Seweta Srivastava Aspak Suvaraj Mukherjee Swagnik Datta Sanchari Burman Meenakshi Rana Rajeev Kumar Kanuri Komala Siva Katyayani Arun Karnwal Shubham Kumar Manash Shukla Ravindra Kumar


Microsatellites or simple sequence repeats (SSRs) markers are a helpful strategy among the various molecular marker techniques for strengthening molecular breeding programs. These are useful markers for genotyping plant populations with tandem repeats of 2-6 base pair length DNA patterns. The expansion of various molecular markers and advances in sequencing technologies has aided crop improvement. Several articles for research scholars with progressive knowledge of molecular genetics have been published in the last three decades to probe the information regarding molecular markers. This article reviews novel advances regarding molecular markers and their implementations in plant breeding for researchers with no expertise in using molecular markers in plant breeding. A superior comprehension of molecular markers, and a better consciousness of the spectrum of crops that can be grown, has resulted from progress in molecular plant breeding, genetics, genomic selection, and genome rectification. Further-generation sequence technology must enable the production of novel genetic markers for multifaceted and amorphous groups through genotyping-by-sequencing and union mapping. The review also discusses almost all the microsatellite markers and their advantages and disadvantages.  




Crop improvement, Microsatellite, Marker development, Marker application, Marker-assisted selection (MAS), Polymerase Chain Reaction (PCR)

Adams, K.L., Qiu, Y.L., Stoutemyer, M. & Palmer, J.D. (2002). Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc Natl Acad Sci USA, 99,: 9905–9912.
Adams, M.D., Kelley, J.M., Gocayne, J.D., Dubnick, M., Polymeropoulos, M.H., Xiao, H., Merril, C.R., Wu, A., Olde, B., Moreno, R.F., Kerlavage, A.R., Mccombie, W.R. & Venter, J.C. (1991). Complementary DNA sequencing: expressed sequence tags and human genome project. Sci, 252(5013),: 1651–1656.
Aitken, K.S., Jackson, P.A. & McIntyre, C.L. (2005). A Combination of AFLP and SSR Markers Provides Extensive Map Coverage and Identification of Homo(eo)logous Linkage Groups in a Sugarcane Cultivar. Theor Appl Genet, 110, 789-801.
Akkaya, M.S., Bhagwat, A.A., & Cregan, P.B. (1992). Length polymorphisms of simple sequence repeat DNA in soybean. Genetics, 132(4), 1131-1139.
Akopyanz, N., Bukanov, N., Westblom, T.U., & Berg, D.E. (1992). PCR-based RFLP analysis of DNA sequence diversity in the gastric pathogen Helicobacter pylori. Nucleic Acid Res, 20,m6221-6225.
Alam, C.M., Iqbal, A., Sharma, A., Schulman, A.H., & Ali, S. (2019). Microsatellite Diversity, Complexity, and Host Range of Mycobacteriophage Genomes of the Siphoviridae Family. Front Genet, 10, 207.
Allen, J.F. (2015). Why chloroplasts and mitochondria retain their own genomes and genetic systems: colocation for redox regulation of gene expression. Proc Natl Acad Sci USA, 112,: 10231–10238.
Alwala, S., Suman, A., Arro, J.A., Veremis, J.C., & Kimbeng, C.A. (2006). Target Region Amplification Polymorphism (TRAP) for Assessing Genetic Diversity in Sugarcane Germplasm Collections. Crop Sci, 46, 448-455.
Amiteye, S. (2021). Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon, 7(10), e08093.
Andersen, J.R. & Lübberstedt, T. (2003). Functional markers in plants. Trends Plant Sci, 8, 554–560.
Arnholdt-Schmitt, B. (2005). Functional markers and a “systemic strategy”: convergency between plant breeding, plant nutrition and molecular biology. Plant Physiol Bioch, 43, 817–820.
Atheeswaran, A., Raghavender, K.V., Lakshmi Chaganti, B.N., Maram, A. & Herencsar, N. (2023). Expert system for smart farming for diagnosis of sugarcane diseases using machine learning. Computers and Electrical Engineering, 109(Part A), 108739.
Aydın, F., Özer, G., Alkan, M. & Çakır, I. (2020). The utility of iPBS retrotransposons markers to analyse genetic variation in yeast. Inter J Food Microbiol, 325, 108647.
Bachem, C.W., van der Hoeven, R.S., de Bruijn, S.M., Vreugdenhil, D., Zabeau, M. & Visser, R.G. (1996). Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J, 9, 745–53.
Badoni, S., Das, S., Sayal, Y. K., Gopalakrishnan, S., Singh, A.K., Rao, A.R., Agarwal, P., Parida, S.K. & Tyagi, A.K. (2016). Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice. Sci Rep, 6, 23765.
Biswas, M.K., Xu, Q. & Deng, X.X. (2010). Utility of RAPD, ISSR, IRAP and REMAP markers for the genetic analysis of Citrus spp. Sci Hort, 124, 254–261.
Botstein, D., White, R.L., Skolnick, M. & Davis, R.W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet, 32, 314-331.
Braglia, L., Gavazzi, F., Gianì, S., Morello, L. & Breviario, D. (2023). Tubulin-Based Polymorphism (TBP) in Plant Genotyping. Methods Mol Biol, 2638, 387-401.
Braglia, L., Gavazzi, F., Morello, L., Gianì, S., Nick, P. & Breviario, D. (2020). On the applicability of the Tubulin-Based Polymorphism (TBP) genotyping method: a comprehensive guide illustrated through the application on different genetic resources in the legume family. Plant Methods, 16, 86.
Bryan, G.J., Stephenson, P., Collins, A., Kirby, J., Smith, J.B. & Gale, M.D. (1999). Low levels of DNA sequence variation among adapted genotypes of hexaploid wheat. Theor Appl Genet, 99, 192–198.
Cai, C., Wu, S., Niu, E., Cheng, C. & Guo, W. (2017). Identification of genes related to salt stress tolerance using intron-length polymorphic markers, association mapping and virus-induced gene silencing in cotton. Scientific Report, 7(1), 528.
Cato, S., Gardner, R., Kent, J., Richardson, T. (2001). A rapid PCR based method for genetically mapping ESTs. Theor Appl Genet, 102, 296–306.
Chadha, S. & Gopalakrishna, T. (2005). Retrotransposon-microsatellite amplified polymorphism (REMAP) markers for genetic diversity assessment of the rice blast pathogen (Magnaporthe grisea). Genome, 48, 943–945.
Chandra, A., Grisham, M.P. & Pan, Y.B. (2014). Allelic Divergence and Cultivar-Specific SSR Alleles Revealed by Capillary Electrophoresis Using Fluorescence-Labeled SSR Markers in Sugarcane. Genome, 57, 363-372.
Chandra, A., Jain, R., Solomon, S., Shrivastava, S. & Roy, A.K. (2013). Exploiting EST databases for the development and characterisation of 3425 gene-tagged CISP markers in biofuel crop sugarcane and their transferability in cereals and orphan tropical grasses. BMC Res Notes, 6, 47.
Cheraghi, A., Rahmani, F. & Hassanzadeh-Ghorttapeh, A. (2018). IRAP and REMAP based genetic diversity among varieties of Lallemantia iberica. Mol Biol Res Commun, 7(3), 125-132.
Choi, I.S., Ruhlman, T.A. & Jansen, R.K. (2020). Comparative mitogenome analysis of the genus Trifoliumreveals independent gene fission of ccmFn and intracellular gene transfers in fabaceae. Int J Mol Sci, 21,1959.
Christensen, A.C. (2020). More than just a powerhouse. Nat Plants, 6, 5–6.
Collard, B.C.Y. & Mackill, D.J. (2009). Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol Biol Rep, 27, 86-93.
Cordeiro, G.M., Eliott, F., McIntyre, C.L., Manners, J.M. & Henry, R.J. (2006). Characterization of Single Nucleotide Polymorphisms in Sugarcane ESTs. Theor Appl Genet, 113, 331-343.
Cordeiro, G.M., Taylor, G.O. & Henry, R.J. (2000). Characterization of Microsatellite Markers from Sugarcane (Saccharum spp.). A Highly Polyploidy Species. Plant Sci, 155, 161-168.
Cuevas, H.E. & Vermerris, W. (2022). Linkage map construction using limited parental genotypic information. Euphytica, 218, 58.
Cui, H., Ding, Z., Zhu, Q., Wu, Y., Qiu, B. & Gao, P. (2021). Comparative analysis of nuclear, chloroplast, and mitochondrial genomes of watermelon and melon provides evidence of gene transfer. Sci Rep, 11, 1595.
Da Silva, J.A.G. (2001). Preliminary Analysis of Microsatellite Markers Derived from Sugarcane Expressed Sequence Tags (ESTs). Genet Mol Biol, 24, 155-159.
Das, R., Arora, V., Jaiswa, S., Iquebal, M.A., Angadi, U.B., Fatma, S., Singh, R., Shil, S., Rai, A. & Kumar, D. (2019). PolyMorphPredict: A Universal Web-Tool for Rapid Polymorphic Microsatellite Marker Discovery from Whole Genome and Transcriptome Data. Front Plant Sci, 9, 1966.
de Abreu, N.L., Alves, R.J.V., Cardoso, S.R.S., Bertrand, Y.J.K., Sousa, F., Hall, C.F., Pfeil, B.E. & Antonelli, A. (2018). The use of chloroplast genome sequences to solve phylogenetic incongruences in Polystachya Hook (Orchidaceae Juss) PeerJ, 6, e4916.
de Cesare, M., Hodkinson, T.R. & Barth, S. (2010). Chloroplast DNA markers (cpSSRs, SNPs) for Miscanthus, Saccharum and related grasses (Panicoideae, Poaceae). Mol Breeding, 26(3), 539-544.
Debibakas, S., Rocher, S., Garsmeur, O., Toubi, L., Roques, D., D’Hont, A., Hoarau, J.Y. & Daugrois, J.H. (2014). Prospecting sugarcane resistance to Sugarcane yellow leaf virus by genome-wide association. Theor Appl Genet, 127, 1719–1732.
Devarumath, R., Kalwade, S., Bundock, P., Eliott, F.G. & Henry, R. (2013). Independent Target Region Amplification Polymorphism and Single-Nucleotide Polymorphism Marker Utility in Genetic Evaluation of Sugarcane Genotypes. Plant Breed, 132, 736-747.
Devarumath, R.M., Kalwade, S.B., Kawar, P.G. & Sushir, K.V. (2012). Assessment of Genetic Diversity in Sugarcane Germplasm Using ISSR and SSR Markers. Sugar Tech, 4, 334-344.
Dhingani, R.M., Umrania, V.V., Tomar, R.S., Parakhia, M.V. & Golakiya, B.A. (2015). Introduction to QTL mapping in plants. Ann Pl Sci, 4(04), 1072-1079.
Donald, R. (2001). The science of plant morphology: definition, history, and role in modern biology. Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102 USA.
Eagles, H.A., Bariana, H.S., Ogbonnaya, F.C., Rebetzke, G.J., Hollamby, G.J., Henry, R.J., Henschke, P.H. & Carter, M. (2001). Implementation of markers in Australian wheat breeding. Australian J Agri Res, 52(11-12), 1349-1356.
Edwards, A., Civitello, A., Hammond, H.A. & Caskey, C.T. (1991). DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am J Hum Genet, 49, 746-756.
El Dessoky, S.D., Attia O.A., Ismail A.I., Saqer S.A. & Bandar S.A. (2020). Molecular Assessment of Genetic Stability Using CDDP and DNA-barcoding Assays in Long-term Micropropagated Rose Plant. Pakistan J Biological Sci, 23, 1176-1183.
Fabriki, O.S. & Azarkhanian, M.Y. (2018). Genetic variability and relationships among Salvia ecotypes/species revealed by TRAP-CoRAP markers. Biotechnol Biotechnological Equip, 32(6), 1486–1495.
Feltus, F.A., Singh, H.P., Lohithaswa, H.C., Schulze, S.R., Silva, T.D. & Paterson, A.H. (2006). A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops. Plant Physiol, 140, 1183–1191.
Fu, Y., Pan, Y., Lei, C., Grisham, M.P., Yang, C. & Meng, Q. (2016). Genotype-Specific Microsatellite (SSR) Markers for the Sugarcane Germplasm from the Karst Region of Guizhou, China. American J Pl Sci, 7(15), 2209-2220.
Gali, K.K., Sackville, A., Tafesse, E.G., Lachagari, V.B.R., McPhee, K., Hybl, M., Mikić, A., Smýkal, P., McGee, R., Burstin, J., Domoney, C., Ellis, T.H.N., Tar'an, B. & Warkentin, T.D. (2019). Genome-Wide Association Mapping for Agronomic and Seed Quality Traits of Field Pea (Pisum sativum L.). Front Pl Sci, 10, 1538.
Gorji, A.M., Matyas, K.K., Dublecz, Z., Decsi, K., Cernak, I., Hoffmann, B., Taller, J. & Polgar, Z. (2012). In vitro osmotic stress tolerance in potato and identification of major QTLs. Am J Pot Res, 89, 453-464.
Govindaraj, M., Vetriventhan, M. & Srinivasan, M. (2015). Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet Res Int, 2015, 431487.
Grivet, L., D’Hont, A., Roques, D., Feldmann, P., Lanaud, C. & Glaszmann, J.C. (1996). RFLP Mapping in Cultivated Sugarcane (Saccharum spp.): Genome Organization in a Highly Polypoid and Aneuploid Interspecific Hybrid. Genet, 142, 987-1000.
Gui, Y., Yan, G., Bo, S., Tong, Z., Wang, Y. Xiao, B., Lu, X., Li, Y., Wu, W. & Fan, L. (2011). iSNAP: a small RNA-based molecular marker technique. Plant Breed, 1-6.
Gurumurthy, C.B., Joshi, P.S., Kurz, S.G., Ohtsuka, M., Quadros, R.M., Harms, D.W. & Lloyd, K.C.K. (2015). Validation of Simple Sequence Length Polymorphism Regions of Commonly Used Mouse Strains for Marker Assisted Speed Congenics Screening. Inter J Genomics, 2015, 735845.
Hasan, N., Choudhary, S., Naaz, N., Sharma, N. & Laskar, R.A. (2021). Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. J Genet Eng Biotechnol, 19(1),128.
Hayashi, K. (1992). PCR-SSCP: a method for detection of mutations. Genetic Analysis: Techniques and Applications, 9, 73-79.
Hill, G.E., Havird, J.C., Sloan, D.B., Burton, R.S., Greening, C. & Dowling, D.K. (2019). Assessing the fitness consequences of mitonuclear interactions in natural populations. Biol Rev, 94, 1089–1104.
Hu, J. & Vick, B.B.A. (2003). Target region amplification polymorphism: a novel marker technique for plant genotyping. Plant Mol Biol Rep, 21(3), 289-294.
Hunter, R.L. & Markert, C.L. (1957). Histochemical demonstration of enzymes separated by zone electrophoresis in starch gels. Sci, 125, 1294-1295.
Igwe, D.O., Ihearahu, O.C., Osano, A.A., Acquaah, G. & Ude, G.N. (2021). Genetic Diversity and Population Assessment of Musa L. (Musaceae) Employing CDDP Markers. Plant Mol Biol Rep, 39, 801–820.
Jaccoud, D., Peng, K., Feinstein, D. & Kilian, A. (2001). Diversity arrays: a solid-state technology for sequence information independent genotyping. Nucleic Acids Res, 29 (4), 25e–25.
Jannoo, N., Grivet, L., Seguin, M., Paulet, F., Domaingue, R., Rao, P.S., Dookun, A., D’Hont, A. & Glaszmann, J.C. (1999). Molecular Investigation of the Genetic Base of Sugarcane Cultivars. Theoret Appl Genet, 99, 171-184.
Jarne, P. & Lagoda, P.J.L. (1996). Microsatellites, from molecules to populations and back. Trends Ecol Evol, 11, 424–429.
Jiang, G.L. (2013). Molecular Markers and Marker-Assisted Breeding in Plants. In: Plant Breeding from Laboratories to Fields, edited by Sven Andersen, IntechOpen, 10.5772/52583.
Jones, N., Ougham, H., Thomas, H. & Pašakinskienë, I. (2009). Markers and mapping revisited: finding your gene. New Phytologist, 183, 935–966.
Junior, C.A.D., Manechini, J.V., Correˆa, R.X., Pinto, A.C.R., da Costa, J.B., Favero, T.M. & Pinto, L.R. (2020). Genetic structure analysis in sugarcane (Saccharum spp.) using target region amplification polymorphism (TRAP) markers based on sugar- and lignin-related genes and potential application in core collection development. Sugar Tech, 22(4), 641–654.
Kakavas, K.V. (2021). Sensitivity and applications of the PCR Single-Strand Conformation Polymorphism method. Mol Biol Rep, 48, 3629–3635.
Kalendar, R., Flavell, A.J., Ellis, T.H., Sjakste, T., Moisy, C. & Schulman, A.H. (2011). Analysis of plant diversity with retrotransposon-based molecular markers. Heredity, 106(4), 520–530.
Kalendar, R., Grob, T., Regina, M., Suoniemi, A. & Schulman, A. (1999). IRAP and REMAP: Two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet, 98, 704–711.
Kalia, R.K., Rai, M.K., Kalia, S., Singh, R. & Dhawan, A.K. (2011). Microsatellite markers: an overview of the recent progress in plants. Euphytica, 177(3), 309–334.
Kantety, R.V., La Rota, M., Matthews, D.E. & Sorrells, M.E. (2002). Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol, 48, 501–510.
Karaköy, T., Baloch, F.S., Toklu, F. & Özkan, H. (2014). Variation for selected morphological and quality-related traits among 178 faba bean landraces collected from Turkey. Plant Genet Resour, 12(01), 5–13.
Khidr, Y.A., Mekuriaw, S.A., Hegazy, A.E. & Amer, E. (2020). Suitability of target region amplified polymorphism (TRAP) markers to discern genetic variability in sweet sorghum. J Genet Eng Biotechnol, 18(1), 59.
Khidr, Y.A., Mekuriaw, S.A., Hegazy, A.E. & Amer, E. (2020). Suitability of target region amplified polymorphism (TRAP) markers to discern genetic variability in sweet sorghum. J Genet Eng Biotechnol, 18(1), 59.
Konieczny, A. & Ausubel, F.M. (1993). A procedure for mapping Arabidopsis mutations using codominant ecotype-specific PCR-based markers. The Pl J, 4, 403-410.
Kozik, A., Rowan, B.A., Lavelle, D., Berke, L., Schranz, M.E., Michelmore, R.W. & Christensen, A.C. (2019). The alternative reality of plant mitochondrial DNA: One ring does not rule them all. PLoS Genet, 15(8), e1008373.
Kumar, P., Gupta, V.K., Misra, A.K., Modi, D.R. & Pandey, B.K. (2009). Potential of molecular markers in plant biotechnology. Plant Omics J, 2, 141–162.
Kumar, P., Kamble, M., Iqbal, A., Tiwari, N.N., Saxena, P., Tiwari, A.K. & Kumar, A. (2012). Role of moleculart markers in plant biotechnology. Agrica, 1, 8-22.
Kumar, R. (2018). Microsatellite Marker. In: Vonk J., Shackelford T. (eds) Encyclopedia of Animal Cognition and Behavior. Springer, Cham. https://doi.org/10.1007/978-3-319-47829-6_167-1
LaMantia, J.M., Chandra, A. & Huff, D.R. (2018). Development of ent-kaurene Oxidase-Based Conserved Intron Spanning Primers for Species Identification in the Genus Poa (Poaceae; Bluegrass). Agronomy, 8(5), 58.
Leister, D., Ballvora, A., Salamini, F. & Gebhardt, C. (1996). A PCR-based approach for isolating pathogen resistance genes from potato with potential for wide application in plants. Nat Genet, 14, 421–429.
Lejman, M., Włodarczyk, M., Styka, B., Pastorczak, A., Zawitkowska, J., Taha, J., Sędek, Ł., Skonieczka, K., Braun, M., Haus, O., Szczepański, T., Młynarski, W. & Kowalczyk, J.R. (2020). Advantages and Limitations of SNP Array in the Molecular Characterization of Pediatric T-Cell Acute Lymphoblastic Leukemia. Front Oncol, 10, 1184
Li, G. & 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. Theor Appl Genet, 103, 455–461.
Li, H., Yang, Y., Hong, W., Huang, M., Wu, M. & Zhao, X. (2020). Applications of genome editing technology in the targeted therapy of human diseases: mechanisms, advances and prospects. Sig Transduct Target Ther, 5, 1.
Li, J., Yang, Y., Sun, X., Liu, R., Xia, W., Shi, P., Zhou, L., Wang, Y., Wu, Y., Lei, X. & Xiao, Y. (2022). Development of Intron Polymorphism Markers and Their Association With Fatty Acid Component Variation in Oil Palm. Front Plant Sci, 13, 885418.
Lima, M.L.A., Garcia, A.A.F., Oliveira, K.M., Matsuoka, S., Arizono, H., de Souza, Jr C.L., de Souza, A.P. (2002). Analysis of Genetic Similarity Detected by AFLP and Coefficient of Parentage among Genotypes of Sugar Cane (Saccharum spp.). Theor Appl Genet, 104, 30-38.
Lindblom, B. & Holmlund, G. (1988). Rapid DNA Purification for restriction fragment length polymorphism analysis. Gene Analysis Techn, 5, 97–101.
Litt, M. & Luty, J.A. (1989). A Hypervariable Microsatellite Revealed by in Vitro Amplification of a Dinucleotide Repeat within the Cardiac Muscle Actin Gene. American Journal of Human Genet, 44, 397-401.
Liu, P., Chandra, A., Que, Y., Chen, P.H., Grisham, M.P., White, W.H., Dalley, C.D., Tew, T.L. & Pan, Y.B. (2016). Identification of QTLs Controlling Sucrose Content Based on an Enriched Genetic Linkage Map of Sugarcane (Saccharum spp. Hybrids) Cultivar “LCP 85-384”. Euphytica, 207, 527-549.
Liu, P., Que, Y. & Pan, Y.B. (2011). Highly Polymorphic Microsatellite DNA Markers for Sugarcane Germplasm Evaluation and Variety Identity Testing. Sugar Tech, 13, 129-136.
Lu, X., Zhou, H., Pan, Y.B., Chen, C.Y., Zhu, J.R., Chen, P.H., Cai, Q. & Chen, R.K. (2015). Segregation Analysis of Microsatellite (SRR) Markers in Sugarcane Polyploids. Genetics and Molecular Research, 14, 18384-18395.
Mackill, D.J. (2003). Applications of genomics to rice breeding. IRRN, 28, 9–15.
Madhumati, B. (2014). Potential and application of molecular markers techniques for plant genome analysis. Int J Pure App Biosci, 2(1), 169–188.
Magdy, M., Ou, L., Yu, H., Chen, R., Zhou, Y., Hassan, H., Feng, B., Taitano, N., van der Knaap, E., Zou, X., Li, F. & Ouyang, B. (2019). Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species. Hortic Res-Engl, 6, 1–15.
Marconi, T.G., Costa, E.A., Miranda, H.R., Mancini, M.C., Cardoso-Silva, C.B., Oliveira, K.M., Pinto, L.R., Mollinari, M., Garcia, A.A.F., Souza, A.P. (2011). Functional Markers for Gene Mapping and Genetic Diversity Studies in Sugarcane. BMC Res Notes, 4, 264.
Martya, E., Buchsa, J., Eugster-Meierb, E., Lacroixa, C. & Meile, L. (2012). Identification of staphylococci and dominant lactic acid bacteria in spontaneously fermented Swiss meat products using PCR–RFLP. Food Microbiol, 29(2),157–166.
Marwal, A. & Gaur, R.K. (2020). Chapter 18 - Molecular markers: tool for genetic analysis. In: Animal Biotechnology (Second Edition), Editor(s): Ashish S. Verma, Anchal Singh, Academic Press, pp. 353-372.
Marwal, A., Srivastava, A.K. & Gaur, R.K. (2020). Improved plant tolerance to biotic stress agronomic management. Agrica, 9(2), 84-100.
Mateu-Andres, I. & De Paco, L. (2005). Allozymic differentiation of the Antirrhinum majus and A. siculum species groups. Ann Bot, 95(3), 465–473.
Matuszczak, M., Spasibionek, S., Gacek, K. & Bartkowiak-Broda, I. (2020). Cleaved amplified polymorphic sequences (CAPS) marker for identification of two mutant alleles of the rapeseed BnaA.FAD2 gene. Mol Biol Rep, 47(10), 7607-7621.
McDew-White, M., Li, X., Nkhoma, S.C., Nair, S., Cheeseman, I. & Anderson, T.J.C. (2019). Mode and Tempo of Microsatellite Length Change in a Malaria Parasite Mutation Accumulation Experiment. Genome Biol Evol, 11(7), 1971–1985.
Medeiros, C., Balsalobre, T.W.A. & Carneiro, M.S. (2020). Molecular diversity and genetic structure of Saccharum complex accessions. PLoS One, 15(5), e0233211.
Meena, M.R., Appunu, C., Arun Kumar, R., Manimekalai, R., Vasantha, S., Krishnappa, G., Kumar, R., Pandey, S.K. & Hemaprabha, G. (2022). Recent Advances in Sugarcane Genomics, Physiology, and Phenomics for Superior Agronomic Traits. Front Genet, 13, 854936.
Miah, G., Rafii, M.Y., Ismail, M.R., Puteh, A.B., Rahim, H.A., Kh. Islam, N., Latif, M.A. (2013). A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance. Int J Mol Sci, 14, 22499-22528.
Mondini, L., Noorani, A. & Pagnotta, M.A. (2009). Assessing plant genetic diversity by molecular tools. Diversity, 1(1), 19–35.
Morgante, M., Hanafey, H. & Powell, W. (2002). Microsatellites are preferentially associated with nonrepetitive DNA in plant genome. Nat Genet, 30, 194–200.
Morley, S.A. & Nielsen, B.L. (2017). Plant mitochondrial DNA. Front Biosci (Landmark Ed), 22, 1023-1032.
Nadeem, M.A., Nawaz, M.A., Shahid, M.Q., Dogan, Y., Comertpay, G., Yıldız, M., Hatipoglu, R., Ahmad, F., Alsaleh, A., Labhane, N., Ozkan, H., Chung, G., Balocha, F.S. (2017). DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnology & Biotechnolog Equip, 32(2), 261–285.
Nair, N.V., Selvi, A., Sreenivasan, T.V. & Pushpalatha, K.N. (2002). Molecular Diversity in Indian Sugarcane Cultivars as Revealed by Randomly Amplified DNA Polymorphisms. Euphytica, 127, 219-225.
Nakamura, Y., Leppert, M., O'Connell, P., Wolff, R., Holm, T., Culver, M., Martin, C., Fujimoto, E., Hoff, M., Kumlin, E. & White, R. (1987). Variable number of tandem repeat (VNTR) markers for human gene mapping. Sci, 235, 1616–1622.
Ng, W.L. & Tan, S.G. (2015). Inter-simple sequence repeat (ISSR) markers: are we doing it right? ASM Sci J, 9, 30–39.
Oliveira, K.M., Pinto, L.R., Marconi, T.G., Margarido, G.R.A., Pastina, M.M., Teixeira, L.H.M., Figueira, A.V., Ulian, E.C., Garcia, A.A.F. & Souza, A.P. (2007). Functional Integrated Genetic Linkage Map Based on EST-Markers for a Sugarcane (Saccharum spp.) Commercial Cross. Mol Breed, 20, 189-208.
Oliveira, K.M., Pinto, L.R., Marconi, T.G., Mollinari, M., Ulian, E.C., Chabregas, S.M., Falco, M.C., Burnquist, W., Garcia, A.A. & Souza, A.P. (2009). Characterization of New Polymorphic Functional Markers for Sugarcane. Genome, 52, 191-209.
Olson, M., Hood, L., Cantor, C. & Botstein, D. (1989). A common language for physical mapping of the human genome. Sci, 245(4925), 1434-1435.
Orita, M., Iwahana, H., Kanazawa, H., Hayashi, K. & Sekiya, T. (1989). Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci USA, 86, 2766–2770.
Pan, Y.B. (2006). Highly Polymorphic Microsatellite DNA Markers for Sugarcane Germplasm Evaluation and Variety Identity Testing. Sugar Tech, 8, 246-256.
Pan, Y.B., Burner, D.M. & Legendre, B.L. (2000). An Assessment of the Phylogenetic Relationship among Sugarcane and Related Taxa Based on the Nucleotide Sequence of 5S rRNA Intergenic Spacers. Genetica, 108, 285-295.
Pan, Y.B., Burner, D.M. & Wei, Q. (2001). Developing Species-Specific DNA Markers to Assist in Sugarcane Breeding. Proceed Inter Soc Sugar Cane Technologists, 24, 337-342.
Pan, Y.B., Burner, D.M., Legendre, B.L., Grisham, M.P. & White, W.H. (2004). An Assessment of the Genetic Diversity within a Collection of Saccharum spontaneum with RAPD-PCR. Genet Res Crop Evol, 51, 895-903.
Pan, Y.B., Cordeiro, G.M., Richard, Jr E.P. & Henry, R.J. (2003). Molecular Genotyping of Sugarcane Clones with Microsatellite DNA Markers. Maydica, 48, 319-329.
Pan, Y.B., Liu, P. & Que, Y. (2014). Independently Segregating Simple Sequence Repeats (SSR) Alleles in Polyploid Sugarcane. Sugar Tech, 17, 235-242.
Pang, M., Percy, R.G., Hughs, E. & Zhang, J. (2008). Promoter anchored amplified polymorphism based on random amplified polymorphic DNA (PAAP-RAPD) in cotton. Euphytica, 167, 281–291.
Paran, I. & Michelmore, R.W. (1993). Development of reliable PCR based markers linked to downy mildew resistance genes in lettuce. Theor Appl Genet, 85, 985-993.
Parida, S.K., Kalia, S.K., Kaul, S., Dalal, V., Hemprapha, G., Selvi, A., Pandit, A., Singh, A., Gaikwad, K., Sharma, T.R., Srivastava, P.S., Singh, N.K. & Mohapatra, T. (2008). Informative Genomic Microsatellite Markers for Efficient Genotyping Application in Sugarcane. Theoretical and Applied Genet, 118, 327-338.
Paun, O. & Schönswetter, P. (2012). Amplified fragment length polymorphism: an invaluable fingerprinting technique for genomic, transcriptomic, and epigenetic studies. Methods Mol Biol, 862, 75-87.
Pinto, L.R., Oliveira, K.M., Marconi, T.G., Garcia, A.F., Ulian, E.C. & Souza, A.P. (2006). Characterization of Novel Sugarcane Expressed Sequence Tag Microsatellites and Their Comparison with Genomic SSRs. Plant Breed, 125, 378-384.
Pinto, L.R., Oliveira, K.M., Ulian, E.C., Garcia, A.A. & Souza, A.P. (2004). Survey in the Expressed Sequence Tag Database (SUCEST) for Simple Sequence Repeats. Genome, 47, 795-804.
Platten, J.D., Cobb, J.N. & Zantua, R.E. (2019). Criteria for evaluating molecular markers: Comprehensive quality metrics to improve marker-assisted selection. PLoS One, 14(1), e0210529.
Poczai, P., Varga, I., Laos, M., Cseh, A., Bell, N., Valkonen, J.P.T. & Hyvönen, J. (2013). Advances in plant gene-targeted and functional markers: a review. Pl Methods, 9, 6.
Powell, W., Morgante, M., Andre, C., McNicol, J.W., Machray, G.C., Doyle, J.J., Tingey, S.V. & Rafalski, J.A. (1995). Hypervariable microsatellites provide a general source of polymorphic DNA markers for the Chloroplast genome. Curr Biol, 5, 1023–1029.
Qi, Y., Gao, X., Zeng, Q., Zheng, Z., Wu, C., Yang, R., Feng, X., Wu, Z., Fan, L. & Huang, Z. (2022). Sugarcane Breeding, Germplasm Development and Related Molecular Research in China. Sugar Tech, 24(1), 73-85.
Rafalski, J.A. & Tingey, S.V. (1993). Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines. Trend Genet, 9, 275–280.
Rai, M.K. (2023). Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects. Planta, 257(2), 34.
Rakoczy-Trojanowska, M. & Bolibok, H. (2004). Characteristics and a comparison of three classes of microsatellite-based markers and their application in plants. Cell Mol Biol Lett, 9(2), 221-238.
Rasouli, M., Martínez-Gómez, P. & Karimi, R. (2015). Application of Random Amplified Microsatellite Polymorphism (RAMP) in Prunus Characterization and Mapping. J Nuts, 6(1), 1-5.
Ravi, R.S.D., Siril, E.A. & Nair, B.R. (2020). The efficiency of Cytochrome P450 gene-based markers in accessing genetic variability of drumstick (Moringa oleifera Lam.) accessions. Mol Biol Rep, 47(4), 2929-2939.
Rosenberg, N.A. (2002). Genetic Structure of Human Populations. Science. American Association for the Advancement of Science (AAAS). 298(5602), 2381–2385.
Roy, J.K., Balyan, H.S., Prasad, M. & Gupta, P.K. (2002) Use of SAMPL for a study of DNA polymorphism, genetic diversity and possible gene tagging in bread wheat. Theor Appl Genet, 104(2-3), 465-472.
Roy, N.S., Choi, J.Y., Lee, S.I. & Kim, N.S. (2015). Marker utility of transposable elements for plant genetics, breeding, and ecology: a review. Genes Genom, 37(2),141–151.
Roy, N.S., Ramekar, R.V. & Kim, N.S. (2021). Sequence-Specific Amplified Polymorphism (SSAP) and Sequence Characterized Amplified Region (SCAR) Markers in Zea mays. Methods Mol Biol, 2250, 207-218.
Salazar, J.A., Rasouli, M., Moghaddam, R.F., Zamani, Z., Imani, A. & Gómez, P.M. (2014). Low-cost strategies for development of molecular markers linked to agronomic traits in Prunus. Agric Sci, 5(05), 430–439.
Sanghera, G.S., Kumar, A., Singh, R.P. & Tiwari, A.K. (2016). Sugarcane improvement in genomic era: opportunity and complexity. Agrica, 5(2), 69-97.
Santos, J.M.D., Filho, L.S.C.D., Soriano, M.L., Silva, P.P.D., Nascimento, V.X., Barbosa, G.V.D.S., Todaro, A.R., Neto, C.E.R.N. & Almeida, C. (2012). Genetic Diversity of the Main Progenitors of Sugarcane from the RIDESA Germplasm Bank Using SSR Markers. Industrial Crops and Products, 40, 145-150.
Seibt, K.M., Wenke, T., Muders, K., Truberg, B. & Schmidt, T. (2016). Short interspersed nuclear elements (SINEs) are abundant in Solanaceae and have a family-specific impact on gene structure and genome organization. The Plant J, 86(3), 268-285.
Seibt, K.M., Wenke, T., Wollrab, C., Junghans, H., Muders, K., Dehmer, K.J., Diekmann, K. & Schmidt, T. (2012). Development and application of SINE-based markers for genotyping of potato varieties. Theor Appl Genet, 125, 185– 196.
Selvi, A., Nair, N.V., Noyer, J.L., Singh, N.K., Balasundaram, N., Bansal, K.C., Koundal, K.R. & Mohapatra, T. (2006). AFLP Analysis of the Phenetic Organization and Genetic Diversity in the Sugarcane Complex, Saccharum and Erianthus. Genet Res Crop Evol, 53, 831-842.
Sharma, M.D., Dobhal, U., Singh, P., Kumar, S., Gaur, A.K., Singh, S.P., Jeena, A.S., Koshy, E.P. & Kumar, S. (2014). Assessment of Genetic Diversity among Sugarcane Cultivars Using Novel Microsatellite Markers. African J Biotech, 13, 1444-1451.
Singh, P., Singh, S.P., Kumar, A. & Kumar, A. (2012). Evaluation of Saccharaum spontaneum clones under subtropical climatic conditions. Agrica, 1, 45-49.
Singh, P., Singh, S.P., Tiwari, A.K. & Sharma, B.L. (2017). Genetic diversity of sugarcane hybrid cultivars by RAPD markers. 3 Biotech, 7, 222.
Singh, R., Guan, T.S., Panandam, J., Rahman, R.A. & Cheah, S.C. (2008). Identification of cDNA-RFLP Markers and Their Use for Molecular Mapping in Oil Palm (Elaeis guineensis). As Pac J Mol Biol Biotechnol, 16(3), 53-63.
Singh, R.B., Mahenderakar, M.D., Jugran, A.K., Singh, R.K. & Srivastava, R.K. (2020). Assessing genetic diversity and population structure of sugarcane cultivars, progenitor species and genera using microsatellite (SSR) markers. Gene, 753, 144800.
Singh, R.B., Srivastava, S., Rastogi, J., Gupta, G.N., Tiwari, N.N., Singh, B. & Singh, R.K. (2014). Molecular markers exploited in crop improvement practices. Res Environ Life Sci, 7(4), 223- 232.
Singh, R.B., Srivastava, S., Verma, A.K., Singh, B. & Singh, R.K. (2014a). Importance and progresses of microsatellite markers in Sugarcane (Saccharum spp. hybrids). Indian J Sugarcane Technol, 29(01), 1-12.
Singh, S.P., Nigam, A. & Singh, R.K. (2015). Significant role of molecular markers in sugarcane improvement. Agrica, 4(2), 67-78.
Sloan, D.B. & Wu, Z.Q. (2014). History of plastid DNA insertions reveals weak deletion and AT mutation biases in angiosperm mitochondrial genomes. Genome Biol Evol, 6, 3210–3221.
Sloan, D.B., Warren, J.M., Williams, A.M., Wu, Z., Abdel-Ghany, S.E., Chicco, A.J. & Havird, J.C. (2018). Cytonuclear integration and co-evolution. Nat Rev Genet, 19, 635–648.
Smith, D.R. & Keeling, P.J. (2015). Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes. Proc Natl Acad Sci USA, 112, 10177–10184.
Sperisen, C., Buchler, U., Gugerli, F., Matyas, G., Geburek, T. & Vendramin, G.G. (2001). Tandem repeats in plant mitochondrial genomes: application to the analysis of population differentiation in the conifer Norway spruce. Mol Ecol, 10, 257-263.
Suhail, K.M., Yadava, S., Srivastava, S., Swapna, M., Chandra, A. & Singh, R.K. (2011). Development and Utilization of Conserved-Intron Scanning Marker in Sugarcane. Australian J Bot, 59, 38-45.
Tew, T.L. & Pan, Y.B. (2010). Microsatellite (Simple Sequence Repeat) Marker-Based Paternity Analysis of a Seven-Parent Sugarcane Polycross. Crop Sci, 50, 1401-1408.
Thakur, J., Dwivedi, M.D., Singh, N., Uniyal, P.L., Goel, S. & Pandey, A.K. (2021). Applicability of Start Codon Targeted (SCoT) and Inter Simple Sequence Repeat (ISSR) markers in assessing genetic diversity in Crepidium acuminatum (D. Don) Szlach. J Appl Res Medicinal and Aromatic Plants, 23(2021), 100310.
Thirugnanasambandam, P.P., Hoang, N.V. & Henry, R.J. (2018). The Challenge of Analyzing the Sugarcane Genome. Front Plant Sci, 9, 616.
Uzun, A., Yesiloglu, T., Aka-Kacar, Y., Tuzcu, O. & Gulsen, O. (2009). Genetic diversity and relationships within citrus and related genera based on sequence related amplified polymorphism markers (SRAPs). Sci Hort, 121(3), 306–312.
Van der Linden, C.G., Wouters, D., Mihalka, V., Kochieva, E.Z., Smulders, M.J.M. & Vosman, B. (2004). Efficient targeting of plant disease resistance loci using NBS profiling. Theor Appl Genet, 109(2), 384-393.
Varshney, R.K., Bohra, A., Yu, J., Graner, A., Zhang, Q. & Sorrells, M.E. (2021). Designing Future Crops: Genomics-Assisted Breeding Comes of Age. Trends in Pl Sci, 26(6), 631-649.
Varshney, R.K., Mahendar, T. & Aggarwal, R.K. (2007). Genic molecular markers in plants: development and applications. In: Genomic-assisted crop improvement: vol.1. genomics approaches and platforms. Varshney RK, Tuberosa R, editor, New York: Springer pp. 13–29.
Vieira, M.L., Santini, L., Diniz, A.L. & Munhoz Cde, F. (2016). Microsatellite markers: what they mean and why they are so useful. Genet Mol Biol, 39(3), 312-328.
Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J. & Kuiper, M. (1995). AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res, 23, 4407–4414.
Wang, D.G., Fan, J.B., Siao, C.J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spencer, J., Kruglyak, L., Stein, L., Hsie, L., Topaloglou, T., Hubbell, E., Robinson, E., Mittmann, M., Morris, M.S., Shen, N., Kilburn, D., Rioux, J., Nusbaum, C., Rozen, S., Hudson, T.J., Lipshutz, R., Chee, M. & Lander, E.S. (1998). Large-scale identification, mapping and genotyping of single-nucleotide polymorphisms in the human genome. Science, 280(5366), 1077-1082.
Wang, M.L., Barkley, N.A. & Jenkins, T.M. (2009). Microsatellite markers in plants and insects. Part I. Applications of biotechnology. Genes Genomes Genomics, 3, 54–67.
Wang, Q., Zhang, B. & Lu, Q. (2008). Conserved region amplification polymorphism (CoRAP), a novel marker technique for plant genotyping in Salvia miltiorrhiza. Plant Mol Biol Rep, 27, 139-143.
Waugh, R., McLean, K., Flavell, A.J., Pearce, S.R., Kumar, A., Thomas, B.B.T. & Powell W. (1997). Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence specific amplification polymorphisms (SSAP). Mol Genet Genomics, 253,687-694.
Weber, J.L. (1990). Informativeness of human (dC-dA)n(dGdT)n polymorphisms. Genomics, 7, 524–530.
Weining, S. & Langridge, P. (1991). Identification and mapping of polymorphisms in cereals based on the polymerase chain reaction. Theor Appl Genet, 82, 209–216.
Welsh, J. & Mc Clelland, M. (1990). Fingerprinting genomes using PCR with arbitrary primers. Nucl Acids Res, 18, 7213-7218.
Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A. & Tingey, S.V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl Acids Res, 18, 6531-6535.
Wright, J.M. & Bentzen, P. (1994). Microsatellites: Genetic markers for the future. Rev Fish Biol Fish, 4, 384–388.
Wu, K.S., Jones, R., Danneberger, L. & Scolnik, P.A. (1994). Detection of microsatellite polymorphisms without cloning. Nucleic Acids Res, 22(15), 3257–3258.
Wu, Q., Su, Y., Pan, Y.B., Xu, F., Zou, W., Que, B., Lin, P., Sun, T., Grisham, M.P., Xu, L. & Que, Y. (2022). Genetic identification of SNP markers and candidate genes associated with sugarcane smut resistance using BSR-Seq. Front Plant Sci, 13, 1035266.
Wu, Z.Q., Sloan, D.B., Brown, C.W., Rosenblueth, M., Palmer, J.D. & Ong, H.C. (2017). Mitochondrial retroprocessing promoted functional transfers of rpl5 to the nucleus in grasses. Mol Biol Evol, 34, 2340–2354.
Wyman, A.R. & White, R. (1980) A highly polymorphic locus in human DNA. Proceedings of the National Acad Sci, 77, 6754–6758.
Yuskianti, V. & Shiraishi, S. (2010). Sequence Characterized Amplified Region (SCAR) Markers in Sengon (Paraseriathes falcataria (L.) Nielsen. Hayati J Biosci, 17(4), 167-172.
Zeid, M., Yu, J.K., Goldowitz, I., Denton, M.E., Costich Denise, E., Jayasuriya, C.T., Saha, M., Elshire, R., Benscher, D., Breseghello, F., Munkvold, J., Varshney, R.K., Belay, G. & Sorrells, M.E. (2010). Cross-amplification of EST-derived markers among 16 grass species. Field Crops Res, 118(1), 28-35.
Zhang, H., Lin, P., Liu, Y., Huang, C., Huang, G., Jiang, H., Xu, L., Zhang, M., Deng, Z. & Zhao, X. (2022). Development of SLAF-Sequence and Multiplex SNaPshot Panels for Population Genetic Diversity Analysis and Construction of DNA Fingerprints for Sugarcane. Genes (Basel), 13(8), 1477.
Zhou, J., Zhang, S., Wang, J., Shen, H., Ai, B., Gao, W., Zhang, C., Fei, Q., Yuan, D., Wu, Z., Tembrock, L.R., Li, S., Gu, C. & Liao, X. (2021). Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution. Sci Rep, 11(1), 9471.
Zietkiewicz, E., Rafalski, A. & Labuda, D. (1994). Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics, 20, 176-183.
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Microsatellite markers for crop improvement: A review: Role of microsatellite markers. (2023). Journal of Applied and Natural Science, 15(3), 1018-1035. https://doi.org/10.31018/jans.v15i3.4615
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Microsatellite markers for crop improvement: A review: Role of microsatellite markers. (2023). Journal of Applied and Natural Science, 15(3), 1018-1035. https://doi.org/10.31018/jans.v15i3.4615