Theoretical and Applied Genetics

, Volume 123, Issue 4, pp 555–569

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

  • Daniele Trebbi
  • Marco Maccaferri
  • Peter de Heer
  • Anker Sørensen
  • Silvia Giuliani
  • Silvio Salvi
  • Maria Corinna Sanguineti
  • Andrea Massi
  • Edwin Andries Gerard van der Vossen
  • Roberto Tuberosa
Original Paper

DOI: 10.1007/s00122-011-1607-7

Cite this article as:
Trebbi, D., Maccaferri, M., de Heer, P. et al. Theor Appl Genet (2011) 123: 555. doi:10.1007/s00122-011-1607-7

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.

Supplementary material

122_2011_1607_MOESM1_ESM.ods (119 kb)
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)

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Daniele Trebbi
    • 1
    • 4
  • Marco Maccaferri
    • 2
  • Peter de Heer
    • 1
  • Anker Sørensen
    • 1
  • Silvia Giuliani
    • 2
  • Silvio Salvi
    • 2
  • Maria Corinna Sanguineti
    • 2
  • Andrea Massi
    • 3
  • Edwin Andries Gerard van der Vossen
    • 1
  • Roberto Tuberosa
    • 2
  1. 1.Keygene N.V., Applied ResearchWageningenThe Netherlands
  2. 2.Dipartimento di Scienze e Tecnologie Agroambientali (DiSTA)Università di BolognaBolognaItaly
  3. 3.Società Produttori Sementi Bologna SpaArgelatoItaly
  4. 4.Dipartimento di Biotecnologie AgrarieUniversità degli Studi di PadovaLegnaroItaly