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GrainGenes Reference Report: PBJ-12-787

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Reference	PBJ-12-787
Title	Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array.
Journal	Plant Biotechnology Journal
Year	2014
Volume	12
Pages	787-796
Author	Wang S [ Show all 40 ]
Abstract	High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.
External Databases	http://dx.doi.org/doi:10.1111/pbi.12183
Locus	IWB1 [ Show all 37426 ]
Map Data	Wheat_2014_90KSNP Wheat AB, Carotenoid QTL, 2017 Wheat_Yr80_2018
Probe	Ra_c23068_380 [ Show all 81586 ]
Sequence	[ Hide all but 1 of 45 ] BobWhite_c11655_343 BobWhite_c12159_729 BobWhite_c12469_173 BobWhite_c14360_420 BobWhite_c14575_323 BobWhite_c1514_523 BobWhite_c15485_590 BobWhite_c17524_242 BobWhite_c18305_366 BobWhite_c1842_612 BobWhite_c1971_839 BobWhite_c21589_200 BobWhite_c25110_98 BobWhite_c260_197 BobWhite_c27287_232 BobWhite_c27541_67 BobWhite_c28971_184 BobWhite_c31599_754 BobWhite_c3208_63 BobWhite_c32883_84 BobWhite_c4500_922 BobWhite_c47168_289 BobWhite_c47168_346 BobWhite_c4729_243 BobWhite_c48435_288 BobWhite_c5235_710 BobWhite_c55284_78 BobWhite_c5655_300 BobWhite_c8266_916 BobWhite_c8680_453 BobWhite_rep_c49500_317 BobWhite_rep_c49803_201 BobWhite_rep_c50314_226 BobWhite_rep_c55035_124 BobWhite_rep_c58171_408 BobWhite_rep_c58803_337 BobWhite_rep_c61871_254 BobWhite_rep_c63322_592 BobWhite_rep_c64211_160 BobWhite_rep_c64288_193 BobWhite_rep_c64934_62 BobWhite_rep_c65765_222 BobWhite_rep_c67506_170 BobWhite_s66737_344 BobWhite_s67322_122

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