Derived Polymorphic Amplified Cleaved Sequence (dPACS) Assay.
Amaranthus retroflexus
Derived polymorphic amplified cleaved sequence
Genotyping
INDELs
PCR-RFLP
SNPs
dPACS
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2023
2023
Historique:
entrez:
13
2
2023
pubmed:
14
2
2023
medline:
16
2
2023
Statut:
ppublish
Résumé
The derived polymorphic amplified cleaved sequence (dPACS) assay is a simple polymerase chain reaction/restriction fragment length polymorphism (PCR-RFLP)-based procedure for detecting known single-nucleotide polymorphisms (SNPs) and deletion-insertion polymorphisms (DIPs). It is relatively straightforward to carry out using basic and commonly available molecular biology kits. The method differs from other PCR-RFLP assays in that it employs 35-55 bp primer pairs that encompass the entire targeted DNA region except for a few diagnostic nucleotides being examined. In so doing, it allows for the introduction of nucleotide mismatches in one or both primers for differentiating wild from mutant sequences following polymerase chain reaction, restriction digestion and MetaPhor gel electrophoresis. Primer design and the selection of discriminating enzymes are achieved with the help of the dPACS 1.0 program. The method is exemplified here with the positive detection of serine 264-psbA, a key determinant for the effective binding of some photosystem II inhibitors to their target. A serine-to-glycine mutation at codon 264 of psbA causes resistance to serine-binding photosystem II herbicides in several grasses and broad-leaf weeds, including Amaranthus retroflexus, which is employed in this study.
Identifiants
pubmed: 36781657
doi: 10.1007/978-1-0716-3024-2_27
doi:
Substances chimiques
Photosystem II Protein Complex
0
Codon
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
373-385Informations de copyright
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Brookes AJ (1999) The essence of SNPs. Gene 234:177–186. https://doi.org/10.1016/s0378-1119(99)00219-x
doi: 10.1016/s0378-1119(99)00219-x
Montgomery S, Goode D, Kvikstad E, Albers C, Zhang Z, Mu X et al (2013) The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Res 23:749–761. https://doi.org/10.1101/gr.148718.112
doi: 10.1101/gr.148718.112
Wang L, Guo W, Fang C, Feng W, Huang Y, Zhang X et al (2021) Functional characterization of a loss-of-function mutant I324M of arginine vasopressin receptor 2 in X-linked nephrogenic diabetes insipidus. Sci Rep 11:11057. https://doi.org/10.1038/s41598-021-90736-z
doi: 10.1038/s41598-021-90736-z
Safi A, Medici A, Szponarski W, Martin F, Clément-Vidal A, Marshall-Colon A et al (2021) GARP transcription factors repress Arabidopsis nitrogen starvation response via ROS-dependent and -independent pathways. J Exp Bot 72:3881–3901. https://doi.org/10.1093/jxb/erab114
doi: 10.1093/jxb/erab114
Veitia RA (2022) Who ever thought genetic mutations were random? Trends Plant Sci 27:733–735. https://doi.org/10.1016/j.tplants.2022.03.003
doi: 10.1016/j.tplants.2022.03.003
Teumer A, Ernst FD, Wiechert A, Uhr K, Nauck M, Petersmann A et al (2013) Comparison of genotyping using pooled DNA samples (allelotyping) and individual genotyping using the affymetrix genome-wide human SNP array 6.0. BMC Genomics 14:506. https://doi.org/10.1186/1471-2164-14-506
doi: 10.1186/1471-2164-14-506
Hidaka A, Sasazuki S, Matsuo K, Ito H, Charvat H, Sawada N et al (2016) CYP1A1, GSTM1 and GSTT1 genetic polymorphisms and gastric cancer risk among Japanese: a nested case–control study within a large-scale population-based prospective study. Int J Cancer 139:759–768. https://doi.org/10.1002/ijc.30130
doi: 10.1002/ijc.30130
Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14. https://doi.org/10.1007/s11032-013-9917-x
doi: 10.1007/s11032-013-9917-x
Arita H, Narita Y, Matsushita Y, Fukushima S, Yoshida A, Takami H et al (2015) Development of a robust and sensitive pyrosequencing assay for the detection of IDH1/2 mutations in gliomas. Brain Tumor Pathol 32:22–30. https://doi.org/10.1007/s10014-014-0186-0
doi: 10.1007/s10014-014-0186-0
Li F, Henderson G, Sun X, Cox F, Janssen PH, Guan LL (2016) Taxonomic assessment of rumen microbiota using total RNA and targeted amplicon sequencing approaches. Front Microbiol 7:987. https://doi.org/10.3389/fmicb.2016.00987
doi: 10.3389/fmicb.2016.00987
Griffin TJ, Smith LM (2000) Single-nucleotide polymorphism analysis by MALDI–TOF mass spectrometry. Trends Biotechnol 18:77–84. https://doi.org/10.1016/s0167-7799(99)01401-8
doi: 10.1016/s0167-7799(99)01401-8
Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L et al (2016) The real cost of sequencing: scaling computation to keep pace with data generation. Genome Biol 17:53. https://doi.org/10.1186/s13059-016-0917-0
doi: 10.1186/s13059-016-0917-0
Neff MM, Neff JD, Chory J, Pepper AE (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidposis thaliana genetics. Plant J 14:387–392. https://doi.org/10.1046/j.1365-313x.1998.00124.x
doi: 10.1046/j.1365-313x.1998.00124.x
Ota M, Asamura H, Oki T, Sada M (2009) Restriction enzyme analysis of PCR products. In: Komar AA (ed) Single nucleotide polymorphisms: methods and protocols. Humana, Totowa, pp 405–414. https://doi.org/10.1007/978-1-60327-411-1_25
doi: 10.1007/978-1-60327-411-1_25
Bottema C, Sommer S (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
doi: 10.1016/0027-5107(93)90211-w
Kaundun SS, Hutchings SJ, Marchegiani E, Rauser R, Jackson LV (2020) A derived Polymorphic Amplified Cleaved Sequence assay for detecting the Δ210 PPX2L codon deletion conferring target-site resistance to protoporphyrinogen oxidase-inhibiting herbicides. Pest Manag Sci 76:789–796. https://doi.org/10.1002/ps.5581
doi: 10.1002/ps.5581
Kaundun SS, Marchegiani E, Hutchings SJ, Baker K (2019) Derived polymorphic amplified cleaved sequence (dPACS): a novel PCR-RFLP procedure for detecting known single nucleotide and deletion-insertion polymorphisms. Int J Mol Sci 20:3193. https://doi.org/10.3390/ijms20133193
doi: 10.3390/ijms20133193
Rogers SO, Bendich AJ (1989) Extraction of DNA from plant tissues. In: Gelvin SB, Schilperoort RA, Verma DPS (eds) Plant molecular biology manual. Springer, Dordrecht, pp 73–83. https://doi.org/10.1007/978-94-009-0951-9_6
doi: 10.1007/978-94-009-0951-9_6
Otto P (2002) MagneSil™ paramagnetic particles: magnetics for DNA purification. JALA: J Assoc Lab Autom 7:34–37. https://doi.org/10.1016/S1535-5535-04-00191-1
doi: 10.1016/S1535-5535-04-00191-1
Green MR, Sambrook J (2018) Hot start polymerase chain reaction (PCR). Cold Spring Harb Protoc 5:pdb.prot095125. https://doi.org/10.1101/pdb.prot095125
doi: 10.1101/pdb.prot095125
Kaundun SS, Downes J, Jackson LV, Hutchings SJ, Mcindoe E (2021) Impact of a novel W2027L mutation and non-target site resistance on acetyl-coA carboxylase-inhibiting herbicides in a French Lolium multiflorum population. Genes 12:1838. https://doi.org/10.3390/genes12111838
doi: 10.3390/genes12111838