DOI: 10.25909/29104916
title: OzBarley: genotypic and expression data of the OzBarley elite panel

description: <b>OzBarley landrace panel SNPchip data: </b>The OzBarley landrace panel was genotyped using the Infinium™ Wheat Barley 40K v1.1 BeadChip (Illumina, San Diego, USA). Marker positions are based on the Barley cv. MorexV3 assembly. OzBarley IDs and line names are provided as concatenated identifier in the first column of the excel file.<b>Genotyping data (HapMap file): </b>The OzBarley germplasm was genotyped using the Infinium™ Wheat Barley 40K v1.0 BeadChip (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)<b>Raw RNA sequencing data: </b>Raw data are deposited in the NCBI Sequence Read Archive under accession number PRJNA1152269 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1152269). The data are provided in FASTQ format.<b>SNP effects (snp_description file): </b>SNPs identified from the RNA-Seq data were combined with genotype calls obtained using the Illumina XT Wheat-Barley SNP chip. The file <b>snp_description.csv</b> provides information on the genomic location of each SNP and their predicted effects on genes. Variant effects were determined using the <b>SnpEff</b> 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/<b>Transcript abundance (cpm_count files): </b><b>cpm_counts.tsv</b> and <b>cpm_count.xlsx</b> contain the results of an RNA-Seq experiment conducted on 217 barley accessions. The sequence reads were aligned to the <i>Morex v3</i> 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 <i>Morex v3</i> genome assembly (version <b>Hv_Morex.pgsb.Jul2020</b>) from GrainGenes (https://wheat.pw.usda.gov/GG3/).<b>OzBarley pedigree: </b>The OzBarley elite panel pedigree is provided in txt format for import and display in Helium software (https://github.com/cardinalb/helium-docs/wiki). A graphic representation of the pedigree is available as png file, where OzBarley elite lines are presented as blue octagons, other lines required for displaying the pedigree, but not part of the OzBarley panel, are presented as black circles. The symbol size represents the relative contribution to the pedigree.<b>Phylogenetic network: </b>A file containing the OzBarley IDs and cultivar names to match the phylogenetic network analysis is provided in excel format. The phylogenetic network using OzBarley SNP data was performed using PLINK and NetViewR and is provided in pdf format.<b>OzBarley Multi-Crop Passport Descriptors: </b>OzBarley lines were described according to the Multi-Crop Passport Descriptor convention (https://hdl.handle.net/10568/105205). Data is provided in Excel format and can also be accessed on the OzBarley Germinate instance (https://ozbarley.plantphenomics.org.au/).<br>