The use of TaqMan® and tetra-primer ARMS-PCR genotyping techniques for identification of single nucleotide polymorphisms associated with genetic determinants of root shape of carrot
Katarzyna Stelmach
*@ibr-urk.plZakład Genetyki, Hodowli Roślin i Nasiennictwa, Instytut Biologii Roślin i Biotechnologii i Ogrodnictwa Uniwersytet Rolniczy w Krakowie (Poland)
Alicja Macko-Podgórni
Zakład Genetyki, Hodowli Roślin i Nasiennictwa, Instytut Biologii Roślin i Biotechnologii i Ogrodnictwa Uniwersytet Rolniczy w Krakowie (Poland)
Rafał Barański
Zakład Genetyki, Hodowli Roślin i Nasiennictwa, Instytut Biologii Roślin i Biotechnologii i Ogrodnictwa Uniwersytet Rolniczy w Krakowie (Poland)
Dariusz Grzebelus
Zakład Genetyki, Hodowli Roślin i Nasiennictwa, Instytut Biologii Roślin i Biotechnologii i Ogrodnictwa Uniwersytet Rolniczy w Krakowie (Poland)
Abstract
Over the last two decades a significant increase has been observed in the pace of development of diverse systems of molecular markers and the corresponding advanced detection platforms. Owing to their ubiquity in genomes, markers based on single nucleotide polymorphism (SNP) promptly gained recognition within research on molecular breeding of plants. Amongst the most widely used genotyping techniques of a single nucleotide polymorphisms are the TaqMan® probes, DNA micro-arrays and the genotyping-by-sequencing (GBS) technology. Techniques based on standard polymerase chain reaction with the use of modified primers, including the tetra-primer ARMS-PCR technique, have also been devised with in order to decrease the costs of genotyping. The current work identifies five SNP markers associated with genetic determinants of the shape of carrot taproot and converts them into markers detectable by the TaqMan® and tetra-primer ARMS-PCR technologies. The usefulness of the above techniques has been verified by genotyping 40 selected cultivars of Western-type carrot. The present authors have also analysed the convergence of the results obtained through the mentioned techniques and a GBS reference method. The techniques have been evaluated in terms of their usefulness for designing reliable specific markers associated with genetic determinants of the shape of the carrot root.
Supporting Agencies
Keywords:
ARMS-PCR, GWAS, carrot, MLNReferences
Armstrong R. A. 2014. When to use the Bonferroni correction. Ophthalmic Physiol. Opt. 34: 502 — 508. DOI:10.1111/opo.12131.
Google Scholar
Banga O. 1963. Origin and distribution of the western cultivated carrot. Genet. Agrar. Period. di Genet. Appl. all’ Agric. 17: 357 — 370.
Google Scholar
Baris I., Etlik O., Koksal V., Arican-Baris S. T. 2010. Rapid diagnosis of spinal muscular atrophy using tetra-primer ARMS PCR assay: Simultaneous detection of SMN1 and SMN2 deletion. DOI:10.1016/j.mcp.2009.12.001. Mol. Cell. Probes 24: 138 — 141.
Google Scholar
Brachi, B., Morris, G. P., Borevitz, J. O. 2011. Genome-wide association studies in plants: the missing heritability is in the field. . DOI:10.1186/gb-2011-12-10-232. Genome Biol. 12: 232.
Google Scholar
Campsall P. A., Au, N. H. C., Prendiville J. S., Speert, D. P., Tan R., Thomas E. E. 2004. Detection and genotyping of varicella-zoster virus by TaqMan allelic discrimination real-time PCR. J. Clin. Microbiol. 42: 1409 — 13. Available at: http://www.ncbi.nlm.nih.gov/pubmed/15070981 [Accessed November 1, 2016].
Google Scholar
Chiapparino E., Lee, D., Donini P. 2004. Genotyping single nucleotide polymorphisms in barley by tetra-primer ARMS–PCR. Genome 47: 414 — 420. Available at: http://www.nrcresearchpress.com/doi/abs/ 10.1139/g03-130#.VzL8g-Qvtng [Accessed May 11, 2016].
Google Scholar
Dry P. 1991. Rapid detection of alpha-1-antitrypsin deficiency by analysis of a PCR-induced TaqI restriction site. DOI:10.1007/BF00201739. Hum. Genet. 87: 742–744.
Google Scholar
Giancola S., McKhann H. I., Bérard A., Camilleri C., Durand S., Libeau P., et al. 2006. Utilization of the three high-throughput SNP genotyping methods, the GOOD assay, Amplifluor and TaqMan, in diploid and polyploid plants. DOI:10.1007/s00122-006-0213-6. Theor. Appl. Genet. 112: 1115 — 1124.
Google Scholar
Holland P. M., Abramson R. D., Watson R., Gelfand D. H. 1991. Detection of specific polymerase chain reaction product by utilizing the 5’----3’ exonuclease activity of Thermus aquaticus DNA polymerase. DOI:10.1073/PNAS.88.16.7276. Proc. Natl. Acad. Sci. U. S. A. 88: 7276 — 7280.
Google Scholar
Huang T., Zhuge J., Zhang W. W. 2013. Sensitive detection of BRAF V600E mutation by Amplification Refractory Mutation System (ARMS)-PCR. DOI:10.1186/2050-7771-1-3. Biomark. Res. 1: 3.
Google Scholar
Iorizzo M., Senalik D. A., Ellison S. L., Grzebelus D., Cavagnaro P. F., Allender C., Brunet J., Spooner D., van Deznye A., Simon P. W. 2013. Genetic structure and domestication of carrot (Daucus carota subsp. sativus) (Apiaceae). DOI:10.3732/ajb.1300055. Am. J. Bot. 100: 930 — 938.
Google Scholar
Korte A., Farlow A. 2013. The advantages and limitations of trait analysis with GWAS: a review. DOI:10.1186/1746-4811-9-29. Plant Methods 9: 29.
Google Scholar
Lindh M., Hannoun C. 2005. Genotyping of hepatitis C virus by Taqman real-time PCR. DOI:10.1016/j.jcv.2005.02.002. J. Clin. Virol. 34: 108 — 114.
Google Scholar
Liu Q., Thorland E. C., Heit J. A., Sommer S. S. 1997. Overlapping PCR for bidirectional PCR amplification of specific alleles: a rapid one-tube method for simultaneously differentiating homozygotes and heterozygotes. Available at: http://www.ncbi.nlm.nih.gov/pubmed/9110178 [Accessed October 30, 2016]. Genome Res. 7: 389 — 398.
Google Scholar
Mammadov J., Aggarwal R., Buyyarapu R., Kumpatla S. 2012. SNP markers and their impact on plant breeding. DOI:10.1155/2012/728398. Int. J. Plant Genomics 72: 83 — 98.
Google Scholar
Medrano R. F. V., de Oliveira C. A. 2014. Guidelines for the tetra-primer ARMS-PCR technique development. DOI:10.1007/s12033-014-9734-4. Mol. Biotechnol. 56: 599 — 608.
Google Scholar
Newton C. R., Graham A., Heptinstall L. E., Powell S. J., Summers C., Kalsheker N., Smith J., Markham A. 1989. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). DOI:10.1093/nar/17.7.2503. Nucleic Acids Res. 17: 2503 — 2516.
Google Scholar
Rubatzky V. E., Quiros C. F., Simon P. W. 1999. Carrots and related vegetable Umbelliferae. CAB International, Wallingford.
Google Scholar
Rubio M., Caranta C., Palloix A. 2008. Functional markers for selection of potyvirus resistance alleles at the pvr2-eIF4E locus in pepper using tetra-primer ARMS-PCR. DOI:10.1139/G08-056. Genome 51: 767 — 771.
Google Scholar
Stolarczyk J., Janick J. 2011. Carrot: History and Iconography. Available at: http://www.hort.purdue.edu /newcrop/pdfs/ch5102-carrot.pdf. Chron. Horticult. 51: 12 — 18.
Google Scholar
Vannucchi A. M., Pancrazzi A., Bogani C., Antonioli E., Guglielmelli P. 2006. A quantitative assay for JAK2V617F mutation in myeloproliferative disorders by ARMS-PCR and capillary electrophoresis. DOI:10.1038/sj.leu.2404209. Leukemia 20: 1055 — 1060.
Google Scholar
Wittwer C. T., Reed G. H., Gundry C. N., Vandersteen J. G., Pryor R. J. 2003. High-resolution genotyping by amplicon melting analysis using LCGreen. DOI:10.1373/49.6.853. Clin. Chem. 49: 853 — 860.
Google Scholar
Ye S., Dhillon S., Ke X., Collins A. R., Day I. N. M. 2001. An efficient procedure for genotyping single nucleotide polymorphisms. DOI:10.1093/nar/29.17.e88. Nucleic Acids Res. 29: 88e — 88.
Google Scholar
Yu J., Pressoir G., Briggs W. H., Vroh Bi I., Yamasaki M., Doebley J. F. et al. 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. DOI:10.1038/ng1702. Nat. Genet. 38: 203 — 208.
Google Scholar
Zhang Z., Ersoz E., Lai C.-Q., Todhunter R. J., Tiwari H. K., Gore M. A., Bradbury P. J., Yu J., Armett D. K., Ordovas J. M., Buckler E. S. 2010. Mixed linear model approach adapted for genome-wide association studies. DOI:10.1038/ng.546. Nat. Genet. 42: 355 — 360.
Google Scholar
Authors
Katarzyna Stelmach*@ibr-urk.pl
Zakład Genetyki, Hodowli Roślin i Nasiennictwa, Instytut Biologii Roślin i Biotechnologii i Ogrodnictwa Uniwersytet Rolniczy w Krakowie Poland
Authors
Alicja Macko-PodgórniZakład Genetyki, Hodowli Roślin i Nasiennictwa, Instytut Biologii Roślin i Biotechnologii i Ogrodnictwa Uniwersytet Rolniczy w Krakowie Poland
Authors
Rafał BarańskiZakład Genetyki, Hodowli Roślin i Nasiennictwa, Instytut Biologii Roślin i Biotechnologii i Ogrodnictwa Uniwersytet Rolniczy w Krakowie Poland
Authors
Dariusz GrzebelusZakład Genetyki, Hodowli Roślin i Nasiennictwa, Instytut Biologii Roślin i Biotechnologii i Ogrodnictwa Uniwersytet Rolniczy w Krakowie Poland
Statistics
Abstract views: 308PDF downloads: 91
License
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
Upon submitting the article, the Authors grant the Publisher a non-exclusive and free license to use the article for an indefinite period of time throughout the world in the following fields of use:
- Production and reproduction of copies of the article using a specific technique, including printing and digital technology.
- Placing on the market, lending or renting the original or copies of the article.
- Public performance, exhibition, display, reproduction, broadcasting and re-broadcasting, as well as making the article publicly available in such a way that everyone can access it at a place and time of their choice.
- Including the article in a collective work.
- Uploading an article in electronic form to electronic platforms or otherwise introducing an article in electronic form to the Internet or other network.
- Dissemination of the article in electronic form on the Internet or other network, in collective work as well as independently.
- Making the article available in an electronic version in such a way that everyone can access it at a place and time of their choice, in particular via the Internet.
Authors by sending a request for publication:
- They consent to the publication of the article in the journal,
- They agree to give the publication a DOI (Digital Object Identifier),
- They undertake to comply with the publishing house's code of ethics in accordance with the guidelines of the Committee on Publication Ethics (COPE), (http://ihar.edu.pl/biblioteka_i_wydawnictwa.php),
- They consent to the articles being made available in electronic form under the CC BY-SA 4.0 license, in open access,
- They agree to send article metadata to commercial and non-commercial journal indexing databases.
Most read articles by the same author(s)
- Ewa Grzebelus, Marek Szklarczyk, Rafał Barański, Aneta Malec, Transfer of cytoplasmic male sterility through somatic hybridization in carrot , Bulletin of Plant Breeding and Acclimatization Institute: No. 286 (2019): Special issue
- Dariusz Grzebelus, Alicja Macko-Podgórni, Katarzyna Stelmach, Kornelia Kwolek, Dariusz Kadłuczka, Zbigniew Gajewski, Rafał Barański, Development and application of high-throughput techniques for genomic selection in the improvement of vegetable crops , Bulletin of Plant Breeding and Acclimatization Institute: No. 286 (2019): Special issue
- Dariusz Grzebelus, Gabriela Machaj, Alicja Macko-Podgórni, Kornelia Kwolek, Rafał Barański, Wojciech Wesołowski, Marcelina Wajdzik, Anna Szlachtowska, Beata Domnicz, Przemysław Gierski, Marek Szklarczyk, Development of methods for global analysis of polymorphisms in the genome of sugar beet , Bulletin of Plant Breeding and Acclimatization Institute: No. 286 (2019): Special issue
