Application of molecular markers in plant sciences; An overview

Document Type : Review paper

Author

Department of Plant Production and Genetics, Razi University, Kermanshah, Iran

Abstract

Recent advances in cellular and molecular genetics have raised new hopes among breeders, including the development of a variety of molecular markers. There are several types of markers, including morphological, molecular, and cytological markers. Molecular markers are one of the most powerful tools for studying genetic diversity. They are used in the study of phylogenetic relationships, selection of superior plants, and the study of similarities or differences between different specimens. Molecular markers are also used in germplasm management and marker-assisted selection (MAS) to increase the efficiency of germplasm breeding. Among molecular markers, DNA-based markers are of particular importance because of the limitations of morphological and isozyme markers. DNA markers are valuable tools in plant sciences. These markers do not have the problems of morphological markers and allow efficient comparisons to distinguish between very similar organisms. These markers are commonly used to assess genetic variation in agronomic germplasm, analyse population structure, localise quantitative traits (QTL), or linkage mapping for gene mapping. The increasing development of new and specific types of markers demonstrates their importance for understanding genomic diversity and diversity between similar species as well as between different plant species. In this review, we will discuss the types of markers, their advantages and disadvantages, and their applications in plant science.

Graphical Abstract

Application of molecular markers in plant sciences; An overview

Highlights

  • Recent advances in molecular biology have led to the use of DNA markers.
  • Molecular markers are not affected by plant growth conditions and stages and do not change due to environmental conditions, and with greater accuracy, speed and sensitivity, they reveal a large number of distinct differences between genotypes at the DNA level.
  • While DNA marker technology cannot replace plant breeding, it certainly increases the effort of breeders by providing new tools.

Keywords

Main Subjects


Adhikari, S., Saha, S., Biswas, A., Rana, T.S., Bandyopadhyay, T.K., Ghosh, P., 2017. Application of molecular markers in plant genome analysis: a review.  Nucleus60(3), 283-297.‏
CrossRef    Google Scholar    full-text PDF    Mendeley     
Agarwal, M., Shrivastava, N., Padh, H., 2008. Advances in molecular marker techniques and their applications in plant sciences.  Plant Cell. Rep., 27(4), 617-631.‏
CrossRef    Google Scholar    full-text PDF    Mendeley    PubMed     
Akasha, I., Campbell, L., Lonchamp, J., Euston, S.R., 2016. The major proteins of the seed of the fruit of the date palm (Phoenix dactylifera L.): Characterisation and emulsifying properties. Food Chem.197, 799-806.‏
CrossRef    Google Scholar    full-text PDF    Mendeley    PubMed   
Allen, F.L., 2020. Usefulness of plant genome mapping to plant breeding. Plant Gen. Anal., CRC Press, 11-18.
Amom, T., Nongdam, P., 2017. The use of molecular marker methods in plants: a review. Int. J. Curr. Res. Rev., 9(17), 1-7.‏
https://doi.org/10.7324/IJCRR.2017.9171
Asadi, N., Jalilian, S., 2021. The effect of methyl jasmonate on the germination of lemon seeds under the influence of salinity stress. Cent. Asian J. Environ. Sci. Technol. Innov., 2(3), 119-128.
Bassil, N.V., Davis, T.M., Zhang, H., Ficklin, S., Mittmann, M., Webster, T., Mahoney, L., Wood, D., Alperin, E.S., Rosyara, U.R. and Putten, H.K.V., 2015. Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria× ananassa. BMC Genom., 16(1), 1-30. ‏
CrossRef    Google Scholar    full-text PDF    Mendeley    PubMed   
Boisset, J.C., Vivié, J., Grün, D., Muraro, M.J., Lyubimova, A., Van Oudenaarden, A., 2018. Mapping the physical network of cellular interactions. Nat. Methods, 15(7), 547-553.
CrossRef    Google Scholar    full-text PDF    Mendeley    PubMed   
Caballo, C., Castro, P., Gil, J., Izquierdo, I., Millan, T., Rubio, J., 2018. STMS (sequence tagged microsatellite site) molecular markers as a valuable tool to confirm controlled crosses in chickpea (Cicer arietinum L.) breeding programs. Euphytica214(12), 1-9.‏
Callahan, B.J., McMurdie, P.J., Holmes, S.P., 2017. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J., 11(12), 2639-2643.
Chukwu, S.C., Rafii, M.Y., Ramlee, S.I., Ismail, S.I., Oladosu, Y., Okporie, E., Onyishi, G., Utobo, E., Ekwu, L., Swaray, S., Jalloh, M., 2019. Marker-assisted selection and gene pyramiding for resistance to bacterial leaf blight disease of rice (Oryza sativa L.). Biotechnol. Biotechnol. Equip., 33(1), 440-455.
Coates, D.J., Byrne, M., Moritz, C., 2018. Genetic diversity and conservation units: dealing with the species-population continuum in the age of genomics. Front. Ecol. Evol., 6, 165.‏
Daly, M., Bromilow, S.N., Nitride, C., Shewry, P.R., Gethings, L.A., Mills, E.N., 2020. Mapping coeliac toxic motifs in the prolamin seed storage proteins of barley, rye, and oats using a curated sequence database. Front. Nutr.7, 87.‏
Dong, M., Wang, Z., He, Q., Zhao, J., Fan, Z., Zhang, J., 2018. Development of EST-SSR markers in Larixprincipis-rupprechtiiMayr and evaluation of their polymorphism and cross-species amplification. Trees., 32(6), 1559-1571.‏
Du, H., Yu, Y., Ma, Y., Gao, Q., Cao, Y., Chen, Z., Ma, B., Qi, M., Li, Y., Zhao, X., Wang, J., 2017. Sequencing and de novo assembly of a near complete indica rice genome. Nat. Commun., 8(1), 1-12.
Etminan, A., Pour-Aboughadareh, A., Mohammadi, R., Ahmadi-Rad, A., Noori, A., Mahdavian, Z., Moradi, Z., 2016. Applicability of start codon targeted (SCoT) and inter-simple sequence repeat (ISSR) markers for genetic diversity analysis in durum wheat genotypes. Biotechnol. Biotechnol. Equip., 30(6), 1075-1081.
Goodwin, S., McPherson, J.D., McCombie, W.R., 2016. Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet., 17(6), 333-351.‏
Grover, A., Sharma, P.C., 2016. Development and use of molecular markers: past and present. Crit. Rev. Biotechnol., 36(2), 290-302.
CrossRef    Google Scholar    full-text PDF    Mendeley    PubMed   
Hamouda, M., 2019. Molecular analysis of genetic diversity in population of Silybum marianum (L.) Gaertn in Egypt.  J. Genet. Eng. Biotechnol.17(1), 1-9.‏
Hilscher, J., Bürstmayr, H., Stoger, E., 2017. Targeted modification of plant genomes for precision crop breeding. Biotechnol. J., 12(1), 1600173.‏ 
CrossRef    Google Scholar    full-text PDF    Mendeley    PubMed   
Husnik, F., McCutcheon, J.P., 2018. Functional horizontal gene transfer from bacteria to eukaryotes. Nat. Rev. Microbiol., 16(2), 67-79.‏
CrossRef    Google Scholar    full-text PDF    Mendeley    PubMed   
Jamali, S.H., Cockram, J., Hickey, L.T., 2019. Insights into deployment of DNA markers in plant variety protection and registration. Theor. Appl. Genet.132(7), 1911-1929.‏
CrossRef    Google Scholar    full-text PDF    Mendeley    PubMed     
Jiang, G.L., 2013. Molecular markers and marker-assisted breeding in plants. Plant breeding from laboratories to fields, 45-83.‏
CrossRef    Google Scholar    full-text PDF    Mendeley     
Kirungu, J.N., Deng, Y., Cai, X., Magwanga, R.O., Zhou, Z., Wang, X., Wang, Y., Zhang, Z., Wang, K., Liu, F., 2018. Simple sequence repeat (SSR) genetic linkage map of D genome diploid cotton derived from an interspecific cross between Gossypiumdavidsonii and Gossypiumklotzschianum. Int. J. Mol. Sci., 19(1), 204-224.
König, P., Beier, S., Basterrechea, M., Schüler, D., Arend, D., Mascher, M., Stein, N., Scholz, U., Lange, M., 2020. BRIDGE–a visual analytics web tool for barley genebank genomics. Front. Plant Sci.11, 701.‏
Kumawat, G., Kumawat, C.K., Chandra, K., Pandey, S., Chand, S., Mishra, U.N., Lenka, D., Sharma, R., 2020. Insights into marker assisted selection and its applications in plant breeding. Intech Open.‏
CrossRef    Google Scholar    full-text PDF    Mendeley    
Kuzay, S., Xu, Y., Zhang, J., Katz, A., Pearce, S., Su, Z., Fraser, M., Anderson, J.A., Brown-Guedira, G., DeWit, N., Haugrud, A.P., Frris, J.D., Akhunov, E., Bai, G., Dubcovsky, J., 2019. Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping. Theor. Appl. Genet., 132(9), 2689-2705.‏
Landry, B.S., Kesseli, R.V., Farrara, B., Michelmore, R.W., 1987. A genetic map of lettuce (Lactuca sativa L.) with restriction fragment length polymorphism, isozyme, disease resistance and morphological markers. Genetics116(2), 331-337.‏
Li, X., Duan, X., Jiang, H., Sun, Y., Tang, Y., Yuan, Z., Guo, J., Liang, Ch., Yin, J., Ma, H., Wang, J., Zhang, D., 2006. Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. Plant physiol., 141(4), 1167-1184.
McGuire, A.L., Gabriel, S., Tishkoff, S.A., Wonkam, A., Chakravarti, A., Furlong, E.E., Treutlein, B., Meissner, A., Chang, H.Y., Lopez-Bigas, N., Segal, E., Kim, J.S., 2020. The road ahead in genetics and genomics. Nat. Rev. Genet., 21(10), 581-596.‏
Merritt, B.J., Culley, T.M., Avanesyan, A., Stokes, R., Brzyski, J., 2015. An empirical review: characteristics of plant microsatellite markers that confer higher levels of genetic variation. Appl. Plant Sci., 3(8), 1500025.‏
Metakovsky, E., Melnik, V., Rodriguez-Quijano, M., Upelniek, V., Carrillo, J.M., 2018. A catalog of gliadin alleles: Polymorphism of 20th-century common wheat germplasm.  Crop J., 6(6), 628-641.‏
‏Mobasheri, A., Bay-Jensen, A.C., Van Spil, W.E., Larkin, J., Levesque, M.C., 2017. Osteoarthritis Year in Review 2016: biomarkers (biochemical markers). Osteoarthr. cartil., 25(2), 199-208.‏
CrossRef    Google Scholar    full-text PDF    Mendeley    PubMed   
Moehs, C.P., Austill, W.J., Holm, A., Large, T.A., Loeffler, D., Mullenberg, J., Schnable, P.S., Skinner, W., Boxtel, J.V., Wu, L., McGuire, C., 2019. Development of decreased-gluten wheat enabled by determination of the genetic basis of lys3a barley. Plant physiol., 179(4), 1692-1703.‏
Nadeem, M.A., Nawaz, M.A., Shahid, M.Q., Doğan, Y., Comertpay, G., Yıldız, M., Hatipoglu, R., Ahmad, F., Alsaleh, A., Labhance, N., Ozkan, H., Chung, G., Baloch, F.S., 2018. DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnol. Biotechnol. Equip., 32(2), 261-285.‏
CrossRef    Google Scholar    full-text PDF    Mendeley     
Ni, J.L., Zhu, A.G., Wang, X.F., Xu, Y., Sun, Z.M., Chen, J.H., Luan, M.B., 2018. Genetic diversity and population structure of ramie (Boehmeria nivea L.). Ind. Crops Prod., 115, 340-347.‏
Oladosu, Y., Rafii, M.Y., Samuel, C., Fatai, A., Magaji, U., Kareem, I., Kamarudin, Z.S., Mohammad, I., Kolapo, K., 2019. Drought resistance in rice from conventional to molecular breeding: a review. Int. J. Mol. Sci., 20(14), 3519.‏ 
Platten, J.D., Cobb, J.N., Zantua, R.E., 2019. Criteria for evaluating molecular markers: comprehensive quality metrics to improve marker-assisted selection. PloS One14(1), e0210529.‏
Sepahvand, D., Matinizadeh, M., Etemad, V., Shirvany, A., 2021. Changes in morphological and biochemical properties of Celtis caucasica L. mycorrhizal fungi-inoculated under drought stress condition. Cent. Asian J. Environ. Sci. Technol. Innov., 2(4), 142-155.