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High-Throughput RAD-SNP Genotyping for Characterization of Sugar Beet Genotypes

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Abstract

High-throughput single-nucleotide polymorphism (SNP) genotyping provides a rapid way of developing resourceful sets of markers for delineating genetic structure and for understanding the basis of the taxonomic discrimination. In this paper, we present a panel of 192 SNPs for effective genotyping in sugar beet using a high-throughput marker array technology, QuantStudio 12K Flex system, coupled with Taqman OpenArray technology. The selected SNPs were evaluated for genetic diversity among a set of 150 individuals representing 15 genotypes (10 individuals each) from five cytoplasmic male steriles (CMSs), five pollinators, and five commercial varieties. We demonstrated that the proposed panel of 192 SNPs effectively differentiated the studied genotypes. A higher degree of polymorphism was observed among the CMSs as compared to pollinators and commercial varieties. PCoA and STRUCTURE analysis revealed that CMSs, pollinators, and varieties clustered into three distinct subpopulations. Our results demonstrate the utility of the identified panel of 192 SNPs coupled with TaqMan OpenArray technology as a wide set of markers for high-throughput SNP genotyping in sugar beet.

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References

  • Arnaud JF, Fénart S, Godé C, Deledicque S, Touzet P, Cuguen J (2009) Fine-scale geographical structure of genetic diversity in inland wild beet populations. Mol Ecol 18:3201–3215

    Article  PubMed  Google Scholar 

  • Aulchenko YS, Ripke S, Isaacs A, van Duijn CM (2007) GenABEL: an R library for genome-wide association analysis. Bioinformatics 23:1294–1296

    Article  CAS  PubMed  Google Scholar 

  • Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3(10):e3376

    Article  PubMed Central  PubMed  Google Scholar 

  • Biancardi E, Lewellen RT, De Biaggi M, Erichsen AW, Stevanato P (2002) The origin of rhizomania resistance in sugar beet. Euphytica 127:383–397

    Google Scholar 

  • Biancardi E, McGrath JM, Panella LW, Lewellen RT, Stevanato P (2010) Sugar beet. In: Bradshow J (ed) Handbook of plant breeding, vol. 4, tuber and root crops. Springer, New York, pp 173–219

    Chapter  Google Scholar 

  • Biancardi E, Panella LW, Lewellen RT (2012) Beta maritima: the origin of beets. Springer, New York, p 293

    Google Scholar 

  • Butler DG, Cullis BR, Gilmour AR, Gogel BJ (2007) Analysis of mixed models for S language environments: ASReml-R reference manual, Technical report, Queensland Department of Primary Industries

  • Frese L (2010) Conservation and access to sugarbeet germplasm. Sugar Tech 12:207–219

    Article  Google Scholar 

  • Ganal MW, Altmann T, Roder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12:211–217

    Article  CAS  PubMed  Google Scholar 

  • Ganal MW, Polley A, Graner EM, Plieske J, Wieseke R, Luerssen H, Durstewitz G (2012) Large SNP arrays for genotyping in crop plants. J Biosci 37:821–828

    Article  CAS  PubMed  Google Scholar 

  • Geidel H, Weber WE, Mechelke W, Haufe W (2000) Selection for sugar yield in sugar beet, Beta vulgaris, using different selection indices. Plant Breed 119:188–190

    Article  Google Scholar 

  • Gupta PK, Rustgi S, Mir RR (2008) Array-based high-throughput DNA markers for crop improvement. Heredity 101:5–18

    Article  CAS  PubMed  Google Scholar 

  • Johnson JA, Burkley BM, Langaee TY, Clare-Salzler MJ, Klein TE, Altman RB (2012) Implementing personalized medicine: development of a cost-effective customized pharmacogenetics genotyping array. Clin Pharm Ther 92:437–439

    Article  CAS  Google Scholar 

  • Kaeuffer R, Reale D, Coltman DW, Pontier D (2007) Detecting population structure using structure software: effect of background linkage disequilibrium. Heredity 99:374–380

    Google Scholar 

  • Li J, Luhmann AK, Weißlede K, Stich B (2011) Genome-wide distribution of genetic diversity and linkage disequilibrium in elite sugar beet germplasm. BMC Genom 12:484

    Article  CAS  Google Scholar 

  • Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S (2012) SNP markers and their impact on plant breeding. Int J Plant Genomics. doi:10.1155/2012/728398

    PubMed Central  PubMed  Google Scholar 

  • McGrath JM, Derrico C, Yu Y (1999) Genetic diversity in selected, historical US sugarbeet germplasm and Beta vulgaris ssp maritima. Theor Appl Genet 98:968–976

    Article  Google Scholar 

  • McGrath JM, Saccomani M, Stevanato P, Biancardi E (2007) Beet. In: Kole C (ed) Genome mapping and molecular breeding in plants. Vol. 5: vegetables. Springer-Verlag, Berlin, pp 191–207

    Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 23:341–369

    CAS  Google Scholar 

  • Panella L, Lewellen RT (2007) Broadening the genetic base of sugar beet: introgression from wild relatives. Euphytica 154:383–400

    Article  CAS  Google Scholar 

  • Peakall R, Smouse PE (2006) Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  • Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed Central  PubMed  Google Scholar 

  • Rafalski JA (2002) Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Sci 162:329–333

    Article  CAS  Google Scholar 

  • Ravel C, Praud S, Murigneux A, Canaguier A, Sapet F, Samson D, Balfourier F, Dufour P, Chalhoub B, Brunel D, Beckert M, Charmeta G (2006) Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.). Genome 49:1131–1139

    Article  CAS  PubMed  Google Scholar 

  • Saccomani M, Stevanato P, Trebbi D, McGrath JM, Biancardi E (2009) Molecular and morpho-physiological characterization of sea, ruderal and cultivated beets. Euphytica 169:19–29

    Article  Google Scholar 

  • Schneider K, Weisshaar B, Borchardt DC, Salamini F (2001) SNP frequency and allelic haplotype structure of Beta vulgaris expressed genes. Mol Breed 8:63–74

    Article  CAS  Google Scholar 

  • Simko I, Eujayl I, van Hintum TJL (2012) Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations. Plant Sci 184:54–62

    Article  CAS  PubMed  Google Scholar 

  • Stevanato P, Trebbi D, Biancardi E, Cacco G, McGrath JM, Saccomani M (2013) Evaluation of genetic diversity and root traits of sea beet accessions of the Adriatic Sea coast. Euphytica 189:135–146

    Article  Google Scholar 

  • SyvŠnen AC (2005) Toward genome-wide SNP genotyping. Nat Genet 37:5–10

    Article  Google Scholar 

  • Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci U S A 98:9161–9166

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Viard F, Arnaud JF, Delescluse M, Cuguen J (2004) Tracing back seed and pollen flow within the crop-wild Beta vulgaris complex: genetic distinctiveness vs. hot spots of hybridization over a regional scale. Mol Ecol 13:1357–1364

    Article  CAS  PubMed  Google Scholar 

  • Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134

    CAS  PubMed Central  PubMed  Google Scholar 

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Acknowledgments

We are grateful to the members of the BeetSeq project for providing access to unpublished data. Gaurav Sablok thanks the Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, Italy for providing the computational support.

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Authors and Affiliations

  1. Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente (DAFNAE), Università degli Studi di Padova, Viale dell’Università 16, 35020, Legnaro, Padua, Italy

    Piergiorgio Stevanato, Chiara Broccanello & Giuseppe Concheri

  2. Fondazione Parco Tecnologico Padano (FPTP), Viale Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy

    Filippo Biscarini, Marcello Del Corvo & Alessandra Stella

  3. Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all’Adige, Trentino, Italy

    Gaurav Sablok

  4. Sugar beet Research Unit, Crops Research Laboratory, USDA-ARS, NPA, 1701 Centre Ave., Fort Collins, CO, 80526-2083, USA

    Lee Panella

Authors
  1. Piergiorgio Stevanato
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  2. Chiara Broccanello
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  3. Filippo Biscarini
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  4. Marcello Del Corvo
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  5. Gaurav Sablok
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  6. Lee Panella
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  7. Alessandra Stella
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  8. Giuseppe Concheri
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Corresponding author

Correspondence to Piergiorgio Stevanato.

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Stevanato, P., Broccanello, C., Biscarini, F. et al. High-Throughput RAD-SNP Genotyping for Characterization of Sugar Beet Genotypes. Plant Mol Biol Rep 32, 691–696 (2014). https://doi.org/10.1007/s11105-013-0685-x

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  • DOI: https://doi.org/10.1007/s11105-013-0685-x

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