Abstract
Microsatellites are codominant molecular genetic markers, which are universally dispersed within genomes. These markers are highly popular because of their high level of polymorphism, relatively small size, and rapid detection protocols. They are widely used in a variety of fundamental and applied fields of biological sciences for plants and animal studies. Microsatellites are also extensively used in the field of agriculture, where they are used in characterizing genetic materials, plant selection, constructing dense linkage maps, mapping economically important quantitative traits, identifying genes responsible for these traits. In addition microsatellites are used for marker-assisted selection in breeding programs, thus speeding up the process. In this chapter, genomic distribution, evolution, and practical applications of microsatellites are considered, with special emphasis on plant breeding and agriculture. Moreover, novel advances in microsatellite technologies are also discussed.
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References
Armour J et al (1999) Minisatellites and mutation processes in tandemly repetitive DNA. Oxford University Press, Oxford
Hancock JM (1999) Microsatellites and other simple sequences: genomic context and mutational mechanisms. Oxford University Press, Oxford
Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44:397–401
Tautz D (1989) Hypervariabflity of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471
McDonald DB, Potts WK (1997) DNA microsatellites as genetic markers for several scales. Academic, New York
Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127–4138
Goldstein DB, Pollock DD (1997) Launching microsatellites: a review of mutation processes and methods of phylogenetic inference. J Hered 88:335–342
Schlötterer C (1998) Microsatellites. IRL, Oxford
Queller DC et al (1993) Microsatellites and kinship. Trends Ecol Evol 8:285–288
Sonah H et al (2011) Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium. PLoS One 6:e21298
Kelkar YD et al (2011) A matter of life or death: how microsatellites emerge in and vanish from the human genome. Genome Res 21:2038–2048
Nadir E et al (1996) Microsatellite spreading in the human genome: evolutionary mechanisms and structural implications. Proc Natl Acad Sci 93:6470–6475
Morgante M et al (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200
Temnykh S et al (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452
Weber J, May P (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388–396
Milbourne D et al (1998) Isolation, characterisation and mapping of simple sequence repeat loci in potato. Mol Gen Genet 259:233–245
Sharopova N et al (2002) Development and mapping of SSR markers for maize. Plant Mol Biol 48:463–481
Song QJ et al (2002) Characterization of trinucleotide SSR motifs in wheat. Theor Appl Genet 104:286–293
Temnykh S et al (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712
Crow J (1993) How much do we know about spontaneous human mutation rates? Environ Mol Mutagen 21:122–129
Zhu Y et al (2000) A phylogenetic perspective on sequence evolution in microsatellite loci. J Mol Evol 50:324–338
Ellegren H (2000) Microsatellite mutations in the germline: implications for evolutionary inference. Trends Genet 16:551–558
Jin L et al (1996) Mutation rate varies among alleles at a microsatellite locus:Phylogenetic evidence. Proc Natl Acad Sci 93:15285–15288
Tachida H, Iizuka M (1992) Persistence of repeated sequences that evolve by replication slippage. Genetics 131:471–478
Tautz D, Schlötterer C (1994) Simple sequences. Curr Opin Genet Dev 4:832–837
Weber JL, Wong C (1993) Mutation of human short tandem repeats. Hum Mol Genet 2:1123–1128
Harding RM et al (1992) The evolution of tandemly repetitive DNA: recombination rules. Genetics 132:847–859
Levinson G, Gutman GA (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4:203–221
Eisen J (1999) Mechanistic basis for microsatellite instability. Oxford University Press, Oxford
Brohede J, Ellegren H (1999) Microsatellite evolution: polarity of substitutions within repeats and neutrality of flanking sequences. Proc Biol Sci 266:825–833
Goldstein D, Schlotterer C (1999) Microsatellites, evolution and applications. Oxford University Press, Oxford
Jakupciak JP, Wells RD (1999) Genetic instabilities in (CTGΒ  ·  CAG) repeats occur by recombination. J Biol Chem 274:23468–23479
Richard GF, Paques F (2000) Mini- and microsatellite expansions: the recombination connection. EMBO Rep 1:122–126
Charlesworth B et al (1994) The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371:215–220
Bruford M et al (1996) Microsatellites and their application to conservation genetics. Oxford University Press, Oxford
Kostia S et al (1995) Microsatellite sequences in a conifer, Pinus sylvestris. Genome 38:1244–1248
Röder MS et al (1995) Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet 246:327–333
Smith DN, Devey ME (1994) Occurrence and inheritance of microsatellites in Pinus radiata. Genome 37:977–983
Gupta PK et al (1999) Molecular markers and their applications in wheat breeding. Plant Breed 118:369–390
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome Nature 436:793–800
Jarne P, Lagoda PJL (1996) Microsatellites, from molecules to populations and back. Trends Ecol Evol 11:424–429
Eujayl I et al (2004) Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theor Appl Genet 108:414–422
Hackauf B, Wehling P (2002) Identification of microsatellite polymorphisms in an expressed portion of the rye genome. Plant Breed 121:17–25
Thiel TT et al (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare). Theor Appl Genet 106:411–422
Chapman M et al (2009) Development, polymorphism, and cross-taxon utility of EST–SSR markers from safflower (Carthamus tinctorius L.). Theor Appl Genet 120:85–91
Choudhary S et al (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor Appl Genet 118:591–608
Gadaleta A et al (2010) Development and characterization of EST-derived SSRs from a ‘totipotent’ cDNA library of durum wheat. Plant Breed 129:715–717
Nunome T et al (2009) Development of SSR markers derived from SSR-enriched genomic library of eggplant (Solanum melongena L.). Theor Appl Genet 119:1143–1153
Wei W et al (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 12:451
Chabane K et al (2005) EST versus genomic derived microsatellite markers for genotyping wild and cultivated barley. Genet Resour Crop Evol 52:903–909
Cho YG et al (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722
Eujayl I et al (2001) Assessment of genotypic variation among cultivated durum wheat based on EST-SSRS and genomic SSRS. Euphytica 119:39–43
Scott KD et al (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726
Gupta PK et al (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics 270:315–323
Wilhelm J et al (2003) Validation of an algorithm for automatic quantification of nucleic acid copy numbers by real-time polymerase chain reaction. Anal Biochem 317:218–225
Wittwer CT (2009) High-resolution DNA melting analysis: advancements and limitations. Hum Mutat 30:857–859
Vossen RHAM et al (2009) High-resolution melting analysis (HRMA)—more than just sequence variant screening. Hum Mutat 30:860–866
Wittwer CT et al (2003) High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem 49:853–860
Stephens AJ et al (2008) High-resolution melting analysis of the spa repeat region of Staphylococcus aureus. Clin Chem 54:432–436
Tindall EA et al (2009) Assessing high-resolution melt curve analysis for accurate detection of gene variants in complex DNA fragments. Hum Mutat 30:876–883
Mackay JF et al (2008) A new approach to varietal identification in plants by microsatellite high resolution melting analysis: application to the verification of grapevine and olive cultivars. Plant Meth 4:8
Wu SB et al (2008) High resolution melting analysis of almond SNPs derived from ESTs. Theor Appl Genet 118:1–14
Reed GH, Wittwer CT (2004) Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin Chem 50:1748–1754
Smith BL et al (2010) High-resolution melting analysis (HRMA): a highly sensitive inexpensive genotyping alternative for population studies. Mol Ecol Resour 10:193–196
Bosmali I et al (2012) Microsatellite and DNA-barcode regions typing combined with high resolution melting (HRM) analysis for food forensic uses: a case study on lentils (Lens culinaris). Food Res Int 46:141–147
Ganopoulos I et al (2011) Adulterations in Basmati rice detected quantitatively by combined use of microsatellite and fragrance typing with high resolution melting (HRM) analysis. Food Chem 129:652–659
Ganopoulos I et al (2011) Microsatellite high resolution melting (SSR-HRM) analysis for authenticity testing of protected designation of origin (PDO) sweet cherry products. Food Contr 22:532–541
Ganopoulos I et al (2012) Microsatellite genotyping with HRM (high resolution melting) analysis for identification of the PGI common bean variety Plake Megalosperma Prespon. Eur Food Res Tech 234:501–508
Mader E et al (2008) A strategy to setup codominant microsatellite analysis for high-resolution-melting-curve-analysis (HRM). BMC Genet 9:69
Reed GH et al (2007) High-resolution DNA melting analysis for simple and efficient molecular diagnostics. Pharmacogenomics 8:597–608
Powell W et al (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238
Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185
Joshi SP et al (1999) Molecular markers in plant genome analysis. Curr Sci 77:230–240
Provan J et al (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 16:142–147
Neeraja C et al (2007) A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor Appl Genet 115:767–776
Kalia R et al (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334
Wang M et al (2009) Microsatellite markers in plants and insects. Part I: applications of Âbiotechnology. Genes Genomes Genomics 3:54–67
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Madesis, P., Ganopoulos, I., Tsaftaris, A. (2013). Microsatellites: Evolution and Contribution. In: Kantartzi, S. (eds) Microsatellites. Methods in Molecular Biology, vol 1006. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-389-3_1
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DOI: https://doi.org/10.1007/978-1-62703-389-3_1
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