Skip to main content
SpringerLink
Log in

Allele-Specific Mutation Genotyping with Mismatches in Primer Design

  • Protocol
  • First Online:
Plant Genotyping

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2638))

  • 1042 Accesses

Abstract

Genotyping technologies for single nucleotide polymorphisms (SNPs) and other mutation types have evolved to become essential tools in various fields. Although high-throughput genotyping technologies occupy a key position in handling large amounts of SNP data, simple, low-cost, and conventional genotyping technologies remain in demand. Allele-specific (AS) polymerase chain reaction (PCR) and its related improved methods can effectively identify target SNPs and allele types using AS primers that introduce instability through mismatched bases at and around the SNP site. In this chapter, we present what is known from the literature on primer design with mismatches for AS-PCR and describe three cases of mutation detection (SNPs and insertions/deletions) associated with functional genes of crop species, which could be useful to guide future AS-PCR experiments.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Schramm C, Shavrukov Y, Anderson P, Kurishbaev A, Jatayev S (2019) Development of single nucleotide polymorphism (SNP) markers for cereal breeding and crop research: current methods and future prospects. In: Ordon F, Friedt W (eds) Advances in breeding techniques for cereal crops. BD Publishing, Cambridge, pp 327–362. https://doi.org/10.19103/AS.2019.0051.16

    Chapter  Google Scholar 

  2. Morgil H, Gercek YC, Tulum I (2020) Single nucleotide polymorphisms (SNPs) in plant genetics and breeding. In: Çalişkan M (ed) The recent topics in genetic polymorphisms. InTech Open, London, pp 825–400. https://doi.org/10.5772/intechopen.91886

    Chapter  Google Scholar 

  3. Ugozzoli L, Yam P, Petz LD, Ferrara GB, Champlin RE, Forman SJ et al (1991) Amplification by the polymerase chain reaction of hypervariable regions of the human genome for evaluation of chimerism after bone marrow transplantation. Blood 77:1607–1615. https://doi.org/10.1182/blood.v77.7.1607.1607

    Article  CAS  Google Scholar 

  4. Bottema CD, Sommer SS (1993) PCR amplification of specific alleles: rapid detection of known mutations and polymorphisms. Mutat Res 288:93–102. https://doi.org/10.1016/0027-5107(93)90211-W

    Article  CAS  Google Scholar 

  5. Sommer SS, Groszbach AR, Bottema CD (1992) PCR amplification of specific alleles (PASA) is a general method for rapidly detecting known single-base changes. BioTechniques 12:82–87

    Google Scholar 

  6. Sarkar G, Cassady J, Bottema CDK, Sommer SS (1990) Characterization of polymerase chain reaction amplification of specific alleles. Anal Biochem 186:64–68. https://doi.org/10.1016/0003-2697(90)90573-R

    Article  CAS  Google Scholar 

  7. Wu DY, Ugozzoli L, Pal BK, Wallace RB (1989) Allele-specific enzymatic amplification of β-globin genomic DNA for diagnosis of sickle cell anemia. Proc Natl Acad Sci U S A 86:2757–2760. https://doi.org/10.1073/pnas.86.8.2757

    Article  CAS  Google Scholar 

  8. Newton CR, Heptinstall LE, Summers C, Super M, Schwarz M, Anwar R et al (1989) Amplification refractory mutation system for prenatal diagnosis and carrier assessment in cystic fibrosis. Lancet 334:1481–1483. https://doi.org/10.1016/S0140-6736(89)92931-0

    Article  Google Scholar 

  9. Liu J, Huang S, Sun M, Liu S, Liu Y, Wang W et al (2012) An improved allele-specific PCR primer design method for SNP marker analysis and its application. Plant Methods 8:34. https://doi.org/10.1186/1746-4811-8-34

    Article  CAS  Google Scholar 

  10. Bru D, Martin-Laurent F, Philippot L (2008) Quantification of the detrimental effect of a single primer-template mismatch by real-time PCR using the 16S rRNA gene as an example. Appl Environ Microbiol 74:1660–1663. https://doi.org/10.1128/AEM.02403-07

    Article  CAS  Google Scholar 

  11. Cha RS, Zarbl H, Keohavong P, Thilly WG (1992) Mismatch amplification mutation assay (MAMA): application to the c-H-ras gene. Genome Res 2:14–20. https://doi.org/10.1101/gr.2.1.14

    Article  CAS  Google Scholar 

  12. Kwok S, Chang SY, Sninsky JJ, Wang A (1994) A guide to the design and use of mismatched and degenerate primers. Genome Res 3:539–547. https://doi.org/10.1101/gr.3.4.S39

    Article  Google Scholar 

  13. Fogle HW (1958) Inheritance of fruit color in sweet cherries (Prunus avium). J Hered 49:294–298. https://doi.org/10.1093/oxfordjournals.jhered.a106830

    Article  Google Scholar 

  14. Schmidt H (1998) On the genetics of fruit colour in sweet cherries. Acta Hortic 468:77–81. https://doi.org/10.17660/actahortic.1998.468.6

    Article  Google Scholar 

  15. Sooriyapathirana SS, Khan A, Sebolt AM, Wang D, Bushakra JM, Lin-Wang K et al (2010) QTL analysis and candidate gene mapping for skin and flesh color in sweet cherry fruit (Prunus avium L.). Tree Genet Genomes 6:821–832. https://doi.org/10.1007/s11295-010-0294-x

    Article  Google Scholar 

  16. Saito Y, Adachi E, Isuzugawa K, Kurosaka S, Takashina T (2017) Development of DNA marker for flesh color derived from sweet cherry (Prunus avium L.) cultivar ‘Benisayaka’. Bull Yamagata Pref Agric Res 9:33–41

    Google Scholar 

  17. Saito Y, Adachi E, Isuzugawa K, Shirasawa K, Ikenaga M, Sato H (2017) Development of DNA marker for distinguishing flesh colour in sweet cherry (Prunus avium L.). Acta Hortic 1235:15–25. https://doi.org/10.17660/ActaHortic.2019.1235.2

    Article  Google Scholar 

  18. Hayashi K, Hashimoto N, Daigen M, Ashikawa I (2004) Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theor Appl Genet 108:1212–1220. https://doi.org/10.1007/s00122-003-1553-0

    Article  CAS  Google Scholar 

  19. Mori K, Shirasawa K, Nogata H, Hirata C, Tashiro K, Habu T et al (2017) Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.). Sci Rep 7:41124. https://doi.org/10.1038/srep41124

    Article  CAS  Google Scholar 

  20. Takahashi Y, Yamamoto T, Adachi E, Ikeda K, Sato Y, Noguchi K (2018) Development of self-incompatibility (S) alleles identification methods and S genotyping in sweet cherry (Prunus avium L.) cultivars. Bull Agric Res Yamagata Prefect 10:15–27

    Google Scholar 

  21. Ikeda K, Watari A, Ushijima K, Yamane H, Hauck NR, Iezzoni AF et al (2004) Molecular markers for the self-compatible S4′-haplotype, a pollen-part mutant in sweet cherry (Prunus avium L.). J Am Soc Hortic Sci 129:724–728. https://doi.org/10.21273/jashs.129.5.0724

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Yamagata Integrated Agricultural Research Center, Horticultural Research Institute, Yamagata, Japan

    Yutaro Saito, Fumito Tada & Tadashi Takashina

  2. Fukuoka Agriculture and Forestry Research Center, Buzen Branch, Yukuhashi, Japan

    Hidetoshi Ikegami

Authors
  1. Yutaro Saito
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Fumito Tada
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tadashi Takashina
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hidetoshi Ikegami
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hidetoshi Ikegami .

Editor information

Editors and Affiliations

  1. College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia

    Yuri Shavrukov

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Saito, Y., Tada, F., Takashina, T., Ikegami, H. (2023). Allele-Specific Mutation Genotyping with Mismatches in Primer Design. In: Shavrukov, Y. (eds) Plant Genotyping. Methods in Molecular Biology, vol 2638. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3024-2_17

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-3024-2_17

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3023-5

  • Online ISBN: 978-1-0716-3024-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation