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GrainGenes Reference Report: TAG-123-555

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Reference	TAG-123-555
Title	High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.)
Journal	Theoretical and Applied Genetics
Volume	123
Pages	555-569
Author	Trebbi D [ Show all 10 ]
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.
External Databases	https://link.springer.com/article/10.1007%2Fs00122-011-1607-7 http://dx.doi.org/10.1007/s00122-011-1607-7
Locus	kbo-0001 [ Show all 446 ]
Probe	[ Hide all but 1 of 232 ] KBO-0287 KBO-0228 KBO-0301 KBO-0434 KBO-0128 KBO-0405 KBO-0417 KBO-0016 KBO-0103 KBO-0014 KBO-0386 KBO-0312 KBO-0303 KBO-0082 KBO-0425 KBO-0203 KBO-0175 KBO-0199 KBO-0200 KBO-0034 KBO-0254 KBO-0407 KBO-0135 KBO-0260 KBO-0051 KBO-0211 KBO-0351 KBO-0295 KBO-0010 KBO-0395 KBO-0102 KBO-0247 KBO-0381 KBO-0067 KBO-0062 KBO-0045 KBO-0375 KBO-0001 KBO-0173 KBO-0161 KBO-0222 KBO-0190 KBO-0089 KBO-0090 KBO-0196 KBO-0171 KBO-0304 KBO-0305 KBO-0013 KBO-0380 KBO-0119 KBO-0350 KBO-0033 KBO-0145 KBO-0431 KBO-0333 KBO-0081 KBO-0080 KBO-0367 KBO-0026 KBO-0159 KBO-0061 KBO-0235 KBO-0290 KBO-0180 KBO-0092 KBO-0075 KBO-0416 KBO-0402 KBO-0335 KBO-0226 KBO-0392 KBO-0125 KBO-0142 KBO-0198 KBO-0214 KBO-0233 KBO-0058 KBO-0376 KBO-0306 KBO-0356 KBO-0357 KBO-0096 KBO-0150 KBO-0064 KBO-0086 KBO-0041 KBO-0170 KBO-0059 KBO-0331 KBO-0237 KBO-0379 KBO-0346 KBO-0236 KBO-0099 KBO-0039 KBO-0282 KBO-0293 KBO-0192 KBO-0227 KBO-0348 KBO-0069 KBO-0426 KBO-0298 KBO-0184 KBO-0435 KBO-0077 KBO-0117 KBO-0309 KBO-0220 KBO-0136 KBO-0130 KBO-0131 KBO-0132 KBO-0109 KBO-0079 KBO-0383 KBO-0053 KBO-0129 KBO-0336 KBO-0137 KBO-0242 KBO-0317 KBO-0091 KBO-0250 KBO-0204 KBO-0421 KBO-0347 KBO-0337 KBO-0291 KBO-0399 KBO-0169 KBO-0252 KBO-0218 KBO-0139 KBO-0166 KBO-0294 KBO-0364 KBO-0420 KBO-0066 KBO-0158 KBO-0172 KBO-0093 KBO-0406 KBO-0029 KBO-0152 KBO-0366 KBO-0389 KBO-0255 KBO-0146 KBO-0183 KBO-0390 KBO-0209 KBO-0019 KBO-0087 KBO-0372 KBO-0325 KBO-0002 KBO-0004 KBO-0008 KBO-0011 KBO-0023 KBO-0040 KBO-0044 KBO-0047 KBO-0048 KBO-0049 KBO-0073 KBO-0074 KBO-0085 KBO-0088 KBO-0108 KBO-0115 KBO-0134 KBO-0155 KBO-0163 KBO-0167 KBO-0176 KBO-0178 KBO-0181 KBO-0186 KBO-0188 KBO-0197 KBO-0207 KBO-0210 KBO-0216 KBO-0217 KBO-0219 KBO-0221 KBO-0224 KBO-0229 KBO-0231 KBO-0232 KBO-0239 KBO-0244 KBO-0246 KBO-0251 KBO-0253 KBO-0258 KBO-0259 KBO-0262 KBO-0267 KBO-0268 KBO-0274 KBO-0278 KBO-0281 KBO-0283 KBO-0284 KBO-0289 KBO-0292 KBO-0307 KBO-0310 KBO-0314 KBO-0320 KBO-0321 KBO-0326 KBO-0329 KBO-0330 KBO-0338 KBO-0363 KBO-0368 KBO-0369 KBO-0370 KBO-0371 KBO-0391 KBO-0393 KBO-0394 KBO-0400 KBO-0401 KBO-0409 KBO-0423 KBO-0430
Sequence	KBO_0287 [ Show all 232 ]

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