DOI: 10.15482/usda.adc/1529123
title: Data from: Genome-wide association mapping of resistance to the foliar diseases septoria nodorum blotch and tan spot in a global winter wheat collection

description: Phenotypic Data
A subset of 264 lines from the National Small Grains Collection global hexaploid winter wheat germplasm collection was evaluated under controlled growth chamber conditions for reaction to the pathogens Parastagonospora nodorum and Pyrenophora tritici-repentis.
Both infiltrations and inoculations were performed on plants planted in plastic cones and when seedlings were at the second leaf stage. Plants were infiltrated with the P. nodorum necrotrophic effectors (NEs) SnTox1, SnToxA, SnTox3, SnTox267, and SnTox5; and the P. tritici-repentis NE Ptr ToxB. The scoring system was 0-3, with reaction types of 2 and 3 considered sensitive and 0 to 1 were insensitive.
Plants were inoculated with the P. nodorum isolates Sn4, Sn2000, AR2-1, SnIr05H71a, and NOR4 and P. tritici-repentis isolates Pti2, 86-124, DW5, and AR CrossB10. After inoculation, plants were placed in a 100 % humidity growth chamber at 21 °C for 24 hours under constant light, then moved to a controlled growth chamber at 21 °C with a 12 h photoperiod. Plants were scored at 7 days post inoculation. For P. nodorum, plants were scored using a 0 to 5 scale, with 0 being highly resistant and 5 being highly susceptible. For P. tritici-repentis, plants were scored using a 1 to 5 scale, with 1 being highly resistance and 5 being highly susceptible.
Three homogeneous replicates (determined by Bartlett’s chi squared analysis) were used to calculate an average value for each trait. This value was used for the rest of the analysis.
Genotypic Data
DNA of the winter wheat panel was extracted and genotyped using the Illumina iSelect 90k wheat SNP array. Clustering data was analyzed using GenomeStudio 2.0.5 from Illumina, Inc. SNPs were ordered based on their physical position in the Chinese Spring IWGSC RefSeq v2.0. In TASSEL v5.2, SNP markers were filtered with a minor allele frequency greater than 0.01 and missing data less than 50%. For the remaining markers, missing values were imputed using the LD-KNNi method.
Genome-wide association analysis data
Association mapping was conducted using the R package GAPIT v.3. The filtered hapmap file was used for the association mapping, along with the average value for each phenotypic trait. The models GLM, MLM, MLMM, FarmCPU, and Blink were run on the averages for each trait.
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Resources in this dataset:


Resource Title: Phenotypic data collected from 264 lines in the NSGC global hexaploid winter wheat collection
Resource Description: The phenotypic file consists of the lines in this panel, their accession numbers, their ACIMPT designation (improvement status), country and continent of origin, and the scores for each phenotypic trait evaluated, in both replicate from and average of all the replicates. SnToxA, Ptr ToxB, SnTox1, SnTox267, SnTox3, and SnTox5 are all purified necrotrophic effectors and were scored on a 0-3 scale. Sn4, Sn2000, AR2-1, SnIr05H71a, and NOR4 are Parastagonospora nodorum isolates and were scored on a 0-5 scale. Pti2, 86-124, DW5, and AR CrossB10 are Pyrenophora tritici-repentis isolates and were scored on a 1-5 scale. An entry of ‘NA’ indicated missing data.


Resource Title: Necrotrophic effector Ptr ToxB GWAS data output from the winter wheat global panel
Resource Title: Necrotrophic effector SnTox1 GWAS data output from the winter wheat global panel
Resource Title: Necrotrophic effector SnTox3 GWAS data output from the winter wheat global panel
Resource Title: Necrotrophic effector SnTox5 GWAS data output from the winter wheat global panel
Resource Title: Necrotrophic effector SnTox267 GWAS data output from the winter wheat global panel
Resource Title: Necrotrophic effector SnToxA GWAS data output from the winter wheat global panel
Resource Title: P. nodorum isolate AR2-1 GWAS data output from the winter wheat global panel
Resource Title: P. nodorum isolate NOR4 GWAS data output from the winter wheat global panel
Resource Title: P. nodorum isolate Sn4 GWAS data output from the winter wheat global panel
Resource Title: P. nodorum isolate Sn2000 GWAS data output from the winter wheat global panel
Resource Title: P. nodorum isolate SnIr05H71a GWAS data output from the winter wheat global panel
Resource Title: P. tritici-repentis isolate 86-124 GWAS data output from the winter wheat global panel
Resource Title: P. tritici-repentis isolate AR CrossB10 GWAS data output from the winter wheat global panel
Resource Title: P. tritici-repentis isolate DW5 GWAS data output from the winter wheat global panel
Resource Title: P. tritici-repentis isolate Pti2 GWAS data output from the winter wheat global panel
Resource Description for GWAS data output files: The GWAS output file consists of the SNP (SNP), chromosome assignment (Chromosome), position on that chromosome (Position), p-value (P.value), minor allele frequency (maf), number of observations (nobs), FDR adjusted p-values (FDR_Adjusted_P-values), and marker effect. Markers are sorted in order of significance, with the most significant first. Sheet 1 consists of the GLM output, sheet 2 MLM, sheet 3 MLMM, sheet 4 FarmCPU, and sheet 5 Blink.


Resource Title: Winter wheat panel_264 lines_90k_refv2
Resource Description: The genotypic hapmap data file consists of the raw SNP data after cluster analysis and includes 79,103 SNPs. The file consists of the rs# (SNP name), alleles, chrom (1 to 21 with 1 being chromosome 1A, 2 1B, 3 1D, so forth until 21 is 7D), pos (chromosome position based on Chinese Spring IWGSC RefSeq v2.0), strand (+ or NA for negative), assembly, center, protLSID, assayLSID, panelLSID, QCcode, and the 264 lines used in this panel with their SNP allele calls. ‘NA’ means no SNP call was detected.


Resource Title: winterwheatpanel_264 lines_genotype90k_refv2_filtered_KNNimp.hmp
Resource Description: The filtered genotypic hapmap data file consists of the SNP data after cluster analysis, filtering for a minor allele frequency greater than 0.01 and missing data less than 50%, and imputation using the LD-KNNi method. The filtered data consists of  and includes 42,022 SNPs. The file consists of the rs# (SNP name), alleles, chrom (1 to 21 with 1 being chromosome 1A, 2 1B, 3 1D, so forth until 21 is 7D), pos (chromosome position based on Chinese Spring IWGSC RefSeq v2.0), strand (+ or NA for negative), assembly, center, protLSID, assayLSID, panelLSID, QCcode, and the 264 lines used in this panel with their SNP allele calls. ‘NA’ means no SNP call was detected.