Query (optional)   in Class  All Allele Author Colleague Collection Assembly Gene Gene Class Gene Product Germplasm Image Journal Keyword Library Locus Map Map Data Marker Pathology Polymorphism Probe Protein QTL Rearrangement Reference Sequence Species Trait Trait Study Two Point Data  

---

GrainGenes Reference Report: TAG-123-555

[Submit comment/correction]

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	[ Hide all but 1 of 446 ] kbo-0001 kbo-0001-2A kbo-0010 kbo-0010-2A kbo-0014 kbo-0014-1B kbo-0016 kbo-0016-1B kbo-0019 kbo-0019-7B kbo-0026 kbo-0026-3A kbo-0029 kbo-0029-7B kbo-0033 kbo-0033-2B kbo-0034 kbo-0034-1B kbo-0039 kbo-0039-5A kbo-0041 kbo-0041-4B kbo-0045 kbo-0045-2A kbo-0051 kbo-0051-1B kbo-0053 kbo-0053-6A kbo-0058 kbo-0058-4A kbo-0059 kbo-0059-4B kbo-0061 kbo-0061-3A kbo-0062 kbo-0062-2A kbo-0064 kbo-0064-4B kbo-0066 kbo-0066-7A kbo-0067 kbo-0067-2A kbo-0069 kbo-0069-5A kbo-0075 kbo-0075-3B kbo-0077 kbo-0077-5B kbo-0079 kbo-0079-6A kbo-0080 kbo-0080-2B kbo-0081 kbo-0081-2B kbo-0082 kbo-0082-1B kbo-0086 kbo-0086-4B kbo-0087 kbo-0087-7B kbo-0089 kbo-0089-2B kbo-0090 kbo-0090-2B kbo-0091 kbo-0091-6A kbo-0092 kbo-0092-3A kbo-0096 kbo-0096-4A kbo-0102 kbo-0102-2A kbo-0103 kbo-0103-1B kbo-0109 kbo-0109-6A kbo-0117 kbo-0117-5B kbo-0119 kbo-0119-2B kbo-0125 kbo-0125-4A kbo-0128 kbo-0128-1A kbo-0130 kbo-0130-6A kbo-0131 kbo-0131-6A kbo-0132 kbo-0132-6A kbo-0135 kbo-0135-1B kbo-0136 kbo-0136-6A kbo-0137 kbo-0137-6A kbo-0139 kbo-0139-7A kbo-0142 kbo-0142-4A kbo-0145 kbo-0145-2B kbo-0146 kbo-0146-7B kbo-0150 kbo-0150-4A kbo-0152 kbo-0152-7B kbo-0161 kbo-0161-2A kbo-0166 kbo-0166-7A kbo-0169 kbo-0169-6B kbo-0170 kbo-0170-4B kbo-0171 kbo-0171-2B kbo-0172 kbo-0172-7A kbo-0173 kbo-0173-2A kbo-0175 kbo-0175-1B kbo-0180 kbo-0180-3A kbo-0183 kbo-0183-7B kbo-0190 kbo-0190-2B kbo-0192 kbo-0192-5A kbo-0196 kbo-0196-2B kbo-0198 kbo-0198-4A kbo-0199 kbo-0199-1B kbo-0200 kbo-0200-1B kbo-0203 kbo-0203-1B kbo-0204 kbo-0204-6B kbo-0209 kbo-0209-7B kbo-0211 kbo-0211-1B kbo-0214 kbo-0214-4A kbo-0218 kbo-0218-7A kbo-0220 kbo-0220-5B kbo-0222 kbo-0222-2A kbo-0226 kbo-0226-3B kbo-0228 kbo-0228-1A kbo-0233 kbo-0233-4A kbo-0235a kbo-0235a-3A kbo-0235b kbo-0235b-3A kbo-0236 kbo-0236-4B kbo-0237 kbo-0237-4B kbo-0242 kbo-0242-6A kbo-0247 kbo-0247-2A kbo-0250-6B kbo-0252 kbo-0252-6B kbo-0254 kbo-0254-1B kbo-0254a-1B kbo-0255 kbo-0255-7B kbo-0260 kbo-0260-1B kbo-0287 kbo-0287-1A kbo-0290 kbo-0290-3A kbo-0291 kbo-0291-6B kbo-0293 kbo-0293-5A kbo-0294 kbo-0294-7A kbo-0295 kbo-0295-2A kbo-0298 kbo-0298-5A kbo-0301 kbo-0301-1A kbo-0303 kbo-0303-1B kbo-0304 kbo-0304-2B kbo-0305 kbo-0305-2B kbo-0306 kbo-0306-4A kbo-0309 kbo-0309-5B kbo-0312 kbo-0312-1B kbo-0317 kbo-0317-6A kbo-0325 kbo-0325-7B kbo-0331 kbo-0331-4B kbo-0333 kbo-0333-2B kbo-0335 kbo-0335-3B kbo-0336 kbo-0336-6A kbo-0337 kbo-0337-6B kbo-0346 kbo-0346-4B kbo-0347 kbo-0347-6B kbo-0348 kbo-0348-5A kbo-0350 kbo-0350-2B kbo-0351 kbo-0351-2A kbo-0356 kbo-0356-4A kbo-0357 kbo-0357-4A kbo-0364 kbo-0364-7A kbo-0366 kbo-0366-7B kbo-0367 kbo-0367-2B kbo-0372 kbo-0372-7B kbo-0375 kbo-0375-2A kbo-0376 kbo-0376-4A kbo-0379 kbo-0379-4B kbo-0380 kbo-0380-2B kbo-0381 kbo-0381-2A kbo-0383 kbo-0383-6A kbo-0386 kbo-0386-1B kbo-0389 kbo-0389-7B kbo-0390 kbo-0390-7B kbo-0392 kbo-0392-3B kbo-0395 kbo-0395-2A kbo-0399 kbo-0399-6B kbo-0402 kbo-0402-3B kbo-0405 kbo-0405-1A kbo-0406 kbo-0406-7B kbo-0407 kbo-0407-1B kbo-0416 kbo-0416-3B kbo-0417 kbo-0417-1A kbo-0420 kbo-0420-7A kbo-0421 kbo-0421-6B kbo-0425 kbo-0425-1B kbo-0426 kbo-0426-5A kbo-0431 kbo-0431-2B kbo-0434 kbo-0434-1A kbo-0435 kbo-0435-5B KBO_0001 KBO_0010 KBO_0014 KBO_0016 KBO_0019 KBO_0026 KBO_0029 KBO_0033 KBO_0034 KBO_0039 KBO_0041 KBO_0045 KBO_0051 KBO_0053 KBO_0058 KBO_0059 KBO_0061 KBO_0062 KBO_0064 KBO_0066 KBO_0067 KBO_0069 KBO_0075 KBO_0077 KBO_0079 KBO_0080 KBO_0081 KBO_0082 KBO_0086 KBO_0087 KBO_0089 KBO_0090 KBO_0091 KBO_0092 KBO_0096 KBO_0102 KBO_0103 KBO_0109 KBO_0117 KBO_0119 KBO_0125 KBO_0128 KBO_0130 KBO_0131 KBO_0132 KBO_0135 KBO_0136 KBO_0137 KBO_0139 KBO_0142 KBO_0145 KBO_0146 KBO_0150 KBO_0152 KBO_0161 KBO_0166 KBO_0169 KBO_0170 KBO_0171 KBO_0172 KBO_0173 KBO_0175 KBO_0180 KBO_0183 KBO_0190 KBO_0192 KBO_0196 KBO_0198 KBO_0199 KBO_0200 KBO_0203 KBO_0204 KBO_0209 KBO_0211 KBO_0214 KBO_0218 KBO_0220 KBO_0222 KBO_0226 KBO_0228 KBO_0233 KBO_0235 KBO_0236 KBO_0237 KBO_0242 KBO_0247 KBO_0250 KBO_0252 KBO_0254 KBO_0255 KBO_0260 KBO_0287 KBO_0290 KBO_0291 KBO_0293 KBO_0294 KBO_0295 KBO_0298 KBO_0301 KBO_0303 KBO_0304 KBO_0305 KBO_0306 KBO_0309 KBO_0312 KBO_0317 KBO_0325 KBO_0331 KBO_0333 KBO_0335 KBO_0336 KBO_0337 KBO_0346 KBO_0347 KBO_0348 KBO_0350 KBO_0351 KBO_0356 KBO_0357 KBO_0364 KBO_0366 KBO_0367 KBO_0372 KBO_0375 KBO_0376 KBO_0379 KBO_0380 KBO_0381 KBO_0383 KBO_0386 KBO_0389 KBO_0390 KBO_0392 KBO_0395 KBO_0399 KBO_0402 KBO_0405 KBO_0406 KBO_0407 KBO_0416 KBO_0417 KBO_0420 KBO_0421 KBO_0425 KBO_0426 KBO_0431 KBO_0434 KBO_0435
Probe	KBO-0287 [ Show all 232 ]
Sequence	KBO_0287 [ Show all 232 ]

GrainGenes is a product of the Agricultural Research Service of the US Department of Agriculture.