed
Assessment of Genetic Variation in Soybean (<i>Glycine max</i>) Accessions from International Gene Pools Using RAPD Markers: Comparison with the ISSR System
Department of Biology, Laurentian University, Sudbury, Ontario, Canada
,
Department of Biology, Laurentian University, Sudbury, Ontario, Canada
Soybean ( Glycine max ) is one of the most important crops in the world in terms of total production and usage. It is also among the least diverse species. The main objectives of the present study were to 1) assess the level of genetic variation among soybean ( G. max ) accessions from different countries using Random Amplified Polymorphic DNA (RAPD) markers and 2) compare Inter Simple Sequence Repeats (ISSR) and RAPD marker systems in detecting polymorphic loci in soybeans ( G. max ). Genomic DNAs from 108 soybeans ( G. max ) accessions from 11 different gene pools were analyzed using several ISSR and RAPD primers. The average level of polymorphic loci detected with the RAPD primers was 35%. The soybean accessions from the China, Netherlands, and Canada gene pools were the least genetically variable with 25%, 26%, and 30% of polymorphic loci, respectively. Accessions from Hungary (43%) and France (48%) showed the highest level of polymorphism based on the RAPD analysis. Overall, RAPD data revealed that the accessions from different countries are closely related with 64% genetic distance values below 0.40. The levels of polymorphic loci detected with the RAPD and ISSR marker systems were in general moderate and similar even if they target different regions of the genome. A combination of different marker systems that include RAPD/ISSR, microsatellites (SSR), and SNPs should provide the most accurate information on genetic variation of soybean ( G. max ) accessions.
Ford, B.A., Ball, P. W. and Ritland K. (1991) Allozyme Diversity and Genetic Relationships among North American Members of the Short-Beaked Taxa of Carex sect. Vesicariae (Cyperaceae). Systematic Botany, 16, 116-131. https://doi.org/10.2307/2418977
Lu, H., Li, J.S., Liu, J.L. and Bernardo, R. (2002) Allozyme Polymorphisms of Maize Populations from Southwestern China. Theoretical and Applied Genetics 104, 119-126. https://doi.org/10.1007/s001220200014
Prasad, M., Varshney, R.K., Roy, J.K., Balyan, H.S. and Gupta, P.K. (2000) The Use of Microsatellites for Detecting DNA Polymorphism, Genotype Identification and Genetic Diversity in Wheat. Theoretical and Applied Genetics, 100, 584-592. https://doi.org/10.1007/s001220050077
Apuya, N., Frazier, B.L., Keim, P.E., Roth, J. and Lark, K.G. (1988) Restriction Length Polymorphisms as Genetic Markers in Soybean, Glycine max (L.) Merrill. Theoretical and Applied Genetics, 75, 889-901. https://doi.org/10.1007/BF00258050
Keim, P., Shoemaker, R.C. and Palmer, R.G. (1989) RFLP Diversity in Soybean. Theoretical and Applied Genetics, 77, 786-792. https://doi.org/10.1007/BF00268327
Keim, P., Diers, B.W., Olson, T.C. and Shoemaker, R.C. (1990) RFLP Mapping in Soybean: Association between Marker Loci and Variation in Quantitative Traits. Genetics, 126, 735-742.
Keim, P., Beavis, W., Schupp, J., et al. (1992) Evaluation of Soybean RFLP Marker Diversity in Adapted Germ Plasm. Theoretical and Applied Genetics, 85, 205-212. https://doi.org/10.1007/BF00222861
Maughan, P.J., Saghai Maroof, M.A., Buss, G.R., et al. (1996) Amplified Fragment Length Polymorphism (AFLP) in Soybean: Species Diversity, Inheritance, and Near-Isogenic Line Analysis. Theoretical and Applied Genetics, 93, 392-401. https://doi.org/10.1007/BF00223181
Li, Z. and Nelson, R.L. (2002) RAPD Marker Diversity among Soybean and Wild Soybean Accessions from Four Chinese Provinces. Crop Science, 42, 1737-1744. https://doi.org/10.2135/cropsci2002.1737
Devaiah, K., Balusubramani, S.P. and Venkatasubramanian, P. (2010) Development of Randomly Amplified Polymorphic DNA Based SCAR Marker for Identification of Ipomoea mauritiana Jacq (Convolvulaceae). Evidence-Based Complementary and Alternative Medicine, 2010, Article ID: 868720. https://doi.org/10.1093/ecam/neq023
Khan, F., Hakeem, K.R., Siddiqi, T.O., et al. (2013) RAPD Markers Associated with Salt Tolerance in Soybean Genotypes Under Salt Stress. Applied Biochemistry and Biotechnology, 170, 257-272. https://doi.org/10.1007/s12010-013-0182-6
Costa, R., Pereira, G., Garrido, I., Tavares-De-Sousa, M.M. and Espinosa, F. (2016) Comparison of RAPD, ISSR, and AFLP Molecular Markers to Reveal and Classify Orchardgrass (Dactylis glomerata L.) Germplasm Variations. PLoS ONE, 11, e0152972. https://doi.org/10.1371/journal.pone.0152972
Thompson, J.A., Nelson, R.L. and Vodkin, L.O. (1998) Identification of Diverse Soybean Germplasm Using RAPD Markers. Crop Science, 38, 1348-1355. https://doi.org/10.2135/cropsci1998.0011183X003800050033x
Brown-Guedira, G.L., Thompson, J.A., Nelson, R.L. and Warburton, M.L. (2000) Evaluation of Genetic Diversity of Soybean Introductions and North American Ancestors Using RAPD and SSR Markers. Crop Science, 40, 815-823. https://doi.org/10.2135/cropsci2000.403815x
Akkaya, M.S., Bhagwat, A.A. and Cregan, P.B. (1992) Length Polymorphism of Simple Sequence Repeat DNA in Soybean. Genetics, 47, 1131-1139.
Diwan, N. and Cregan, P.B. (1997) Automated Sizing of Fluorescent-Labeled Simple Sequence Repeat (SSR) Markers to Assay Genetic Variation in Soybean. Theoretical and Applied Genetics, 95, 723-733. https://doi.org/10.1007/s001220050618
Rongwen, J., Akkaya, M.S., Lavi, U. and Cregan, P.B. (1995) The Use of Micro Satellite DNA Markers for Soybean Genotype Identification. Theoretical and Applied Genetics, 90, 43-48. https://doi.org/10.1007/BF00220994
Kachare S., Tiwari, S., Tripathi, N., et al. (2020) Assessment of Genetic Diversity of Soybean (Glycine max) Genotypes Using Qualitative Traits and Microsatellite Markers. Agricultural Research, 9, 23-34. https://doi.org/10.1007/s40003-019-00412-y
Vieira, M.L.C., Santini, L., Diniz, A.L. and Munhoz, C.F. (2016) Microsatellite Markers: What They Mean and Why They Are So Useful. Genetics and Molecular Research, 39, 312-328. https://doi.org/10.1590/1678-4685-GMB-2016-0027
Nkongolo, K.K., Michael, P. and Demers, T. (2005) Application of ISSR, RAPD, and Cytological Markers to the Certification of Picea mariana, P. glauca, and P. engelmannii Trees, and Their Putative Hybrids. Genome, 48, 302-311. https://doi.org/10.1139/g04-118
Mudibu J., Nkongolo, K.K.C., Mehes-Smith, M. and Kalonji Mbuyi, A. (2011) Genetic Analysis of a Soybean Genetic Pool Using ISSR Marker: Effect of Gamma Radiation on Genetic Variability. International Journal of Plant Breeding and Genetics, 5, 235-245. https://doi.org/10.3923/ijpbg.2011.235.245
Moarefi, N, Michael, P., Beckett, P. and Nkongolo, K.K. (2018) Identification of Molecular Markers Differentiating Betula papyrifera and B. pumila Populations from Northern Ontario (Canada). American Journal of Environmental Sciences, 14, 246-256. https://doi.org/10.3844/ajessp.2018.246.256
Boyd, M., Panoyan, M.A., Michael, P. and Nkongolo, K.K. (2019) Development and Characterization of Species-Diagnostic ISSR and SCAR DNA Markers Differentiating Red Maple (Acer rubrum) and Silver Maple (A. saccharinum). Genome, 62, 527-535. https://doi.org/10.1139/gen-2019-0037
Alamri, S. (2014) Comparative Analysis of Soybean (Glycine max) Accessions Using Inter Simple Sequence Repeat (ISSR) and Random Amplified Polymorphic DNA (RAPD) Markers. M.Sc. Thesis, Laurentian University, Sudbury, Ontario, 106 p. https://zone.biblio.laurentian.ca/handle/10219/2201
Yeh, F.C. and Boyle, T.J.B. (1997) Population Genetic Analysis of Co-Dominant and Dominant Markers and Quantitative Traits. Belgian Journal of Botany, 129, 157.
Pavlicek, A., Hrda, S. and Flegr, J. (1999) Freetree-Freeware Program for Construction of Phylogenetic Trees on the Basis of Distance Data and Bootstrap/Jackknife Analysis of the Tree Robustness. Folia Biologica, 5, 97-99.
Fang, D.Q. and Roose, M.L. (1997) Identification of Closely Related Citrus Cultivars with Inter-Simple Sequence Repeat Markers. Theoretical and Applied Genetics, 95, 408-417. https://doi.org/10.1007/s001220050577
Rus-Kortekaas W., Smulders, M.J.M., Arens, P. and Vosman, B. (1994) Direct Comparison of Levels of Genetic Variation in Tomato Detected by a GACA-Containing Microsatellite Probe and by Random Amplified Polymorphic DNA. Genome, 37, 375-381. https://doi.org/10.1139/g94-053
Nagaoka, T. and Ogihara, Y. (1997) Applicability of Inter-Simple Sequence Repeat Polymorphisms in Wheat for Use as DNA Markers in Comparison to RFLP and RAPD Markers. Theoretical and Applied Genetics, 94, 597-602. https://doi.org/10.1007/s001220050456
Raina S.N., Rani, V., Kojima, T., Ogihara, Y., Singh, K.P. and Devarumath, R.M. (2001) RAPD and ISSR Fingerprints as Useful Genetic Markers for Analysis of Genetic Diversity, Varietal Identification, and Phylogenetic Relationships in Peanut (Arachis hypogaea) Cultivars and Wild Species. Genome, 44, 763-772. https://doi.org/10.1139/g01-064
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. https://doi.org/10.1093/nar/18.22.6531
Semagn K., Bjornstad, A. and Ndjiondjop, M.N. (2006) An Overview of Molecular Markers Methods for Plants. African Journal of Biotechnology, 5, 2540-2568.
Devos, K.M. and Gale, M.D. (1992) The Use of Random Amplified Polymorphic DNA Markers in Wheat. Theoretical and Applied Genetics, 84, 567-572. https://doi.org/10.1007/BF00224153
Ellsworth, D.L., Rittenhouse, D. and Honeycutt, R.L. (1993) Artifactual Variation in Random Amplified Polymorphic DNA Banding Patterns. BioTechniques, 14, 214-217.
Zietkiewicz, E., Rafalski, A. and Labuda, D. (1994) Genome Fingerprinting by Simple Sequence Repeat (SSR)-Anchored Polymerase Chain Reaction Amplification. Genomics, 20, 176-183. https://doi.org/10.1006/geno.1994.1151
Reddy, P.M., Sarla, N. and Siddiq, E.A. (2002) Inter Simplesequence Repeat (ISSR) Polymophism and Its Application in Plant Breeding. Euphytica, 128, 9-17. https://doi.org/10.1023/A:1020691618797
Queller, D.C., Strassmann, J.E. and Hughes, C.R. (1993) Microsatellites and Kinship. Trends in Ecology & Evolution, 8, 285-288. https://doi.org/10.1016/0169-5347(93)90256-O
Verma, K.S., Ul Haq, S., Kachhwaha, S. and Kothari, S.L. (2017) RAPD and ISSR Marker Assessment of Genetic Diversity in Citrullus colocynthis (L.) Schrad: A Unique Source of Germplasm Highly Adapted to Drought and High-Temperature Stress. 3 Biotech, 7, Article No. 288.
Hao, C.Y., Wang, L.F., Zhang, X.Y., You, G.X., Dong, Y.S., Jia, J.Z., Liu, X.W., Shang, X.W., Liu, S.C. and Cao, Y.S. (2006) Genetic Diversity in Chinese Modern Wheat Varieties Revealed by Microsatellite Markers. Science in China Series C, 49, 218-226. https://doi.org/10.1007/s11427-006-0218-z
Roy, J.K., Lakshmikumaran, M.S., Balyan, H.S. and Gupta, P.K. (2004) AFLP-Based Genetic Diversity and Its Comparison with Diversity Based on SSR, SAMPL, and Phenotypic Traits in Bread Wheat. Biochemical Genetics, 42, 43-89. https://doi.org/10.1023/B:BIGI.0000012143.48298.71
Mattioni, C., Casasoli, M., Gonzalez, M. and Ipinza, R. (2002) Comparison of ISSR and RAPD Markers to Characterize Three Chilean Nothofagus Variety. Theoretical and Applied Genetics, 104, 1064-1070. https://doi.org/10.1007/s00122-001-0824-x