Validation of Chromosomal Locations of 90K Array Single Nucleotide Polymorphisms in US Wheat

Abstract

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.

Saturated Genetic Mapping of Wheat Streak Mosaic Virus Resistance Gene Wsm2 in Wheat

“…To conduct genotyping, the DNA was extracted via the cetyltrimethyl ammonium bromide method with minor modifications (Doyle and Doyle, 1990;Liu et al, 2013). Furthermore, genotypic data were converted to linkage scores for linkage mapping: all RILs with the same SNP genotype call as the female parent were designated as A and those with the same as the male parent were designated as B (Liu et al, 2016). The parents were replicated four times and only SNPs with a consistent genotype in at least three parental sets were evaluated to construct genetic maps.…”

“…S1a-f ). Furthermore, genotypic data were converted to linkage scores for linkage mapping: all RILs with the same SNP genotype call as the female parent were designated as A and those with the same as the male parent were designated as B (Liu et al, 2016). In total, 8819 SNPs were used for linkage map construction.…”

Developing KASP Markers on a Major Stripe Rust Resistance QTL in a Popular Wheat TAM 111 Using 90K Array and Genotyping‐by‐Sequencing SNPs

“…After JoinMap analyses, there were 5792 identical markers that were excluded from further analyses. Third, the SNPs with <20% missing values were kept (Liu et al, 2016). The cumulative map length was SNP array, which was conducted at the USDA-ARS Bioscience Research Laboratory in Fargo, ND.…”

“…"Not called (NC)" was assigned to missing values. Third, the SNPs with <20% missing values were kept (Liu et al, 2016). After filtering, a set of 11,839 GBS and 20 simple sequence repeat (SSR) and sequence-tagged site (STS) markers linked to Glu-D1, 1AL.1RS, Gb3, and a set of previously mapped 4861 SNPs from the 90K array were used for map construction.…”

Identification of Quantitative Resistance to Puccinia striiformis and Puccina triticinia in the Soft Red Winter Wheat Cultivar ‘Jamestown’

“…Genome Studio 2.0 software (Illumina, 2016) was used to analyze the SNPs according to genotype. In summary, there were multiple parental clusters called, similar to Liu et al (2016), which were then converted to the A, B, H format (Supplemental Table S1). In summary, there were multiple parental clusters called, similar to Liu et al (2016), which were then converted to the A, B, H format (Supplemental Table S1).…”