title: High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.).
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.
authors: Keygene NV, Applied Research, Agro Business Park 90, 6708, PW, Wageningen, The Netherlands. trebbida@msu.edu
authors: Daniele
authors: D
authors: Trebbi
authors: Marco
authors: M
authors: Maccaferri
authors: Peter
authors: P
authors: de Heer
authors: Anker
authors: A
authors: Sørensen
authors: Silvia
authors: S
authors: Giuliani
authors: Silvio
authors: S
authors: Salvi
authors: Maria Corinna
authors: MC
authors: Sanguineti
authors: Andrea
authors: A
authors: Massi
authors: Edwin Andries Gerard
authors: EA
authors: van der Vossen
authors: Roberto
authors: R
authors: Tuberosa
references: Forensic Sci Int. 2003 Oct 14;137(1):74-84
references: 14550618
references: PCR Methods Appl. 1995 Jun;4(6):357-62
references: 7580930
references: Ann Bot. 2005 Jan;95(1):127-32
references: 15596462
references: Funct Integr Genomics. 2009 Nov;9(4):473-84
references: 19575250
references: Trends Plant Sci. 2007 Feb;12(2):57-63
references: 17224302
references: Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12273-8
references: 19597147
references: Curr Opin Plant Biol. 2009 Apr;12(2):211-7
references: 19186095
references: Genome. 2006 Sep;49(9):1131-9
references: 17110993
references: Curr Opin Plant Biol. 2009 Apr;12(2):218-22
references: 19185530
references: Nat Methods. 2008 Mar;5(3):247-52
references: 18297082
references: Mol Biol Evol. 2007 Jul;24(7):1506-17
references: 17443011
references: Plant J. 2003 Apr;34(2):249-55
references: 12694599
references: BMC Genomics. 2009 Dec 04;10:582
references: 19961604
references: Nucleic Acids Res. 1995 Nov 11;23(21):4407-14
references: 7501463
references: J Exp Bot. 2011 Jan;62(2):409-38
references: 21041372
references: Mutat Res. 2005 Jun 3;573(1-2):70-82
references: 15829238
references: Theor Appl Genet. 2005 Feb;110(3):550-60
references: 15655666
references: Cold Spring Harb Symp Quant Biol. 2003;68:69-78
references: 15338605
references: Nat Methods. 2007 Nov;4(11):903-5
references: 17934467
references: Theor Appl Genet. 2006 Nov;113(8):1409-20
references: 17033786
references: Genome Res. 2009 Jun;19(6):1068-76
references: 19420380
references: Nat Methods. 2007 Nov;4(11):907-9
references: 17934469
references: Cell Mol Biol Lett. 2002;7(2B):695-702
references: 12378229
references: Plant Biotechnol J. 2010 Jan;8(1):2-9
references: 19906089
references: Curr Opin Plant Biol. 2005 Apr;8(2):135-41
references: 15752992
references: Theor Appl Genet. 2010 Aug;121(3):577-88
references: 20401646
references: Trends Biotechnol. 2009 Sep;27(9):522-30
references: 19679362
references: Genome. 2003 Jun;46(3):431-7
references: 12834059
references: Plant Physiol. 2002 Jun;129(2):440-50
references: 12068090
references: Theor Appl Genet. 2009 Aug;119(3):507-17
references: 19449174
references: BMC Genomics. 2008 Feb 25;9:95
references: 18298839
references: Nat Biotechnol. 2008 Oct;26(10):1135-45
references: 18846087
references: BMC Genet. 2002 Oct 7;3:19
references: 12366868
references: Genome Res. 2008 Dec;18(12):2024-33
references: 18818371
references: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D752-7
references: 16381974
references: Plant J. 2007 Sep;51(5):910-8
references: 17662031
references: Bioinformatics. 2005 Apr 15;21(8):1703-4
references: 15598829
references: Theor Appl Genet. 2008 Nov;117(8):1225-40
references: 18712342
references: Science. 2003 Dec 19;302(5653):2115-7
references: 14684820
references: BMC Genomics. 2006 Aug 12;7:206
references: 16904008
references: Plant Biotechnol J. 2009 May;7(4):318-25
references: 19386040
references: Theor Appl Genet. 2008 May;116(7):945-52
references: 18278477
references: Genetics. 2010 Jan;184(1):19-26
references: 19884313
references: BMC Genomics. 2010 Dec 29;11:727
references: 21190581
references: Genome Res. 1999 May;9(5):492-8
references: 10330129
references: BMC Genomics. 2010 Apr 27;11:267
references: 20423466
references: Plant J. 2006 Nov;48(3):463-74
references: 17010109
references: Gene. 1999 Jul 8;234(2):177-86
references: 10395891
references: Philos Trans R Soc Lond B Biol Sci. 2008 Feb 12;363(1491):557-72
references: 17715053
references: Theor Appl Genet. 2007 Aug;115(4):451-61
references: 17571251
references: PLoS One. 2007 Nov 14;2(11):e1172
references: 18000544
references: Brief Funct Genomics. 2010 Mar;9(2):166-77
references: 20156985
references: Nature. 2000 Sep 28;407(6803):513-6
references: 11029002
references: Clin Genet. 2008 Nov;74(5):463-8
references: 18700895
references: Genetics. 2009 Aug;182(4):943-54
references: 19474198
references: Theor Appl Genet. 2008 Jun;117(1):103-15
references: 18437346
references: BMC Genomics. 2010 Dec 14;11:702
references: 21156062
references: Hum Mutat. 2001 Jun;17(6):475-92
references: 11385706
references: Science. 2007 Jun 29;316(5833):1862-6
references: 17600208
references: Mutat Res. 2005 Jun 3;573(1-2):103-10
references: 15829241
references: Trends Biotechnol. 2010 Sep;28(9):452-60
references: 20692061
references: BMC Genomics. 2010 Jan 15;11:38
references: 20078886
references: Biotechniques. 2002 Jun;Suppl:56-8, 60-1
references: 12083399
references: Methods Mol Biol. 2009;529:197-213
references: 19381978
references: Genome Res. 2004 Sep;14(9):1812-9
references: 15342564