Main Article Content


D. Tussipkan

National Center for Biotechnolog, Plant Genetic Engineering Laboratory, 13/5, Qorghalzhyn road., Astana, 010000, Kazakhstan

Zhaoe Pan

State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China


Due to the advanced sequencing technologies, breeders and researchers can use DNA markers to characterize various plants' genetic diversity, kinship, and population structures. This review describes four kinds of genetic markers. Among them, DNA-based molecular markers were discussed in types, basic mechanisms, advantages, and disadvantages in detail. Secondly, we summarize the whole process of a genome-wide association study, and its advantages and disadvantages. We hope that this review provides fundamental information that will be useful for understanding different markers, especially, DNA-based molecular markers, and genome-wide association studies.


polymerase chain reaction (PCR) based marker, simple sequence repeats (SSRs), DNA-based molecular marker,, single nucleotide polymorphisms (SNPs), genome-wide association study (GWS).

Article Details


Nadeem, M.A., et al., DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnology & Biotechnological Equipment, 2018. 32(2): p. 261-285.

Bhandari, H.R., et al., Assessment of Genetic Diversity in Crop Plants: An Overview. 2017.

Khan, N. and S. Singh, Role of Molecular Markers in Assessing Genetic Diversity in Mentha: A Review. 2016.

McCormick, R.F., et al., The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization. The Plant Journal, 2018. 93(2): p. 338-354.

Asghari, A., et al., QTL analysis for cold resistance-related traits in Brassica napus using RAPD markers. Journal of Food Agriculture & Environment, 2015. 5(3): p. 188-192.

Hang, T.T.V., et al., Use of DArT molecular markers for QTL analysis of drought-stress responses in soybean. II. Marker identification and QTL analyses. Crop & Pasture Science, 2016. 66(8): p. 817.

Wen, Y., et al., Construction of a High-Density Genetic Map Based on SLAF Markers and QTL Analysis of Leaf Size in Rice. Frontiers in Plant Science, 2020. 11(1143).

NAGEL, M., et al., Genome-wide association mapping and biochemical markers reveal that seed ageing and longevity are intricately affected by genetic background and developmental and environmental conditions in barley. Plant, Cell & Environment, 2015. 38(6): p. 1011-1022.

Dilnur, T., et al., Association Analysis of Salt Tolerance in Asiatic cotton (Gossypium arboretum) with SNP Markers. International Journal of Molecular Sciences, 2019. 20(9): p. 2168.

Wang, Z., et al., A genome-wide association study approach to the identification of candidate genes underlying agronomic traits in alfalfa (Medicago sativa L.). Plant biotechnology journal, 2020. 18(3): p. 611-613.

White, T.L., W.T. Adams, and D.B. Neale, Genetic markers - morphological, biochemical and molecular markers. 2007.

Semagn, K., B. Rnstad, and M.N. Ndjiondjop, An overview of molecular marker methods for plants. African Journal of Biotechnology, 2006. 5(25): p. 2540-2568.

Seibt, K.M., et al., Development and application of SINE-based markers for genotyping of potato varieties. Theoretical and Applied Genetics, 2012. 125(1): p. 185-196.

Yang, R., et al., Electrochemical Voltammogram Recording for Identifying Varieties of Ornamental Plants. Micromachines, 2020. 11(11): p. 967.

Winter, P. and a.G. Kahl, Molecular marker technologies for plant improvement. World Journal of Microbiology & BiofechnoIogy 1995. 11: p. 438-448.

Boscaiu, M., et al., Osmolyte biosynthesis: A biochemical marker for salt tolerance of halophytes in their natural habitats. Current Opinion in Biotechnology, 2011. 22: p. S138-S139.

Elbaz, F.K., A.A. Mohamed, and A.A. Aly, Development of Biochemical Markers for Salt Stress Tolerance in Cucumber Plants. Pakistan Journal of Biological Sciences, 2003. 6(1).

Metwali, E.M.R., M.H. Eid, and T.Y. Bayoumi, Agronomical Traits and Biochemical Genetics Markers Associated with Salt Tolerance in Wheat Cultivars (Triticum aestivum L). Australian Journal of Basic & Applied Sciences, 2011. 5(5): p. 174-183.

Linda, et al., Assessing Plant Genetic Diversity by Molecular Tools. Diversity, 2009. 1(1): p. 19-35.

Preetha, S., Molecular marker technology in cotton. Biotechnology & Molecular Biology Reviews, 2008. 3: p. 32-45.

Agarwal, M., N. Shrivastava, and H. Padh, Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Reports, 2008. 27(4): p. 617-31.

Khan, F., Molecular Markers: An Excellent Tool for Genetic Analysis. Journal of Molecular Biomarkers & Diagnosis, 2015. 06.

Duran, C., et al., Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation. Current Bioinformatics, 2009. 4: p. 16-27.

Kearsey, M.J. and A.G.L. Farquhar, QTL analysis in plants; where are we now? Heredity, 1998. 80(2): p. 137–142.

Paterson, A.H., et al., Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 2012. 492(7429): p. 423.

Acquaah, G., Principles of Plant Genetics and Breeding, Second Edition. 2012.

Grodzicker, T., et al., Physical mapping of temperature-sensitive mutations of adenoviruses. Journal of Molecular Biology, 1975. 39 Pt 1(3): p. 439.

Botstein, D., et al., Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 1980. 32(3): p. 314.

Helentjaris, T., et al., Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphisms. Theoretical and Applied Genetics, 1986. 72(6): p. 761.

Weber, D., Mapping RFLP loci in maize using B-A translocations. Genetics, 1989. 121(3): p. 583.

Semagn, K., Å. Bjørnstad, and M. Ndjiondjop, An overview of molecular marker methods for plants. 2006. 5(25).

WR, M., RFLP association with varietal origin and heterosis. In: Proc. Beltwide Cotton Conf. (ed. D. Herber), Nashville, TN., 1992: p. 607.

Reinisch, A.J., et al., A detailed RFLP map of cotton, Gossypium hirsutum x Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics, 1994. 138(3): p. 829.

Wright, R., et al., Molecular mapping of genes affecting pubescence of cotton. Journal of Heredity, 1999. 90(1): p. 215-219.

Shappley, Z., et al., An RFLP linkage map of Upland cotton, Gossypium hirsutum L. Theor Appl Genet, 1998. 97: p. 756-761.

Ulloa, M. and M. Wrjr, Genetic linkage map and QTL analysis of agronomic and fiber quality traits in an intraspecific population. Journal of Cotton Science, 2000. 4(3): p. 161-170.

Ulloa, M., et al., Chromosomal assignment of RFLP linkage groups harboring important QTLs on an intraspecific cotton (Gossypium hirsutum L.) Joinmap. Journal of Heredity, 2005. 96(2): p. 132-144.

Rashidismaelhag, I., A. Junichi, and S. Masahiro, PCR-RFLP analysis of the whole chloroplast DNA from three cultivated species of cotton (Gossypium L.). Euphytica, 2007. 156(1): p. 47-56.

Mullis, K., et al., Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harbor Symp. Quant. Biol., 1986. 51: p. 263-273.

Mandaliya, V.B., Single nucleotide polymorphism (SNP): a trend in genetics and genome analyses of plants. General & Applied Plant Physiology, 2010.

Bernatzky, R. and S.D. Tanksley, Toward a saturated linkage map in tomato based on isozymes and random cDNA sequences. Genetics, 1986. 112(4): p. 887-98.

Hadrys, H., M. Balick, and B. Schierwater, Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Molecular Ecology, 1992. 1(1): p. 55.

Kumar, N.S. and G. Gurusubramanian, Random amplified polymorphic DNA (RAPD) markers and its applications. Science Vision, 2011. 3.

Tanksley, S.D., Mapping polygenes. Annual Review of Genetics, 1993. 27(4): p. 205.

NCBI, Random Amplified Polymorphic DNA (RAPD), Available at: URL.

Smith, P.J., Random Amplified Polymorphic DNA (RAPD). 2005.

Savelkoul, P.H., et al., Amplified-fragment length polymorphism analysis: the state of an art. Journal of Clinical Microbiology, 1999. 37(10): p. 3083.

Maughan, P.J., et al., Amplified fragment length polymorphism (AFLP) in soybean: species diversity, inheritance, and near-isogenic line analysis. Theoretical and Applied Genetics, 1996. 93(3): p. 392-401.

Vos, P., et al., AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research, 1995. 23(21): p. 4407.

Abdel-Mawgood, A.L., DNA Based Techniques for Studying Genetic Diversity. 2012: InTech.

Collard, B.C.Y., et al. An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts. in Euphytica. 2005.

Sunnucks, P., Marking the spot : Microsatellites: Evolution and Applications edited by D.B. Goldstein and C. Schlötterer. Trends in Ecology & Evolution, 2000. 15(3): p. 126-126.

Miesfeld, R., M. Krystal, and N. Amheim, A member of a new repeated sequence family which is conserved throughout eucaryotic evolution is found between the human δ and β globin genes. Nucleic Acids Res 9:5931-5947. Nucleic Acids Research, 1981. 9(22): p. 5931-47.

Chambers, G.K. and E.S. Macavoy, Microsatellites: consensus and controversy. Comparative Biochemistry & Physiology Part B Biochemistry & Molecular Biology, 2000. 126(4): p. 455-476.

Reddy, M.P., N. Sarla, and E.A. Siddiq, Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica, 2002. 128(1): p. 9-17.

Powell, W., G.C. Machray, and J. Provan, Polymorphism revealed by simple sequence repeats. Trends in Plant Science, 1996. 1(7): p. 215-222.

Dilnur, T., Association Analysis of Salt Tolerance Traits with SSR and SNP Markers in Asiatic Cotton; Available at: URL

: p. 1-146.

Hao, D.-C., Chapter 1 - Genomics and Evolution of Medicinal Plants, in Ranunculales Medicinal Plants, D.-C. Hao, Editor. 2019, Academic Press. p. 1-33.

Collard, B., et al., An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica, 2005. 142(1-2): p. 169-196.

Kumar, P., et al., Potential of Molecular Markers in Plant Biotechnology. Plant Omics, 2009. 2(4): p. 141-162.

Gupta, P., et al., Molecular markers and their applications in wheat breeding. Plant Breeding, 1999. 118(5): p. 369-390.

Wang, S., et al., Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes. Genome Biology, 2015. 16(1): p. 1-18.

Su, J., et al., Identification of favorable SNP alleles and candidate genes for traits related to early maturity via GWAS in upland cotton. Bmc Genomics, 2016. 17(1).

Liu, Z.J. and J.F. Cordes, DNA marker technologies and their applications in aquaculture genetics. Biotechnology Bulletin, 2007. 238(1–4): p. 1-37.

Orsini, L., et al., Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna. BMC Genomics, 2011. 12: p. 309-309.

Wang, X., et al., Mining and Analysis of SNP in Response to Salinity Stress in Upland Cotton (Gossypium hirsutum L.). Plos One, 2016. 11(6).

Liu, Z. and J. Cordes, DNA marker technologies and their applications in aquaculture genetics. Aquaculture, 2004. 238(1): p. 1-37.

Wang, D.G., et al., Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome. Science, 1998. 280(5366): p. 1077.

Parida, S.K., et al., SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure. Bmc Genomics, 2012. 13(1): p. 157-157.

Yonemaru, J.I., et al., Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars. Bmc Genomics, 2014. 15(1): p. 1-12.

Yamamoto, T., et al., Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. Bmc Genomics, 2010. 11(1): p. 1-14.

Descalsota, G.I.L., et al., Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification. Frontiers in Plant Science, 2018. 9(1347).

Chen, C., G.J. Norton, and A.H. Price, Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel. Frontiers in Plant Science, 2020. 11(1633).

Close, T.J., et al., Development and implementation of high-throughput SNP genotyping in barley. Bmc Genomics, 2009. 10(12): p. 1-13.

Lee, T.H., et al., SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. Bmc Genomics, 2014. 15(1): p. 120-121.

Shi, Z., et al., SNP identification and marker assay development for high-throughput selection of soybean cyst nematode resistance. Bmc Genomics, 2015. 16(1): p. 1-12.

Guimaraes, C.T., et al., Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan. Bmc Genomics, 2014. 15(1): p. 1-14.

Tiwari, V.K., et al., SNP Discovery for mapping alien introgressions in wheat. Bmc Genomics, 2014. 15(1): p. 687-694.

Chao, S., et al., Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum. Bmc Genomics, 2010. 11(6): p. 393-406.

Akhunov, E.D., et al., Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. Bmc Genomics, 2010. 11(6): p.: 702.

Cantu, D., et al., Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. triticireveal polymorphic and haustorial expressed secreted proteins as candidate effectors. Bmc Genomics, 2013. 14(1): p. 1-18.

Genome-wide association analysis on pre-harvest sprouting resistance and grain color in U.S. winter wheat. BMC Genomics, 2016. 17.

Deulvot, C., et al., Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea. Bmc Genomics, 2010. 11(32): p. 468.

Duarte, J., et al., Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea. Bmc Genomics, 2014. 15(1): p. 1-15.

Boutet, G., et al., SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population. Bmc Genomics, 2016. 17(1): p. 1-14.

Li, X., et al., Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping. Bmc Genomics, 2014. 15(1): p. 1-11.

Hulse-Kemp, A.M., et al., Development and bin mapping of gene-associated interspecific SNPs for cotton ( Gossypium hirsutum L.) introgression breeding efforts. Bmc Genomics, 2014. 15(1): p. 1-14.

Flagel, L.E., J.F. Wendel, and J.A. Udall, Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton. Bmc Genomics, 2012. 13(1): p. 1-13.

Gómez, G., M.F. Álvarez, and T. Mosquera, Association mapping, a method to detect quantitative trait loci: statistical bases. Agronomía Colombiana, 2011. 29(3): p. 367-376.

Yano, K., et al., Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice. Nature Genetics, 2016. 48(8): p. 927.

Sajjad, M., S.H. Khan, and R.M. Rana, Family and/or Friends? Gene Mapping at Crossroads. American Journal of Plant Sciences, 2014. 5(1): p. 112-118.

Almaskri, A.Y., M. Sajjad, and S.H. Khan, Association mapping: a step forward to discovering new alleles for crop improvement. International Journal of Agriculture & Biology, 2012. 14(14): p. 153-160.

Flint-Garcia, S.A. and J.M. Thornsberry, Structure of linkage disequilibrium in plants. Annual Review of Plant Biology, 2003. 54(4): p. 357.

Argan, P., et al., An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.). Molecular Breeding, 2005. 15(3): p. 233-245.

Kraakman, A.T.W., et al., Linkage Disequilibrium Mapping of Morphological, Resistance, and Other Agronomically Relevant Traits in Modern Spring Barley Cultivars. Molecular Breeding, 2006. 17(1): p. 41-58.

Neumann, K., et al., Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.). Molecular Breeding, 2011. 27(1): p. 37-58.

Zeng, L., et al., Identification of associations between SSR markers and fiber traits in an exotic germplasm derived from multiple crosses among Gossypium tetraploid species. Theoretical and Applied Genetics, 2009. 119(1): p. 93-103.

Xu, J., et al., Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species. Theoretical and Applied Genetics, 2013. 126(3): p. 567.