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Simple Sequence Repeats Amplification

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Microsatellites

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1006))

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Abstract

The technique of SSR amplification is a prerequisite to generate the molecular profiles of various alleles of an individual or genotype. Amplification is the multifold duplication and accumulation of a targeted region which is achieved by polymerase chain reaction. It needs ingredients such as buffer, MgCl2, dNTPs, primers, and DNA polymerase enzyme. The utilization of these essential PCR components in optimal concentrations determines the success of amplification. Thus SSRs, as primers, play an important role in enhancing the amplification and thereby generating the genotype profile. With the advent of technology, fluorophore-labeled primers along with automated capillary electrophoresis system have enhanced the efficiency of detection.

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References

  1. Rajwant KK, Manoj KR, Sanjay K, Rohtas S, Dhawan AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334

    Article  Google Scholar 

  2. Parida SK, Kalia SK, Sunita K, Dalal V, Hemaprabha G, Selvi A, Pandit A, Singh A, Gaikwad K, Sharma TR, Srivastava PS, Singh NK, Mohapatra T (2009) Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theor Appl Genet 118:327–338

    Article  PubMed  CAS  Google Scholar 

  3. Ravishankar KV, Mani BH, Anand L, Dinesh MR (2011) Development of new microsatellite markers from Mango (Mangifera indica) and cross-species amplification. Am J Bot 98:e96–e99. doi:10.3732/ajb.1000263

    Article  PubMed  Google Scholar 

  4. Narina SS, d’Orgeix CA, Sayre BL (2011) Optimization of PCR conditions to amplify microsatellite loci in the bunchgrass lizard (Sceloporus slevini) genomic DNA. BMC Res Notes 4:26. doi:10.1186/1756-0500-4-26

    Article  PubMed  CAS  Google Scholar 

  5. Mishra MK, Patrizia T, De Barbara N, Elisa A, René D, Lorenzo DT, Rajkumar R, Paola R, Alberto P, Giorgio G (2011) Genome organization in coffee as revealed by EST PCRRFLP, SNPs and SSR analysis. J Crop Sci Biotech 14:25–37

    Article  Google Scholar 

  6. Wang H, Huan P, Xia L, Baozhong L (2011) Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome. Genes Genet Syst 86:197–205

    Article  PubMed  CAS  Google Scholar 

  7. Blair MW, Hurtado N, Chavarro CM, Monica CM, Martha CG, Fabio P, Jeff T, Wing R (2011) Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series. BMC Plant Biol 11:50

    Article  PubMed  CAS  Google Scholar 

  8. Risterucci AM, Duval MF, Rohde W, Billotte N (2005) Isolation and characterization of microsatellite loci from Psidium guajava L. Mol Ecol Notes 5:745–748

    Article  CAS  Google Scholar 

  9. Schuelke M (2000) An economic method for fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234

    Article  PubMed  CAS  Google Scholar 

  10. Guichoux E, Lagache L, Wagner S, Chaumeil P, Leger P, Lepais O, Lepoittevin C, Malausa T, Revardel E, Salin F, Petit RJ (2011) Current trends in microsatellite genotyping. Mol Ecol Res 11:591–611

    Article  CAS  Google Scholar 

  11. Livingstone D et al (2009) Improvement of highthroughput genotype analysis after implementation of a dual-curve Sybr Green I-based quantification and normalization procedure. Hort Sci 44:1228–1232

    Google Scholar 

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Ravishankar, K.V., Bommisetty, P. (2013). Simple Sequence Repeats Amplification. 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_9

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  • DOI: https://doi.org/10.1007/978-1-62703-389-3_9

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-388-6

  • Online ISBN: 978-1-62703-389-3

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