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

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)

本数据集汇聚了多样化的大麦品种，并利用三种北美地区的 Pyrenophora teres f. teres 分离株对其进行了表型分析。通过关联分析，在16个基因组位点检测到78个显著的标记-性状关联。Pyrenophora teres f. teres 为一种坏死性真菌病原体，是导致大麦经济性重要叶部病害——网状斑驳病（NFNB）的病原菌。有效且持久的抗性部署受到数量性状抗性和易感性的复杂性所阻碍。已利用多个双亲本作图群体来识别与NFNB病害相关的QTL，这些QTL分布于大麦的七个染色体上。本研究首次报告了针对P. teres f. teres的抗性或易感性进行全基因组关联分析（GWAS），以检测标记-性状关联。来自全球大麦核心收集（957个）的地理多样性大麦基因型利用Illumina大麦iSelect芯片进行了基因分型，并使用收集于美国两个地理区域的三个P. teres f. teres分离株（15A、6A和LDNH04Ptt19）进行了表型分析。针对每个分离株，确定了九种回归模型中表现最佳的模型，并用于关联分析，从而识别出78个显著的标记-性状关联（MTA；-log10p值>3.0）。所识别的MTA对应于16个独特的基因组位点，通过分析未达到相关性阈值R2≥0.1的标记之间的局部连锁不平衡确定。这些标记代表不同的位点。其中五个位点所识别的QTL为新型QTL，并被命名为QRptts-3HL、QRptts-4HS、QRptts-5HL.1、QRptts-5HL.2和QRptts-7HL.1。此外，所检验的55个大麦品种对三种分离株均表现出高度抗性，所识别的单核苷酸多态性（SNP）标记将为大麦育种计划提供有价值的遗传资源。本数据集包含的资源：

资源标题：指向补充材料的网络指针。
文件名：网页，网址：https://link.springer.com/article/10.1007/s00122-017-2860-1#Sec19
指向《理论与应用遗传学》中的电子补充材料的链接。
文件包括：

在线资源1：包含用于关联分析的所有957个大麦亲本的平均病害反应得分的表格。（XLSX 68 KB）
在线资源2：显示接种P. teres f. teres分离株15A的所有957个大麦亲本表型值分布的直方图。（TIFF 1088 KB）
在线资源3：显示接种P. teres f. teres分离株6的所有957个大麦亲本表型值分布的直方图。（TIFF 1088 KB）
在线资源4：显示接种P. teres f. teres分离株LDN的所有957个大麦亲本表型值分布的直方图。（TIFF 1088 KB）
在线资源5：包含与P. teres f. teres分离株15A、6A和LDN的病害反应相关的19个显著SNP标记的等位基因信息的表格。（XLSX 14 KB）
在线资源6：发现对P. teres f. teres分离株15A、6A和LDN具有高度抗性的52个大麦亲本的地理起源、行型和生长习性。（XLS 31 KB）
在线资源7：使用大麦Illumina 9K iSelect芯片基因分型的大麦957个品系的三个主成分分析的三维表示。PC1表示在x轴上，PC2列在z轴上，PC3表示在y轴上。红色点对应于二行品种，蓝色点对应于六行品种，灰色点代表行型未知的个体。大麦基因型在两组之间明显的聚类反映了二行和六行大麦种群。（PDF 12 KB）
在线资源8：使用957个多样的大麦品系进行的STRUCTURE分析的结果。假设亚群体水平列在x轴上，Delta K值列在y轴上。最大的Delta K值对应于一个假设的亚群体，代表二行和六行大麦种群。（PNG 196 KB）
在线资源9：使用957个大麦基因型进行的STRUCTURE分析的图形表示。使用iSelect共识图（Muñoz-Amatriaín等，2014）的遗传位置，从每个位点选择一个标记进行分析，从而总共得到1744个SNP标记。结果表明，本研究中使用的的大麦品种被分为两个亚群体。亚群体成员列在y轴上，范围为0.00-1.00。红色表示属于亚群体一，绿色表示属于亚群体二。属于单个亚群体的成员小于0.80的个体被认为是混合的。（PNG 51 KB）
在线资源10：在线资源的标题和描述。（DOCX 11 KB）