Back
 OJE  Vol.4 No.7 , May 2014
Assessment of Genetic Variability of 142 Sweet Sorghum Germplasm of Diverse Origin with Molecular and Morphological Markers
A. Lekgari, I. Dweikat*
Show more
Abstract: Sorghum bicolor (L.) Moech is the fifth most important crop in the world. Recently, its agronomics and genetics have drawn interest among scientists. Sweet sorghum, a variety of sorghum, may potentially become a bioenergy source because of the high sugar content in its juicy stems. Exploring the diversity of sweet sorghum around the world is important to the development and improvement of the crop as an energy source. In exploring the diversity of sweet sorghum, three types of markers (simple sequence repeats [SSR], sequence-related amplified polymorphisms [SRAP], and morphological markers) are used on 142 sweet sorghum accessions from around the world. The accessions show a high significance (P < 0.05) for all the morphological traits measured. The morphological markers cluster the accessions into five groups based primarily on plant height (PH), anthesis data (AD), and moisture content (ML), with the principal component analysis (PCA) showing these traits to explain 92.5% of the total variation. The furthest accessions were PI571103 from Sudan, and N99 from the United States. The Nei’s genetic standard distances ranged from 0.024 to 1.135 and 0.078 to 0.866 for SSR and SRAP, respectively. As expected, accessions of the same origin or breeding history had the lowest genetic distance (e.g. Mokula and Marupantse, both from Botswana; NSL83777 and NSL83779 from Cameroon). Neighbor joining clusters the sweet sorghum accessions into five major groups using SSR and four major groups using SRAP, based on their origin, or breeding history. The three marker types complement each other, and the presence of accessions of different origins across clusters indicate similar genetics, and evidence of germplasm movement between countries.
Keywords: SRAPs, SSRs, Energy Crops, Genetic Distance
Cite this paper: Lekgari, A. and Dweikat, I. (2014) Assessment of Genetic Variability of 142 Sweet Sorghum Germplasm of Diverse Origin with Molecular and Morphological Markers. Open Journal of Ecology, 4, 371-393. doi: 10.4236/oje.2014.47034.
References

[1]   Ritter K.B., McIntyre, C.L. Godwin, I.D. Jordan, D.R. and Chapman, S.C. (2007) An Assessment of the Genetic Relationship between Sweet and Grain Sorghums, within Sorghum bicolor ssp. bicolor (L.) Moench, Using AFLP Markers. Euphytica, 157, 161-176. http://dx.doi.org/10.1007/s10681-007-9408-4

[2]   Hart, G., Schertz, K., Peng, Y. and Syed, N. (2001) Genetic Mapping of Sorghum bicolor (L.) Moench QTLs That Control Variation in Tillering and Other Morphological Character. Theoretical and Applied Genetics, 103, 1232-1242.
http://dx.doi.org/10.1007/s001220100582

[3]   Ferraris, R. (1981) Early Assessment of Sweet Sorghum as an Agro-Industrial Crop. I. Varietal Evaluation. Australian Journal of Experimental Agriculture and Animal Husbandry, 21, 75-82.
http://dx.doi.org/10.1071/EA9810075

[4]   Vietor, D.M. and Miller, F.R. (1990) Assimilation, Partitioning, and Nonstructural Carbohydrate in Sweet Compared with Grain Sorghum. Crop Science, 30, 1109-1115.
http://dx.doi.org/10.2135/cropsci1990.0011183X003000050030x

[5]   Murray, S.C., Rooney, W.L., Hamblin, M.T., Mitchell, S.E. and Kresovich, S. (2009) Sweet Sorghum Genetic Diversity and Association Mapping for Brix and Height. Plant Genome, 2, 48-62.
http://dx.doi.org/10.3835/plantgenome2008.10.0011

[6]   Vaidyanathan, S., Rao, K.E.P., Mengesha, M.H. and Jambunathan, R. (1987) Total Sugar Content in Sorghum Stalks and Grains of Selected Cultivars from the World Germplasm Collection. Journal of the Science of Food and Agriculture, 39, 289-295. http://dx.doi.org/10.1002/jsfa.2740390403

[7]   Lipinsky, E.S., Kresovich, S., McClure, T.A. and Lawhon, W.T. (1977) Fuels from Sugar Crops. First Quarterly Report, Battelle Columbus Labs, Columbus.

[8]   Paterson, A.H. (2008) Genomics of Sorghum: A Review. International Journal of Plant Genomics, 2008, Article ID: 362451, 6 p. http://dx.doi.org/10.1155/2008/362451

[9]   Swanson, A. and Laude, H. (1934) Varieties of Sorghum in Kansas. Kansas Bulletin, 266, 2-50.

[10]   Freeman, K.C. (1979) Germplasm Release of Sweet Sorghum Lines with Resistance to Downy Mildew, Leaf Anthracnose and Rust with Adequate Combining Ability to Produce Progeny with Agronomic Characters Acceptable for Commercial Sirup and/or Sugar Production. Mississippi Agricultural and Forestry Experiment Station Research Report, Vol. 4, No. 2.

[11]   Schulman, A. (2007) Molecular Markers to Assess Genetic Diversity. Euphytica, 158, 313-321.
http://dx.doi.org/10.1007/s10681-006-9282-5

[12]   Franco, J., Crossa, J., Ribaout, J.M., Betran, J., Warburton, M.L. and Khairallah, M. (2001) A Method for Combining Molecular Markers and Phenotype Attributes for Classifying Plant Genotypes. Theoretical and Applied Genetics, 103, 944-952. http://dx.doi.org/10.1007/s001220100641

[13]   Ramakrishnan, A.P., Meyer, S.E., Walters, J., Stevens, M.R., Coleman, C.E. and Fairbanks, D.J. (2004) Correlation between Molecular Markers and Adaptively Significant Genetic Variation in Bromus tectorum (Poaceae), an Inbreedingannual Grass. American Journal of Botany, 91, 797-803.
http://dx.doi.org/10.3732/ajb.91.6.797

[14]   Li, G. and Quiros, C.F. (2001) 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, 103, 455-461. http://dx.doi.org/10.1007/s001220100570

[15]   Tao, Y., Manners, J., Ludlow, M. and Henzell, R. (1993) DNA Polymorphisms in Grain Sorghum (Sorghum bicolor (L.) Moench). Theoretical and Applied Genetics, 86, 679-688.
http://dx.doi.org/10.1007/BF00222656

[16]   Ahnert, D., Lee, M., Austin, D., Livini, C., Woodman, W., Openshaw, S., Smith, J., Porter, K. and Dalon, G. (1996) Genetic Diversity among Elite Sorghum Inbred Lines Assessed with DNA Markers and Pedigree Information. Crop Science, 36, 1385-1392.
http://dx.doi.org/10.2135/cropsci1996.0011183X003600050049x

[17]   Uptmoor, R., Wenzel, W., Friedt, W., Donaldson, G., Ayisi, K. and Ordon, F. (2003) Comparative Analysis on the Genetic Relatedness of Sorghum bicolor Accessions from Southern Africa by RAPDs, AFLPs and SSRs. Theoretical and Applied Genetics, 106, 1316-1325.

[18]   Anas and Yoshida, T. (2004) Genetic Diversity among Japanese Cultivated Sorghum Assessed with Simple Sequence Repeats Markers. Plant Production Science, 7, 217-223.

[19]   Menz, M.A., Klein, R.R., Unruh, N.C., Rooney, W.L., Klein, P.E. and Mullet, J.E. (2004) Genetic Diversity of Public Inbreds of Sorghum Determined by Mapped AFLP and SSR Markers. Crop Science, 44, 1236-1244.
http://dx.doi.org/10.2135/cropsci2004.1236

[20]   Warburton, M.L., Reif, J.C., Frisch, M., Bohn, M., Bedoya, C., Xia, X.C., Crossa, J., Franco, J., Hoisington, D., Pixley, K., Taba, S. and Melchinger, A.E. (2008) Genetic Diversity in CIMMYT Nontemperate Maize Germplasm: Landraces, Open Pollinated Varieties, and Inbred Lines. Crop Science, 48, 617-624.
http://dx.doi.org/10.2135/cropsci2007.02.0103

[21]   Sharon, D., Cregan, P.B., Mhameed, S., Kusharska, M., Hillel, J., Lahav, E. and Lavi, U. (1997) An Integrated Genetic Linkage Map of Avocado. Theoretical and Applied Genetics, 95, 911-921. http://dx.doi.org/10.1007/s001220050642

[22]   Brown, S.M., Hopkins, M.S., Mitchell, S.E., Senior, M.L., Wang, T.Y., Duncan, R.R., Gonzalez-Candelas, F. and Kresovich, S. (1996) Multiple Methods for the Identification of Polymorphic Simple Sequence Repeats (SSRs) in Sorghum [Sorghum bicolor (L.) Moench]. Theoretical and Applied Genetics, 93, 190-198.
http://dx.doi.org/10.1007/BF00225745

[23]   Powell, W., Morgante, M., Andre, C., Hanafey, M., Vogel, J., Tingey, S. and Rafalski, A. (1996) The Comparison of RFLP, RAPD, AFLP and SSR (Microsatellite) Markers for Germplasm Analysis. Molecular Breeding, 3, 225-238.
http://dx.doi.org/10.1007/BF00564200

[24]   Casa, A.M., Mitchell, S.E., Hamblin, M.T., Sun, H., Bowers J.E., Paterson, A.H., Aquadro, C.F. and Kresovich, S. (2005) Diversity and Selection in Sorhum: Simultaneous Analyses Using Simple Sequence Repeats. Theoretical and Applied Genetics, 111, 23-30. http://dx.doi.org/10.1007/s00122-005-1952-5

[25]   Perumal, R., Krishnaramanujan, R., Menz, M.A., Katilé, S., Dahlberg, J., Magill, C.W. and Rooney, W.L. (2007) Genetic Diversity among Sorghum Races and Working Groups Based on AFLPs and SSRs. Crop Science, 47, 1375-1383.
http://dx.doi.org/10.2135/cropsci2006.08.0532

[26]   Ali, M.L., Rajewski, J.F., Baenziger, P.S., Gill, K.S., Eskridge, K.M. and Dweikat, I. (2008) Assessment of Genetic Diversity and Relationship among a Collection of US Sweet Sorghum Germplasm by SSR Markers. Molecular Breeding, 21, 497-509. http://dx.doi.org/10.1007/s11032-007-9149-z

[27]   Klein, R.R., Mullet, J.E., Jordan, D.R., Miller, F.R., Rooney, W.L., Menz, M.A., Franks, C.D. and Klein, P.E. (2008) The Effect of Tropical Sorghum Conversion and Inbred Development on Genome Diversity as Revealed by High-Resolution Genotyping. Crop Science, 48, 512-526.

[28]   Budak, H., Shearman, R.C., Parmaksiz, I., Gaussoin, R.E., Riordan, T.P. and Dweikat, I. (2004) Molecular Characterization of Buffalograss Germplasm Using Sequence-Related Amplified Polymorphism Markers. Theoretical and Applied Genetics, 108, 328-334. http://dx.doi.org/10.1007/s00122-003-1428-4

[29]   Ariss, J.J. and Vandemark, G.J. (2007) Assessment of Genetic Diversity among Non-Dormant and Semi-Dormant Alfalfa Populations Using Sequence-Related Amplified Polymorphism. Crop Science, 47, 2274-2284.
http://dx.doi.org/10.2135/cropsci2006.12.0782

[30]   Zhao, W., Fang, R., Pan, Y., Yang, Y., Chung, J.W., Chung, I.M. and Park, Y.J. (2009) Analysis of Genetic Relationships of Mulberry (Morus L.) Germplasm Using Sequence-Related Amplified Polymorphism (SRAP) Markers. African Journal of Biotechnology, 8, 2604-2610.

[31]   Han, X., Wang, L., Liu, Z.A., Jan, D.R. and Shu, Q. (2008) Characterization of Sequence-Related Amplified Polymorphism Markers Analysis of Tree Peony Bud Sports. Scientia Horticulturae, 115, 261-267.
http://dx.doi.org/10.1016/j.scienta.2007.09.003

[32]   Budak, H., Shearman, R.C., Parmaksiz, I. and Dweikat, I. (2004) Comparative Analysis of Seeded and Vegetative Biotype Buffalograss Based on Phylogenetic Relationship Using ISSRs, SSRs, RAPDs, and SRAPs. Theoretical and Applied Genetics, 109, 280-288. http://dx.doi.org/10.1007/s00122-004-1630-z

[33]   Lin, Z.X., Zhang, X.L. and Nie, Y.C. (2004) Evaluation of Application of a New Molecular Marker SRAP on Analysis of F2 Segregation Population and Genetic Diversity in Cotton. Acta Genetica Sinica, 31, 622-626.

[34]   Ferriol, M., Pico, B. and Nuze, F. (2003) Genetic Diversity of a Germplasm Collection of Cucurbita pepo Using SRAP and AFLP Markers. Theoretical and Applied Genetics, 107, 271-282.
http://dx.doi.org/10.1007/s00122-003-1242-z

[35]   Fufa, H., Baenziger, P.S., Beecher, B.S., Dweikat, I., Graybosch, R.A. and Eskridge, K.M. (2005) Comparison of Phenotypic and Molecular Marker-Based Classifications of Hard Red Winter Wheat Cultivars. Euphytica, 145, 133-146.
http://dx.doi.org/10.1007/s10681-005-0626-3

[36]   Zaefizadeh, M. and Goliev, R. (2009) Diversity and Relationships among Durum Wheat Landraces (Subconvars) by SRAP and Phenotypic Marker Polymorphism. Research Journal of Biological Sciences, 4, 960-966.

[37]   Folkertsma R., Frederick, H., Rattunde, W., Chandra, S., Raju, G. and Hash, C. (2005) The Pattern of Genetic Diversity of Guinea-Race Sorghum bicolor (L.) Moench Landraces as Revealed with SSR Markers. Theoretical and Applied Genetics, 111, 399-409. http://dx.doi.org/10.1007/s00122-005-1949-0

[38]   Gorz, H.J., Haskins, F.A. and Johnson, B.E. (1990) Registration of 15 Germplasm Lines of Grain Sorghum and Sweet Sorghum. Crop Science, 30, 762-763.
http://dx.doi.org/10.2135/cropsci1990.0011183X003000030089x

[39]   Dweikat, I. (2005) A Diploid, Interspecific, Fertile Hybrid from Cultivated Sorghum, Sorghum bicolor, and the Common Johnsongrass Weed Sorghum halepense. Molecular Breeding, 16, 93-101.
http://dx.doi.org/10.1007/s11032-005-5021-1

[40]   Schloss, S.J., Mitchell, S.E., White, G.M., Kukatla, R., Bowers, J.E., Paterson, A.H. and Kresovich, S. (2002) Characterization of RFLP Probe Sequences for Gene Discovery and SSR Development in Sorghum bicolor (L.) Moench. Theoretical and Applied Genetics, 105, 912-920. http://dx.doi.org/10.1007/s00122-002-0991-4

[41]   Riaz, A., Li, G., Quresh, Z., Swati, M.S. and Quiros, C.F. (2001) Genetic Diversity of Oilseed Brassica napus Inbred Lines Based on Sequence-Related Amplified Polymorphism and Its Relation to Hybrid Performance. Plant Breeding, 120, 411-415. http://dx.doi.org/10.1046/j.1439-0523.2001.00636.x

[42]   Kuleung, C., Baenziger, P. S. and Dweikat, I. (2004) Transferability of SSR Markers among Wheat, Rye and Triticale. Theoretical and Applied Genetics, 108, 1147-1150. http://dx.doi.org/10.1007/s00122-003-1532-5

[43]   Flury, B., and Riedwyl, H. (1986) Standard Distance in Univariate and Multivariate Analysis. The American Statistician, 40, 249-251.

[44]   SAS Institute Inc. (2008) User’s Guide, Version 9.2. SAS Institute Inc., Cary.

[45]   Anderson, J.A., Churchill, G.A., Autrique, J.E., Sorells, M.E. and Tanksley, S.D. (1993) Optimizing Parental Selection for Genetic Linkage Maps. Genome, 36, 181-186. http://dx.doi.org/10.1139/g93-024

[46]   Botstein, D., White, R.L. Skolnick, M. and Davis, R.W. (1990) Construction of a Genetic Linkage Map in Man Using Restriction Fragment Length Polymorphism. The American Journal of Human Genetics, 32, 314-331.

[47]   Nei, M. and Li, W.H. (1979) Mathematical Model for Studying Genetic Variation in Terms of Restriction Endonucleases. Proceedings of the National Academy of Sciences of the United States of America, 76, 5269-5273.
http://dx.doi.org/10.1073/pnas.76.10.5269

[48]   Weising, K., Nyborn, H., Wolff, K. and Kahl, G. (2005) DNA Fingerprinting in Plants: Principles, Methods, and Applications. 2nd Edition, CRC Press, New York. http://dx.doi.org/10.1201/9781420040043

[49]   Nei, M. (1972) Genetic Distance between Populations. The American Naturalist, 106, 283-292.
http://dx.doi.org/10.1086/282771

[50]   Takezaki, N. and Nei, M. (1996) Genetic Distances and Reconstruction of Phylogenetic Tree from Microsatellite DNA. Genetics, 144, 389-399.

[51]   Page, R.D.M. (1996) TreeView: An Application to Display Phylogenetic Trees on Personal Computers. Computer Applications in the Biosciences, 12, 357-358.

[52]   Wang, M.L., Zhu, C., Barkley, N.A., Chen, Z., Erpelding, J.E., Murray, S.C., Tuinstra, M.R., Tesso, T., Paterson, G.A. and Yu, J. (2009) Genetic Diversity and Population Structure Analysis of Accessions in the US Historic Sweet Sorghum Collection. Theoretical and Applied Genetics, 120, 13-23. http://dx.doi.org/10.1007/s00122-009-1155-6

 
 
Top