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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	KBO-0287 [ Show all 232 ]
Sequence	[ 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

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