Artículo

Fusari, C.M.; Lia, V.V.; Nishinakamasu, V.; Zubrzycki, J.E.; Puebla, A.F.; Maligne, A.E.; Hopp, H.E.; Heinz, R.A.; Paniego, N.B. "Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (Helianthus annuus L.)" (2011) Molecular Breeding. 28(1):73-89
Estamos trabajando para incorporar este artículo al repositorio
Consulte el artículo en la página del editor
Consulte la política de Acceso Abierto del editor

Abstract:

Single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) are increasingly used for cultivar identification, construction of genetic maps, genetic diversity assessment, association mapping and marker-assisted breeding. Although there are several highly sensitive methods for the detection of polymorphisms, most of them are often beyond the budget of medium-throughput academic laboratories or seed companies. Heteroduplex analysis by enzymatic cleavage (CEL1CH) or denaturing high-performance liquid chromatography (dHPLC) has been successfully used to examine genetic variation in several plant and animal species. In this work, we assess and compare the performance of both methods in sunflower by genotyping SNPs from a set of 24 selected polymorphic candidate genes. The CEL1CH method allowed us to accurately detect allele differences in 10 out of 24 regions using an in-house prepared CEL1 enzyme (celery single strand endonuclease 1, Apium graveolens L.). Similarly, a total of 11 regions were successfully optimized for dHPLC analysis. As a scaling-up approach, both strategies were tested to genotype either 42 SNPs/indels in 22 sunflower accessions from the local germplasm bank or 33 SNPs/indels in 90 recombinant inbred lines (RILs) for genetic mapping purposes. Summarizing, a total of 601 genotypes were efficiently analyzed either with CEL1CH (110) or dHPCL (491). In conclusion, CEL1CH and dHPLC proved to be robust, complementary methods, allowing medium-scale laboratories to scale up the number of both SNPs and individuals to be included in genetic studies and targeted germplasm diversity characterization (EcoTILLING). © 2010 Springer Science+Business Media B.V.

Registro:

Documento: Artículo
Título:Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (Helianthus annuus L.)
Autor:Fusari, C.M.; Lia, V.V.; Nishinakamasu, V.; Zubrzycki, J.E.; Puebla, A.F.; Maligne, A.E.; Hopp, H.E.; Heinz, R.A.; Paniego, N.B.
Filiación:Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Hurlingham, Buenos Aires 1686, Argentina
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria 1428, Argentina
Palabras clave:CEL1; dHPLC; Heteroduplex analysis; High-throughput genotyping; SNPs; Sunflower; Animalia; Apium graveolens; Apium graveolens var. dulce; Helianthus; Helianthus annuus
Año:2011
Volumen:28
Número:1
Página de inicio:73
Página de fin:89
DOI: http://dx.doi.org/10.1007/s11032-010-9462-9
Título revista:Molecular Breeding
Título revista abreviado:Mol. Breed.
ISSN:13803743
CODEN:MOBRF
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13803743_v28_n1_p73_Fusari

Referencias:

  • Abbas, A., Lepelley, M., Lechevrel, M., Sichel, F., Assessment of DHPLC usefulness in the genotyping of GSTP1 exon 5 SNP: comparison to the PCR-RFLP method (2004) J Biochem Biophys Meth, 59, pp. 121-126
  • Al-Chaarani, G.R., Gentzbittel, L., Huang, X.Q., Sarrafi, A., Genotypic variation and identification of QTLs for agronomic traits. using AFLP and SSR Markers in RILs of Sunflower (Helianthus Annuus L.) (2004) Theor Appl Genet, 109, pp. 1353-1360
  • Al-Chaarani, G.R., Roustaee, A., Gentzbittel, L., Mokrani, G., Barrault, G., A QTL analysis of sunflower partial resistance to downy mildew (Plasmopara halstedii) and black stem (Phoma macdonaldii) by the use of recombinant inbred lines (RILs) (2002) Theor Appl Genet, 104, pp. 490-496
  • Alfadil, A.T., Poormohammad Kiani, G., Dechamp-Guillaume, L., Gentzbittel, L., Sarrafi, A., QTL mapping of partial resistance to Phoma basal stem and root necrosis in sunflower (Helianthus annuus L.) (2007) Plant Sci, 172, pp. 815-823
  • Arnaud, D., Dejardin, A., Leple, J.C., Lesage-Descauses, M.C., Pilate, G., Genome-wide analysis of LIM gene family in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa (2007) DNA Res, 14, pp. 103-116
  • Bagge, M., Lübberstedt, T., Functional markers in wheat: technical and economic aspects (2008) Mol Breed, 22, pp. 319-328
  • Barkley, N.A., Wang, M.L., Application of TILLING and EcoTILLING as Reverse Genetic Approaches to Elucidate the Function of Genes in Plants and Animals (2008) Curr Genomics, 9, pp. 212-226
  • Barreiro, L.B., Henriques, R., Mhlanga, M.M., High-throughput SNP genotyping: combining tag SNPs and molecular beacons (2009) Meth Mol Biol, 578, pp. 255-276
  • Collard, B.C.Y., Cruz, C.M.V., McNally, K.L., Virk, P.S., Mackill, D.J., Rice molecular breeding laboratories in the genomics era: current status and future considerations (2008) Int J Plant Genomics, 2008, p. 524847
  • Comai, L., Young, K., Till, B.J., Reynolds, S.H., Greene, E.A., Codomo, C.A., Enns, L.C., Henikoff, S., Efficient discovery of DNA polymorphisms in natural populations by Ecotilling (2004) Plant J, 37, pp. 778-786
  • Cooper, J.L., Till, B.J., Laport, R.G., Darlow, M.C., Kleffner, J.M., Jamai, A., El-Mellouki, T., Henikoff, S., TILLING to detect induced mutations in soybean (2008) BMC Plant Biol, 8, p. 9
  • Costabile, M., Quach, A., Ferrante, A., Molecular approaches in the diagnosis of primary immunodeficiency diseases (2006) Hum Mutat, 27, pp. 1163-1173
  • Dracatos, P.M., Cogan, N.O., Dobrowolski, M.P., Sawbridge, T.I., Spangenberg, G.C., Smith, K.F., Forster, J.W., Discovery and genetic mapping of single nucleotide polymorphisms in candidate genes for pathogen defence response in perennial ryegrass (Lolium perenne L.) (2008) Theor Appl Genet, 117, pp. 203-219
  • Ehrenreich, I., Hanzawa, Y., Chou, L., Roe, J., Kover, P., Purugganan, M., Candidate gene association mapping of Arabidopsis flowering time (2009) Genetics, , doi:10.1534/genetics.109.105189
  • Elias, R., Till, B.J., Mba, C., Al-Safadi, B., Optimizing TILLING and Ecotilling techniques for potato (Solanum tuberosum L) (2009) BMC Res Notes, 2, p. 141
  • Fusari, C.M., Lia, V.V., Hopp, H.E., Heinz, R.A., Paniego, N.B., Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach (2008) BMC Plant Biol, 8, p. 7
  • Galeano, C.H., Gomez, M., Rodriguez, L.M., Blair, M.W., CEL I nuclease digestion for SNP discovery and marker development in common bean (Phaseolus vulgaris L.) (2009) Crop Sci, 49, pp. 1-14
  • Gilchrist, E.J., Haughn, G.W., Ying, C.C., Otto, S.P., Zhuang, J., Cheung, D., Hamberger, B., Cronk, Q.C.B., Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa (2006) Mol Ecol, 15, pp. 1367-1378
  • Gilles, P.N., Wu, D.J., Foster, C.B., Dillon, P.J., Chanock, S.J., Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips (1999) Nat Biotechnol, 17, pp. 365-370
  • Giordano, M., Oefner, P.J., Underhill, P.A., Cavalli Sforza, L.L., Tosi, R., Richiardi, P.M., Identification by denaturing high-performance liquid chromatography of numerous polymorphisms in a candidate region for multiple sclerosis susceptibility (1999) Genomics, 56, pp. 247-253
  • Haldane, J.B., Waddington, C.H., Inbreeding and linkage (1931) Genetics, 16, pp. 357-374
  • Han, W., Yip, S.P., Wang, J., Yap, M.K., Using denaturing HPLC for SNP discovery and genotyping, and establishing the linkage disequilibrium pattern for the all-trans-retinol dehydrogenase (RDH8) gene (2004) J Hum Genet, 49, pp. 16-23
  • Higuchi, R., Fockler, C., Dollinger, G., Watson, R., Kinetic PCR analysis: real-time monitoring of DNA amplification reactions (1993) Biotechnology (NY), 11, pp. 1026-1030
  • Hung, C.C., Su, Y.N., Lin, C.Y., Chang, Y.F., Chang, C.H., Cheng, W.F., Chen, C.A., Lin, W.L., Comparison of the mismatch-specific endonuclease method and denaturing high-performance liquid chromatography for the identification of HBB gene mutations (2008) BMC Biotechnol, 8, p. 62
  • Jones, A.C., Austin, J., Hansen, N., Hoogendoorn, B., Oefner, P.J., Cheadle, J.P., O'Donovan, M.C., Optimal temperature selection for mutation detection by denaturing HPLC and comparison to single-stranded conformation polymorphism and heteroduplex analysis (1999) Clin Chem, 45, pp. 1133-1140
  • Kolkman, J.M., Berry, S.T., Leon, A., Slabaugh, M.B., Tang, S., Gao, W., Shintani, D.K., Knapp, S.J., Single nucleotide polymorphism and linkage disequilibrium in sunflower (2007) Genetics, 177, pp. 457-468
  • Kosambi, D.D., The estimation of a map distance from recombination values (1944) Ann Eugen, 12, pp. 172-175
  • Kota, R., Varshney, R.K., Prasad, M., Zhang, H., Stein, N., Graner, A., EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome (2008) Funct Integr Genomics, 8, pp. 223-233
  • Kota, R., Wolf, M., Michalek, W., Graner, A., Application of denaturing high-performance liquid chromatography for mapping of single nucleotide polymorphisms in barley (Hordeum vulgare L.) (2001) Genome, 44, pp. 523-528
  • Lai, Z., Livingstone, K., Zou, Y., Church, S.A., Knapp, S.J., Andrews, J., Rieseberg, L.H., Identification and mapping of SNPs from ESTs in sunflower (2005) Theor Appl Genet, 111, pp. 1532-1544
  • Lander, E.S., Green, P., Abrahamson, J., Barlow, A., Daly, M.J., Lincoln, S.E., Newberg, L.A., MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations (1987) Genomics, 1, pp. 174-181
  • Lexer, C., Lai, Z., Rieseberg, L.H., Candidate gene polymorphisms associated with salt tolerance in wild sunflower hybrids: implications for the origin of Helianthus paradoxus, a diploid hybrid species (2003) New Phytol, 161, pp. 225-233
  • Lijavetzky, D., Cabezas, J.A., Ibanez, A., Rodriguez, V., Martinez-Zapater, J.M., High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology (2007) BMC Genomics, 8, p. 424
  • Lin, C.H., Yeakley, J.M., McDaniel, T.K., Shen, R., Medium- to high-throughput SNP genotyping using VeraCode Microbeads (2009) In: DNA and RNA profiling in human blood: Methods and protocols, pp. 129-142. , Bugert P (ed) Humana Press
  • Liu, A., Burke, J.M., Patterns of nucleotide diversity in wild and cultivated sunflower (2006) Genetics, 173, pp. 321-330
  • Livak, K.J., Flood, S.J., Marmaro, J., Giusti, W., Deetz, K., Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization (1995) PCR Meth Appl, 4, pp. 357-362
  • Makridakis, N.M., Reichardt, J.K., Multiplex automated primer extension analysis: simultaneous genotyping of several polymorphisms (2001) Biotechniques, 31, pp. 1374-1380
  • Nieto, C., Piron, F., Dalmais, M., Marco, C.F., Moriones, E., Gómez-Guillamón, M.L., Truniger, V., Bendahmane, A., EcoTILLING for the identification of allelic variants of melon eIF4E, a factor that controls virus susceptibility (2007) BMC Plant Biol, 7, p. 34
  • Oefner, P., Underhill, P., DNA mutation detection using denaturing high-performance liquid chromatography (DHPLC) (1998) Current protocols in human genetics, (SUPPL. 19), pp. 7-10+11-17+10-12. , Wiley, New York, 7. 10. 1-7. 10. 12
  • Oleykowski, C.A., Bronson Mullins, C.R., Godwin, A.K., Yeung, A.T., Mutation detection using a novel plant endonuclease (1998) Nucleic Acids Res, 26, pp. 4597-4602
  • Pajerowska-Mukhtar, K., Stich, B., Achenbach, U., Ballvora, A., Lubeck, J., Strahwald, J., Tacke, E., Gebhardt, C., Single nucleotide polymorphisms in the allene oxide synthase 2 gene are associated with field resistance to late blight in populations of tetraploid potato cultivars (2009) Genetics, 181, pp. 1115-1127
  • Pease, A.C., Solas, D., Sullivan, E.J., Cronin, M.T., Holmes, C.P., Fodor, S.P., Light-generated oligonucleotide arrays for rapid DNA sequence analysis (1994) Proc Natl Acad Sci USA, 91, pp. 5022-5026
  • Perry, J.A., Wang, T.L., Welham, T.J., Gardner, S., Pike, J.M., Yoshida, S., Parniske, M., A TILLING reverse genetics tool and a web-accessible collection of mutants of the legume Lotus japonicus (2003) Plant Physiol, 131, pp. 866-871
  • Poormohammad Kiani, S., Grieu, P., Maury, P., Hewezi, T., Gentzbittel, L., Sarrafi, A., Genetic variability for physiological traits under drought conditions and differential expression of water stress-associated genes in sunflower (Helianthus annuus L.) (2007) Theor Appl Genet, 114, pp. 193-207
  • Poormohammad Kiani, S., Maury, P., Sarrafi, A., Grieu, P., QTL analysis of chlorophyll fluorescence parameters in sunflower (Helianthus annuus L.) under well-watered and water-stressed conditions (2008) Plant Sci, 175, pp. 565-573
  • Poormohammad Kiani, S., Talia, P., Grieu, P., Maury, P., Hewezi, T., Gentzbittel, L., Sarrafi, A., Genetic analysis of plant water status and osmotic adjustment in recombinant inbred lines of sunflower under two water treatments (2007) Plant Sci, 178, pp. 773-787
  • Rafalski, A., Applications of single nucleotide polymorphisms in crop genetics (2002) Curr Opin Plant Biol, 5, pp. 94-100
  • Randall, L.P., Coldham, N.G., Woodward, M.J., Detection of mutations in Salmonella enterica gyrA, gyrB, parC and parE genes by denaturing high performance liquid chromatography (DHPLC) using standard HPLC instrumentation (2005) J Antimicrob Chemother, 56, pp. 619-623
  • Ren, B., Zhou, J.-M., Komiyama, M., Straightforward detection of SNPs in doublestranded DNA by using exonuclease III/nuclease S1/PNA system (2004) Nucleic Acids Res, 34, pp. e42
  • Rozen, S., Skaletsky, H., Primer3 on the WWW for general users and for biologist programmers (2000) Bioinformatics methods and protocols: Methods in molecular biology, pp. 365-386. , http://www.frodo.wi.mit.edu/, In: Krawetz S, Misener S (eds) Humana Press, Totowa, NJ
  • Sala, C.A., Bulos, M., Echarte, M., Whitt, S.R., Ascenzi, R., Molecular and biochemical characterization of an induced mutation conferring imidazolinone resistance in sunflower (2008) Theor Appl Genet, 118, pp. 105-112
  • Schiex, T., Gaspin, C., CARTHAGENE: constructing and joining maximum likelihood genetic maps (1997) Proc Int Conf Intell Syst Mol Biol, 5, pp. 258-267
  • Shirasawa, K., Maeda, H., Monna, L., Kishitani, S., Nishio, T., The number of genes having diVerent alleles between rice cultivars estimated by SNP analysis (2007) Theor Appl Genet, 115, pp. 1067-1074
  • Southern, E.M., High-density gridding: techniques and applications (1996) Curr Opin Biotechnol, 7, pp. 85-88
  • Spiegelman, J.I., Mindrinos, M.N., Oefner, P.J., High-accuracy DNA sequence variation screening by DHPLC (2000) Biotechniques, 29, pp. 1084-1090+1092
  • Tang, S., Kishore, V.K., Knapp, S.J., PCR-multiplexes for a genome-wide framework of simple sequence repeat marker loci in cultivated sunflower (2003) Theor Appl Genet, 107, pp. 6-19
  • Till, B.J., Burtner, C., Comai, L., Henikoff, S., Mismatch cleavage by single-strand specific nucleases (2004) Nucleic Acids Res, 32, pp. 2632-2641
  • Till, B.J., Colbert, T., Tompa, R., Enns, L.C., Codomo, C.A., Johnson, J.E., Reynolds, S.H., Henikoff, S., High-throughput TILLING for functional genomics (2003) Plant Functional Genomics: Methods and Protocols, pp. 205-220. , E. Grotewold (Ed.), Totowa, NJ: Humana Press
  • Till, B.J., Cooper, J., Tai, T.H., Colowit, P., Greene, E.A., Henikoff, S., Comai, L., Discovery of chemically induced mutations in rice by TILLING (2007) BMC Plant Biol, 7, p. 19
  • Tsuchihashi, Z., Dracopoli, N.C., Progress in high throughput SNP genotyping methods (2002) Pharmacogenomics J, 2, pp. 103-110
  • Tyagi, S., Kramer, F.R., Molecular beacons: probes that fluoresce upon hybridization (1996) Nat Biotechnol, 14, pp. 303-308
  • Uauy, C., Paraiso, F., Colasuonno, P., Tran, R.K., Tsai, H., Berardi, S., Comai, L., Dubcovsky, J., A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheat (2009) BMC Plant Biol, 9, p. 115
  • Voorrips, R.E., MapChart: software for the graphical presentation of linkage maps and QTLs (2002) J Hered, 93, pp. 77-78
  • Wagner, T., Stoppa-Lyonnet, D., Fleischmann, E., Muhr, D., Pages, S., Sandberg, T., Caux, V., Oefner, P., Denaturing high-performance liquid chromatography detects reliably BRCA1 and BRCA2 mutations (1999) Genomics, 62, pp. 369-376
  • Wang, H.-Y., Luo, M., Tereshchenko, I.V., Frikker, D.M., Cui, X., Li, J.Y., Hu, G., Li, H., A genotyping system capable of simultaneously analyzing > 1000 single nucleotide polymorphisms in a haploid genome (2005) Genome Res, 15, pp. 276-283
  • Wang, J., Wang, W., Liu, Y., Duo, L., Huang, L., Jiang, X., The method of single-nucleotide variations detection using capillary electrophoresis and molecular beacons (2009) Mol Biol Rep, 36, pp. 1903-1908
  • Wang, N., Wang, Y., Tian, F., King, G.J., Zhang, C., Long, Y., Shi, L., Meng, J., A functional genomics resource for Brassica napus: development of an EMS mutagenized population and discovery of FAE1 point mutations by TILLING (2008) New Phytol, 180, pp. 751-765
  • Weil, C.F., Monde, R.-A., Getting the point-mutations in maize (2007) Crop Sci, 47, pp. 60-67
  • Xiao, W., Oefner, P.J., Denaturing high-performance liquid chromatography: A review (2001) Hum Mutat, 17, pp. 439-474
  • Xin, Z., Wang, M.L., Barkley, N.A., Burow, G., Franks, C., Pederson, G., Burke, J., Applying genotyping (TILLING) and phenotyping analyses to elucidate gene function in a chemically induced sorghum mutant population (2008) BMC Plant Biol, 8, p. 103
  • Yang, W., Bai, X., Kabelka, E., Eaton, C., Kamoun, S., van der Knaap, E., Francis, D., Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags (2004) Mol Breed, 14, pp. 21-34
  • Yu, B., Sawyer, N.A., Caramins, M., Yuan, Z.G., Saunderson, R.B., Pamphlett, R., Richmond, D.R., Trent, R.J., Denaturing high performance liquid chromatography: high throughput mutation screening in familial hypertrophic cardiomyopathy and SNP genotyping in motor neurone disease (2005) J Clin Pathol, 58, pp. 479-485

Citas:

---------- APA ----------
Fusari, C.M., Lia, V.V., Nishinakamasu, V., Zubrzycki, J.E., Puebla, A.F., Maligne, A.E., Hopp, H.E.,..., Paniego, N.B. (2011) . Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (Helianthus annuus L.). Molecular Breeding, 28(1), 73-89.
http://dx.doi.org/10.1007/s11032-010-9462-9
---------- CHICAGO ----------
Fusari, C.M., Lia, V.V., Nishinakamasu, V., Zubrzycki, J.E., Puebla, A.F., Maligne, A.E., et al. "Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (Helianthus annuus L.)" . Molecular Breeding 28, no. 1 (2011) : 73-89.
http://dx.doi.org/10.1007/s11032-010-9462-9
---------- MLA ----------
Fusari, C.M., Lia, V.V., Nishinakamasu, V., Zubrzycki, J.E., Puebla, A.F., Maligne, A.E., et al. "Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (Helianthus annuus L.)" . Molecular Breeding, vol. 28, no. 1, 2011, pp. 73-89.
http://dx.doi.org/10.1007/s11032-010-9462-9
---------- VANCOUVER ----------
Fusari, C.M., Lia, V.V., Nishinakamasu, V., Zubrzycki, J.E., Puebla, A.F., Maligne, A.E., et al. Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (Helianthus annuus L.). Mol. Breed. 2011;28(1):73-89.
http://dx.doi.org/10.1007/s11032-010-9462-9