Genomic resources for a historical collection of cultivated two-row European spring barley genotypes

Abstract

Barley genomic resources are increasing rapidly, with the publication of a barley pangenome as one of the latest developments. Two-row spring barley cultivars are intensely studied as they are the source of high-quality grain for malting and distilling. Here we provide data from a European two-row spring barley population containing 209 different genotypes registered for the UK market between 1830 to 2014. The dataset encompasses RNA-sequencing data from six different tissues across a range of barley developmental stages, phenotypic datasets from two consecutive years of field-grown trials in the United Kingdom, Germany and the USA; and whole genome shotgun sequencing from all cultivars, which was used to complement the RNA-sequencing data for variant calling. The outcomes are a filtered SNP marker file, a phenotypic database and a large gene expression dataset providing a comprehensive resource which allows for downstream analyses like genome wide association studies or expression associations.

Major chromosome 5H haplotype switch structures the European two-rowed spring barley germplasm of the past 190 years

“…The datasets used in this study are described in detail in Schreiber et al ( 2023 ). Briefly, we utilized genotypic and transcript data of 209 barley varieties from the past 190 years which were selected for their representativeness of the European two-rowed spring barley germplasm (Schreiber et al 2023 , Online Resource 1).…”

“…The datasets used in this study are described in detail in Schreiber et al ( 2023 ). Briefly, we utilized genotypic and transcript data of 209 barley varieties from the past 190 years which were selected for their representativeness of the European two-rowed spring barley germplasm (Schreiber et al 2023 , Online Resource 1). The genotypic dataset comprised 1,509,446 biallelic SNP markers derived from 150 bp paired-end RNAseq data from six tissues (seedling crown, seedling root, peduncle, developing inflorescence, spikelet at green anther stage and developing grain five days post anthesis), WGS skim sequencing at threefold haploid genome coverage and the 50 k Illumina Infinium iSelect array (Bayer et al 2017 ).…”

“…Here, we present a high-resolution characterization of barley diversity in a panel of 209 landraces and cultivars representative of 190 years of breeding history in the European two-rowed spring barley germplasm (Schreiber et al 2023 ). Based on a high-density SNP dataset comprising 1.5 million SNPs from transcript and whole genome shotgun (WGS) sequencing data derived from the entire diversity panel and a gene expression survey of six tissues sampled during plant development, the genetic and multi-omic characterization allowed us to track major haplotype and transcript changes in the European barley breeding history (Schreiber et al 2023 ). To fully exploit this rich resource of high-density multi-omics datasets, we thoroughly studied the genetic and structural aspects of this panel.…”

A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity

“…Finally, given access to a complementary pan-genome, we assessed whether variation in transcription factor binding sites (TFBSs) in the proximal regions of orthologous genes could influence transcript abundance. We computed the location and occurrence of 30 TFBSs [20][21][22] in 2,000bp upstream of the coding sequence and compared these to a bona fide set representing all genes of cv. Morex (Methods).…”

“…20 different inversions over 10Mb in size in relation to the cultivar Morex 8 were aligned on a per chromosome basis using minimap2 (-2 -I 6G -K 5G -f 0.005 -x asm5 -c --eqx) followed by variant identification using SyRI 50 and plotting using plotsr 51 with default parameters. Differential gene expression analyses using RNA-sequencing reads from PRJEB49069 21 were as described above. PCR primers as described 8 were used to identify genotypes with the 141Mb 7H inversion (Supplementary Data 7).…”