GrainGenes is a popular repository for information about genetic maps, mapping probes and primers, genes, alleles and QTLs for the following crops: wheat, barley, rye and oat. Documentation includes such data as primer sequences, polymorphism descriptions, genotype and trait scoring data, experimental protocols used, and photographs of marker polymorphisms, disease symptoms and mutant phenotypes. These data, curated with the help of many members of the research community, are integrated with sequence and bibliographic records selected from external databases and results of BLAST searches of the ESTs. Records are linked to corresponding records in other important databases, e.g. Gramene's EST homologies to rice BAC/PACs, TIGR's Gene Indices and GenBank. In addition to this information within the GrainGenes database itself, the GrainGenes homepage at http://wheat.pw.usda.gov provides many other community resources including publications (the annual newsletters for wheat, barley and oat, monographs and articles), individual datasets (mapping and QTL studies, polymorphism surveys, variety performance evaluations), specialized databases (Triticeae repeat sequences, EST unigene sets) and pages to facilitate coordination of cooperative research efforts in specific areas such as SNP development, EST-SSRs and taxonomy. The goal is to serve as a central point for obtaining and contributing information about the genetics and biology of these cereal crops Resources in this dataset:Resource Title: GrainGenes, the genome database for small-grain crops (main web site). File Name: Web Page, url: http://wheat.pw.usda.gov/GG3/ GrainGenes is the primary repository for information about genetic maps, mapping probes and primers, genes, alleles and QTLs; crops are wheat, barley, rye and oat. Documentation includes such data as primer sequences, polymorphism descriptions, genotype and trait scoring data, experimental protocols used, and photographs of marker polymorphisms, disease symptoms and mutant phenotypes. These data, curated with the help of many members of the research community, are integrated with sequence and bibliographic records selected from external databases and results of BLAST searches of the ESTs. Records are linked to corresponding records in other important databases, e.g. Gramene's EST homologies to rice BAC/PACs, TIGR's Gene Indices and GenBank.

GrainGenes is an international, centralized crop database for peer-reviewed small grains data and information portal that serves the small grains research and breeding communities (wheat, barley, oat, and rye). The GrainGenes project ensures long-term data curation, accessibility, and sustainability so that small grains researchers can develop new, more nutritious, disease and pest resistant, high yielding cultivars. As a digital platform, GrainGenes houses peer-reviewed and curated genetic, genomic, and protein data. It has been hard-funded by the U.S. Department of Agriculture-Agricultural Research Service to ensure long-term data sustainability through a functional and integrated web interface for wheat, barley, oat, and rye.

Genotyping data (HapMap file)The OzBarley germplasm was genotyped using the Infinium™ Wheat Barley 40K v1.0 BeadChip (Elite Panel) and v1.1 BeadChip (Landraces) (Illumina, San Diego, USA).In addition, RNA sequencing of the OzBarley elite panel was conducted using 4-day old seedlings germinated on filter paper (roots, embryo and coleoptile).Library preparation and sequencing was conducted at the Australian Genome Research Facility.SNP data from the chip and RNAseq data was combined and aligned to Barley cv. MorexV3.(refer to readme file for more details)Transcript abundance (cpm_count files)cpm_counts.tsv and cpm_count.xlsx contain the results of an RNA-Seq experiment conducted on 217 barley accessions. The sequence reads were aligned to the Morex v3 reference genome, followed by read counting and normalization. The read counts are expressed in CPM (counts per million reads). The final column provides gene annotations, which were obtained alongside the Morex v3 genome assembly (version Hv_Morex.pgsb.Jul2020) from GrainGenes (https://wheat.pw.usda.gov/GG3/).SNP effects (snp_description file)SNPs identified from the RNA-Seq data were combined with genotype calls obtained using the Illumina XT Wheat-Barley SNP chip. The file snp_description.csv provides information on the genomic location of each SNP and their predicted effects on genes. Variant effects were determined using the SnpEff software (https://pcingola.github.io/SnpEff/). For detailed explanations of the effect terms used, refer to Table 2 in the publication by Cingolani et al. (2012): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679285/Supplementary Data 1A file containing the OzBarley IDs and cultivar names to match the phylogenetic network analysis presented in the OzBarley manuscript (Figure 4)

Phenotypic data: A total of 510 lines from the global durum panel (GDP) were evaluated for reaction to five isolates of the fungal pathogen Pyrenophora tritici-repentis. The five isolates were Pti2 (race 1), 86-124 (race 2), 331-9 (race 3), L13-192 (race 4), and DW5 (race 5). The GDP lines were inoculated in a greenhouse when plants were at the two- or three-leaf stage. Plants were grown in a randomized complete block design consisting of one replicate per experiment, and each experiment was repeated three times. Following inoculation, the plants were placed in misting chambers with 100% relative humidity at 21 °C for 24 h, and then placed in a growth chamber under a 12-h photoperiod at 21 °C. Disease reactions were scored 7 days after inoculation following the 1–5 scale where 1 was highly resistant and 5 was highly susceptible. Seedlings of the GDP were also infiltrated with cultures containing the necrotrophic effectors (NEs) Ptr ToxA and Ptr ToxB. Approximately 20 μl of NE-containing culture filtrate (CF) was infiltrated into two plants (1 leaf per plant) in each cone using a needleless 1-ml syringe. The infiltrated area (~3 cm) was marked with permanent marker on the leaves, and the plants were placed in a growth chamber (21 °C, 12-h photoperiod) for 5 days. The reactions were scored using a 0–3 scale where 0 indicated no reaction and 3 indicated severe necrosis or chlorosis. The expansion of chlorosis beyond the boundaries of Ptr ToxB infiltration to the distal end of the leaf was scored separately using 0 or 1 meaning the absence or presence of the symptom, respectively. This trait is noted as ‘ToxB_Spread’ in the data file. Genotypic data: The GDP lines were genotyped using the Illumina iSelect 90K SNP array. Markers were filtered using previously published genetic maps, and marker sequences were aligned to the Svevo.v1 reference genome. SNP imputation was performed, and the redundant markers were pruned based on genome wide linkage disequilibrium, which resulted in a data set with no missing SNP calls. The hapmap information of 855 genotypes and 13,373 SNPs developed by M. Maccaferri is located on the GrainGenes website (https://wheat.pw.usda.gov/GG3/global_durum_genomic_resources). The haplotype map of the 855 genotypes was reduced to 510 genotypes that were selected for phenotypic tests. The SNP data set was selected according to the set filtering for minor allele frequency (MAF) > 5% that resulted in a marker set containing 12,222 SNPs.