Validation of Chromosomal Locations of 90K Array Single Nucleotide Polymorphisms in US Wheat
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Crop Science Society of America. All rights reserved. Mapping single nucleotide polymorphisms (SNPs) in wheat (Triticum aestivum L.) can help to develop high throughput molecular markers for important traits. The 90K Infinium iSelect SNP array was used to screen three recombinant inbred line (RIL) populations derived from three crosses, CO 960293-2/TAM 111 (CT), TAM 112/TAM 111 (TT), and Halberd/Len (HL). The objective of this study was to compare and validate the chromosomal locations of mapped SNPs in wheat. A set of 152, 124, and 180 RILs were used in CT, TT, and HL. Among the 91,829 SNPs, 54,258 SNPs were called at least in one mapping population. A set of 5950, 4861, and 8376 SNPs were mapped onto chromosomes of CT, TT, and HL, respectively, with a total of 15,604 unique SNPs. Only 374 SNPs (2.4%) were commonly mapped across three populations, and 3025 SNPs (19.4%) were mapped across all combinations of two of the three populations. The number of uniquely mapped SNPs specific to each population was 3291 (21.1%) in CT, 2418 (15.5%) in TT, and 6224 (40.0%) in HL. With known chromosomal locations of the mapped 40K out of 90K array SNPs, linkage groups in all three mapping populations were assigned onto chromosomes. More than 76% of the mapped SNPs have consistent chromosomal locations with the previously mapped 40K SNPs. A set of 2190 (14.0%) unique newly mapped SNPs and 1316 (8.4%) SNPs mapped onto multiple chromosomes were presented. These chromosome maps are essential for the discoveries of genes and quantitative trait loci (QTL) of important traits in wheat.
