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Data from: Association mapping utilizing diverse barley lines reveals net form net blotch seedling resistance/susceptibility loci

dataset
posted on 2024-02-13, 13:12 authored by Jonathan K. Richards, Timothy L. Friesen, Robert S. Brueggeman

A diverse collection of barley lines was phenotyped with three North American Pyrenophora teres f. teres isolates and association analyses detected 78 significant marker-trait associations at 16 genomic loci.

Pyrenophora teres f. teres is a necrotrophic fungal pathogen and the causal agent of the economically important foliar disease net form net blotch (NFNB) of barley. The deployment of effective and durable resistance against P. teres f. teres has been hindered by the complexity of quantitative resistance and susceptibility. Several bi-parental mapping populations have been used to identify QTL associated with NFNB disease on all seven barley chromosomes. Here, we report the first genome-wide association study (GWAS) to detect marker-trait associations for resistance or susceptibility to P. teres f. teres. Geographically diverse barley genotypes from a world barley core collection (957) were genotyped with the Illumina barley iSelect chip and phenotyped with three P. teres f. teres isolates collected in two geographical regions of the USA (15A, 6A and LDNH04Ptt19). The best of nine regression models tested were identified for each isolate and used for association analysis resulting in the identification of 78 significant marker-trait associations (MTA; −log10p value >3.0). The MTA identified corresponded to 16 unique genomic loci as determined by analysis of local linkage disequilibrium between markers that did not meet a correlation threshold of R 2 ≥ 0.1, indicating that the markers represented distinct loci. Five loci identified represent novel QTL and were designated QRptts-3HL, QRptts-4HS, QRptts-5HL.1, QRptts-5HL.2, and QRptts-7HL.1. In addition, 55 of the barley lines examined exhibited a high level of resistance to all three isolates and the SNP markers identified will provide useful genetic resources for barley breeding programs.


Resources in this dataset:

  • Resource Title: Web pointer to supplementary material.

    File Name: Web Page, url: https://link.springer.com/article/10.1007/s00122-017-2860-1#Sec19

    Link to the Electronic Supplementary Material at Theoretical and Applied Genetics. Files are:

    Online Resource 1. Table containing average disease reaction score for all 957 barley accessions used in the association analyses. (XLSX 68 KB)

    Online Resource 2. Histogram illustrating the distribution of phenotypic values for all 957 barley accessions used in association mapping inoculated with P. teres f. teres isolate 15A. (TIFF 1088 KB)

    Online Resource 3. Histogram illustrating the distribution of phenotypic values for all 957 barley accessions used in association mapping inoculated with P. teres f. teres isolate6. (TIFF 1088 KB)

    Online Resource 4. Histogram illustrating the distribution of phenotypic values for all 957 barley accessions used in association mapping inoculated with P. teres f. teres isolate LDN. (TIFF 1088 KB)

    Online Resource 5. Table containing allele information of 19 significant SNP markers associated with disease reaction to P. teres f. teres isolates 15A, 6A, and LDN from 52 barley accessions which were highly resistant to all three P. teres f. teres isolates used in this study. (XLSX 14 KB)

    Online Resource 6. Geographic origin, row type, and growth habit of 52 barley accessions found to be highly resistant to P. teres f. teres isolates 15A, 6A, and LDN. (XLS 31 KB)

    Online Resource 7. A three dimensional representation of the principal components analysis conducted using 957 barley lines genotyped with the barley Illumina 9K iSelect chip. PC1 is illustrated on the x-axis, PC2 is listed on the z-axis, and PC3 is represented on the y-axis. Red dots correspond to 2-row accessions, blue dots correspond to 6-row accessions, and grey dots represent individuals with an unknown row-type. The distinct clustering of the barley genotypes into two groups is representative of 2-row and 6-row barley populations. (PDF 12 KB)

    Online Resource 8. Results of a STRUCTURE analysis conducted using 957 diverse barley lines. Hypothetical subpopulation levels are listed on the x-axis and Delta K values are listed on the y-axis. The largest Delta K value corresponds to a hypothetical sub-population of two, representing 2-row and 6-row barley classes. (PNG 196 KB)

    Online Resource 9. Graphical representation of a STRUCTURE analysis using 957 barley genotypes. Using genetic positions of the iSelect consensus map (Muñoz‐Amatriaín et al. 2014), a single marker was selected from each locus and used in the analysis, resulting in a total of 1744 SNP markers. The results indicate that the barley lines used in this study are divided into two subpopulations. Subpopulation membership is listed on the y-axis ranging from 0.00-1.00. Red indicates membership to subpopulation one and green to subpopulation two. Individuals with membership to a single subpopulation of less than 0.80 were considered admixture. (PNG 51 KB)

    Online Resource 10. Titles and descriptions of online resources. (DOCX 11 KB)

Funding

USDA-NIFA: 2011-68002-30029

National Science Foundation: 11A-1355466

History

Data contact name

Brueggeman, Robert S.

Data contact email

robert.brueggeman@ndsu.edu

Publisher

Springer

Theme

  • Not specified

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

barley; Pyrenophora teres; genomics; loci; fungi; pathogens; net blotch; quantitative trait loci; genome-wide association study; genotype; genotyping; United States; regression analysis; linkage disequilibrium; single nucleotide polymorphism; breeding programs; chromosome mapping; seedlings; genome

Primary article PubAg Handle

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Richards, Jonathan K.; Friesen, Timothy L.; Brueggeman, Robert S. (2018). Data from: Association mapping utilizing diverse barley lines reveals net form net blotch seedling resistance/susceptibility loci. Springer.

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