DNA Marker Technologies in Plants and Applications for Crop Improvements

Abstract

Over the past several decades, especially through traditional breeding programme, intensive attempts have been made for the improvement of a large number of cereal varieties which adjusted to diverse agro-ecologies. However, increasing biotic and abiotic stresses, increasing populations, and sharply reducing natural resources especially water for agricultural purposes, push the breeders for organizing and developing improved cereal varieties with higher yield potential. In combination with developments in agricultural technology, plant breeding has made remarkable progress in increasing crop yields for over a century. Molecular markers are widely employed in plant breeding. DNA markers are being used for the acceleration of plant selection through marker-assisted selection (MAS). Genes of agronomic and scientific importance can be isolated especially on the basis of their position on the genetic map by using molecular markers technologies. In this review, the current status of marker development technologies for crop improvements will be discussed. It will also provide an outlook into the future approaches and most widely used applications in plant breeding in crop plants on the basis of present development.

Share and Cite:

Lateef, D. (2015) DNA Marker Technologies in Plants and Applications for Crop Improvements. Journal of Biosciences and Medicines, 3, 7-18. doi: 10.4236/jbm.2015.35002.

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1] Kalia, R.K., et al. (2011) Microsatellite Markers: An Overview of the Recent Progress in Plants. Euphytica, 177, 309- 334.
http://dx.doi.org/10.1007/s10681-010-0286-9
[2] Poland, J.A., et al. (2012) Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two- Enzyme Genotyping-by-Sequencing Approach. PloS One, 7, e32253.
http://dx.doi.org/10.1371/journal.pone.0032253
[3] Mir, R.R., et al. (2013) Evolving Molecular Marker Technologies in Plants: From RFLPs to GBS. In: Lübberstedt, T. and Varshney, R.K., Eds., Diagnostics in Plant Breeding, Springer, Berlin, 229-247.
http://dx.doi.org/10.1007/978-94-007-5687-8_11
[4] Xu, Y., et al. (2013) Marker-Assisted Selection in Cereals: Platforms, Strategies and Examples. In: Cereal Genomics II, Springer, Berlin, 375-411.
[5] Conway, G.R. and Barbier, E.B. (2013) After the Green Revolution: Sustainable Agriculture for Development. Rout- ledge, London.
[6] Gupta, P.K., Langridge, P. and Mir, R.R. (2010) Marker-Assisted Wheat Breeding: Present Status and Future Possibilities. Molecular Breeding, 26, 145-161.
http://dx.doi.org/10.1007/s11032-009-9359-7
[7] Paux, E., et al. (2010) Insertion Site—Based Polymorphism Markers Open New Perspectives for Genome Saturation and Marker-Assisted Selection in Wheat. Plant Biotechnology Journal, 8, 196-210.
http://dx.doi.org/10.1111/j.1467-7652.2009.00477.x
[8] Henry, R.J. (2012) Molecular Markers in Plants. Wiley.
http://dx.doi.org/10.1002/9781118473023
[9] Paux, E., et al. (2012) Sequence-Based Marker Development in Wheat: Advances and Applications to Breeding. Biotechnology Advances, 30, 1071-1088.
http://dx.doi.org/10.1016/j.biotechadv.2011.09.015
[10] Jones, N., et al. (2009) Markers and Mapping Revisited: Finding Your Gene. New Phytologist, 183, 935-966.
http://dx.doi.org/10.1111/j.1469-8137.2009.02933.x
[11] Tanksley, S., et al. (1989) RFLP Mapping in Plant Breeding: New Tools for an Old Science. Nature Biotechnology, 7, 257-264.
http://dx.doi.org/10.1038/nbt0389-257
[12] Cho, Y., et al. (1998) Integrated Map of AFLP, SSLP and RFLP Markers Using a Recombinant Inbred Population of Rice (Oryza sativa L.). Theoretical and Applied Genetics, 97, 370-380.
http://dx.doi.org/10.1007/s001220050907
[13] Smith, O., et al. (1990) Similarities among a Group of Elite Maize Inbreds as Measured by Pedigree, F1 Grain Yield, Grain Yield, Heterosis, and RFLPs. Theoretical and Applied Genetics, 80, 833-840.
http://dx.doi.org/10.1007/BF00224201
[14] 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.
http://dx.doi.org/10.1007/s001220050456
[15] Wong, L.-J.C. (2013) Next Generation Molecular Diagnosis of Mitochondrial Disorders. Mitochondrion, 13, 379-387.
http://dx.doi.org/10.1016/j.mito.2013.02.001
[16] Edwards, J.D. and McCouch, S.R. (2007) Molecular Markers for Use in Plant Molecular Breeding and Germplasm Evaluation. Marker-Assisted Selection-Current Status and Future Perspectives in Crops, Livestock, Forestry and Fish, Food and Agriculture Organization of the United Nations (FAO), Rome, 29-49.
[17] Edwards, D. and Batley, J. (2009) Plant Genome Sequencing: Applications for Crop Improvement. Plant Biotechnology Journal, 8, 2-9.
http://dx.doi.org/10.1111/j.1467-7652.2009.00459.x
[18] Williams, J.G., et al. (1990) DNA Polymorphisms Amplified by Arbitrary Primers Are Useful as Genetic Markers. Nucleic Acids Research, 18, 6531-6535.
http://dx.doi.org/10.1093/nar/18.22.6531
[19] Gupta, P.K. and Varshney, R.K. (2013) Cereal Genomics II. Springer-Verlag GmbH.
[20] Gupta, P., et al. (1999) Molecular Markers and Their Applications in Wheat Breeding. Plant Breeding, 118, 369-390.
http://dx.doi.org/10.1046/j.1439-0523.1999.00401.x
[21] Jiang, G.-L. (2013) Molecular Markers and Marker-Assisted Breeding in Plants. Plant Breeding from Laboratories to Fields.
[22] Dunn, G., et al. (2005) Microsatellites versus Single-Nucleotide Polymorphisms in Linkage Analysis for Quantitative and Qualitative Measures. BMC Genetics, 6, S122.
http://dx.doi.org/10.1186/1471-2156-6-S1-S122
[23] Ellegren, H. (2000) Microsatellite Mutations in the Germline: Implications for Evolutionary Inference. Trends in Genetics, 16, 551-558.
http://dx.doi.org/10.1016/S0168-9525(00)02139-9
[24] Koelling, J., et al. (2012) Development of New Microsatellite Markers (SSRs) for Humulus Lupulus. Molecular Breed- ing, 30, 479-484.
http://dx.doi.org/10.1007/s11032-011-9637-z
[25] Varshney, R.K., Graner, A. and Sorrells, M.E. (2005) Genic Microsatellite Markers in Plants: Features and Applications. Trends in Biotechnology, 23, 48-55.
http://dx.doi.org/10.1016/j.tibtech.2004.11.005
[26] Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., et al. (1995) AFLP: A New Technique for DNA Fingerprinting. Nucleic Acids Research, 23, 4407-4414.
http://dx.doi.org/10.1093/nar/23.21.4407
[27] Nicod, J.C. and Largiadèr, C.R. (2003) SNPs by AFLP (SBA): A Rapid SNP Isolation Strategy for Non-Model Organisms. Nucleic Acids Research, 31, e19.
http://dx.doi.org/10.1093/nar/gng019
[28] Meudt, H.M. and Clarke, A.C. (2007) Almost Forgotten or Latest Practice? AFLP Applications, Analyses and Advances. Trends in Plant Science, 12, 106-117.
http://dx.doi.org/10.1016/j.tplants.2007.02.001
[29] Colomba, M., Vischi, M. and Gregorini, A. (2012) Molecular Characterization and Comparative Analysis of Six Durum Wheat Accessions Including Graziella Ra. Plant Molecular Biology Reporter, 30, 168-175.
http://dx.doi.org/10.1007/s11105-011-0328-z
[30] Xu, Y. (2010) Molecular Plant Breeding. CABI International, Wallingford, Oxfordshire.
[31] Ganal, M.W., Altmann, T. and Roder, M.S. (2009) SNP Identification in Crop Plants. Current Opinion in Plant Biology, 12, 211-217.
http://dx.doi.org/10.1016/j.pbi.2008.12.009
[32] Edwards, D., Forster, J.W., Chagné, D., Batley, J., et al. (2007) What Are SNPs? In: Oraguzie, N., et al., Eds., Association Mapping in Plants, Springer, New York, 41-52.
http://dx.doi.org/10.1007/978-0-387-36011-9_3
[33] Syvanen, A.-C. (2005) Toward Genome-Wide SNP Genotyping. Nature Genetics, 37, S5-S10.
http://dx.doi.org/10.1038/ng1558
[34] Gupta, P.K., Rustgi, S. and Mir, R.R. (2008) Array-Based High-Throughput DNA Markers for Crop Improvement. Heredity, 101, 5-18.
http://dx.doi.org/10.1038/hdy.2008.35
[35] Weising, K., Nybom, H., Wolff, K. and Kahl, G. (2005) DNA Fingerprinting in Plants: Principles, Methods, and Applications. 2nd Edition, Taylor & Francis, UK.
http://dx.doi.org/10.1201/9781420040043
[36] Thudi, M., Li, Y., Jackson, S.A., May, G.D. and Varshney, R.K. (2012) Current State-of-Art of Sequencing Technologies for Plant Genomics Research. Briefings in Functional Genomics, 11, 3-11.
http://dx.doi.org/10.1093/bfgp/elr045
[37] Winfield, M.O., Wilkinson, P.A., Allen, A.M., Barker, G.L.A., Coghill, J.A., Burridge, A., et al. (2012) Targeted Re-Sequencing of the Allohexaploid Wheat Exome. Plant Biotechnology Journal, 10, 733-742.
http://dx.doi.org/10.1111/j.1467-7652.2012.00713.x
[38] Edwards, D., Wilcox, S., Barrero, R.A., Fleury, D., Cavanagh, C.R., Forrest, K.L., et al. (2012) Bread Matters: A National Initiative to Profile the Genetic Diversity of Australian Wheat. Plant Biotechnology Journal, 10, 703-708.
http://dx.doi.org/10.1111/j.1467-7652.2012.00717.x
[39] Allen, A.M., Barker, G.L.A., Berry, S.T., Coghill, J.A., Gwilliam, R., Kirby, S., et al. (2011) Transcript-Specific, Single-Nucleotide Polymorphism Discovery and Linkage Analysis in Hexaploid Bread Wheat (Triticum aestivum L.). Plant Biotechnology Journal, 9, 1086-1099.
http://dx.doi.org/10.1111/j.1467-7652.2011.00628.x
[40] Lorenc, M.T., Hayashi, S., Stiller, J., Lee, H., Manoli, S., Ruperao, P., et al. (2012) Discovery of Single Nucleotide Polymorphisms in Complex Genomes Using SGSautoSNP. Biology, 1, 370-382.
http://dx.doi.org/10.3390/biology1020370
[41] McCouch, S.R., Zhao, K.Y., Wright, M., Tung, C.-W., Ebana, K., Thomson, M., et al. (2010) Development of Genome-Wide SNP Assays for Rice. Breeding Science, 60, 524-535.
http://dx.doi.org/10.1270/jsbbs.60.524
[42] LGC Genomics (2013) KASPtm Genotyping Chemistry User Guide and Manual.
http://www.lgcgenomics.com/genotyping/kasp-genotyping-reagents/?download_file
=22_1_kasp_manual.pdf&download_cat=downloads
[43] Mammadov, J., Chen, W., Mingus, J., Thompson, S. and Kumpatla, S. (2012) Development of Versatile Gene-Based SNP Assays in Maize (Zea mays L.). Molecular Breeding, 29, 779-790.
http://dx.doi.org/10.1007/s11032-011-9589-3
[44] Wheeler, D.A., Srinivasan, M., Egholm, M., Shen, Y.F., Chen, L., McGuire, A., et al. (2008) The Complete Genome of an Individual by Massively Parallel DNA Sequencing. Nature, 452, 872-876.
http://dx.doi.org/10.1038/nature06884
[45] Kiani, S., Akhunova, A. and Akhunov, E. (2013) Application of Next-Generation Sequencing Technologies for Genetic Diversity Analysis in Cereals. In: Gupta, P.K. and Varshney, R.K., Eds., Cereal Genomics II, Springer, Dordrecht, 77-99.
[46] van Oeveren, J., de Ruiter, M., Jesse, T., van der Poel, H., Tang, J., Yalcin, F., et al. (2011) Sequence-Based Physical Mapping of Complex Genomes by Whole Genome Profiling. Genome Research, 21, 618-625.
http://dx.doi.org/10.1101/gr.112094.110
[47] Gupta, P.K., Kumar, J., Mir, R.R. and Kumar, A. (2010) Marker-Assisted Selection as a Component of Conventional Plant Breeding. Plant Breeding Reviews, 33, 145-217.
http://dx.doi.org/10.1002/9780470535486.ch4
[48] Bonnett, D.G., Rebetzke, G.J. and Spielmeyer, W. (2005) Strategies for Efficient Implementation of Molecular Markers in Wheat Breeding. Molecular Breeding, 15, 75-85.
http://dx.doi.org/10.1007/s11032-004-2734-5
[49] Rae, S.J., Macaulay, M., Ramsay, L., Leigh, F., Matthews, D., O’Sullivan, D.M., et al. (2007) Molecular Barley Breeding. Euphytica, 158, 295-303.
http://dx.doi.org/10.1007/s10681-006-9166-8
[50] Gracia, M.P. and Casas, A.M. (2012) Barley Adaptation: Teachings from Landraces Will Help to Respond to Climate Change. In: Zhang, G.P., Li, C.D. and Liu, X., Eds., Advance in Barley Sciences: Proceedings of 11th International Barley Genetics Symposium, Springer, Dordrecht.
[51] Werner, K., Friedt, W. and Ordon, F. (2005) Strategies for Pyramiding Resistance Genes against the Barley Yellow Mosaic Virus Complex (BaMMV, BaYMV, BaYMV-2). Molecular Breeding, 16, 45-55.
http://dx.doi.org/10.1007/s11032-005-3445-2
[52] Wang, J.K., Chapman, S.C., Bonnett, D.G. and Rebetzke, G.J. (2009) Simultaneous Selection of Major and Minor Genes: Use of QTL to Increase Selection Efficiency of Coleoptile Length of Wheat (Triticum aestivum L.). Theoretical and Applied Genetics, 119, 65-74.
http://dx.doi.org/10.1007/s00122-009-1017-2
[53] Crosbie, T.M., Eathington, S.R., Johnson, G.R., Edwards, M., Reiter, R., Stark, S., et al. (2006) Plant Breeding: Past, Present, and Future. In: Lamkey, K.R. and Lee, M., Eds., Plant Breeding: The Arnel R. Hallauer International Symposium, Wiley-Blackwell, Hoboken.
http://dx.doi.org/10.1002/9780470752708.ch1
[54] Bernardo, R. and Charcosset, A. (2006) Usefulness of Gene Information in Marker-Assisted Recurrent Selection: A Simulation Appraisal. Crop Science, 46, 614-621.
http://dx.doi.org/10.2135/cropsci2005.05-0088

Journals Menu
Follow SCIRP
Contact us
customer@scirp.org
WhatsApp +86 18163351462(WhatsApp)
Click here to send a message to me 1655362766
Paper Publishing WeChat

Copyright © 2022 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.