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High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.)

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Abstract

We describe the application of complexity reduction of polymorphic sequences (CRoPS®) technology for the discovery of SNP markers in tetraploid durum wheat (Triticum durum Desf.). A next-generation sequencing experiment was carried out on reduced representation libraries obtained from four durum cultivars. SNP validation and minor allele frequency (MAF) estimate were carried out on a panel of 12 cultivars, and the feasibility of genotyping these SNPs in segregating populations was tested using the Illumina Golden Gate (GG) technology. A total of 2,659 SNPs were identified on 1,206 consensus sequences. Among the 768 SNPs that were chosen irrespective of their genomic repetitiveness level and assayed on the Illumina BeadExpress genotyping system, 275 (35.8%) SNPs matched the expected genotypes observed in the SNP discovery phase. MAF data indicated that the overall SNP informativeness was high: a total of 196 (71.3%) SNPs had MAF >0.2, of which 76 (27.6%) showed MAF >0.4. Of these SNPs, 157 were mapped in one of two mapping populations (Meridiano × Claudio and Colosseo × Lloyd) and integrated into a common genetic map. Despite the relatively low genotyping efficiency of the GG assay, the validated CRoPS-derived SNPs showed valuable features for genomics and breeding applications such as a uniform distribution across the wheat genome, a prevailing single-locus codominant nature and a high polymorphism. Here, we report a new set of 275 highly robust genome-wide Triticum SNPs that are readily available for breeding purposes.

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Acknowledgments

The financial contribution of the European Project “BioExploit Food CT 2005-513959” is gratefully acknowledged. The AFLP® and CRoPS® technologies are subjected to patents and patent applications owned by Keygene N.V. AFLP and CroPS are registered trademarks of Keygene N.V.

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  1. Daniele Trebbi

    Present address: Dipartimento di Biotecnologie Agrarie, Università degli Studi di Padova, Viale dell’ Università 16, 35020, Legnaro, PD, Italy

Authors and Affiliations

  1. Keygene N.V., Applied Research, Agro Business Park 90, 6708, PW, Wageningen, The Netherlands

    Daniele Trebbi, Peter de Heer, Anker Sørensen & Edwin Andries Gerard van der Vossen

  2. Dipartimento di Scienze e Tecnologie Agroambientali (DiSTA), Università di Bologna, Viale Fanin 44, 40127, Bologna, Italy

    Marco Maccaferri, Silvia Giuliani, Silvio Salvi, Maria Corinna Sanguineti & Roberto Tuberosa

  3. Società Produttori Sementi Bologna Spa, Via Macero 1, 40050, Argelato, BO, Italy

    Andrea Massi

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122_2011_1607_MOESM1_ESM.ods

Online Resource 1 Details of the 768 SNP-harboring sequences selected for the two OPA assays. A = Keygene and University of Bologna (KBO) SNP name B = Nucleotide identified during the CRoPS analysis. Dots indicate insufficient number of sequence to identify nucleotides C = Genotype identified during the Golden Gate (GG) assay. Scores A, B, H and U indicate homozygosity for the first allele, homozygosity for the second allele, heterozygosity and undetermined genotype, respectively (ODS 118 kb)

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Trebbi, D., Maccaferri, M., de Heer, P. et al. High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.). Theor Appl Genet 123, 555–569 (2011). https://doi.org/10.1007/s00122-011-1607-7

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