Abstract
BackgroundBarley is the world’s fourth most cultivated cereal and is an important crop model for genetic studies. One layer of genomic information that remains poorly explored in barley is presence/absence variation (PAV), which has been suggested to contribute to phenotypic variation of agronomic importance in various crops.ResultsAn mRNA sequencing approach was used to study genomic PAV and transcriptomic variation in 23 spring barley inbreds. 1502 new genes identified here were physically absent from the Morex reference sequence, and 11,523 previously unannotated genes were not expressed in Morex. The procedure applied to detect expression PAV revealed that more than 50% of all genes of our data set are not expressed in all inbreds. Interestingly, expression PAV were not in strong linkage disequilibrium with neighboring sequence variants (SV), and therefore provided an additional layer of genetic information. Optimal combinations of expression PAV, SV, and gene abundance data could enhance the prediction accuracy of predicting three different agronomic traits.ConclusionsOur results highlight the advantage of mRNA sequencing for genomic prediction over other technologies, as it allows extracting multiple layers of genomic data from a single sequencing experiment. Finally, we propose low coverage mRNA sequencing based characterization of breeding material harvested as seedlings in petri dishes as a powerful and cost efficient approach to replace current single nucleotide polymorphism (SNP) based characterizations.
Highlights
Barley is the world’s fourth most cultivated cereal and is an important crop model for genetic studies
This technology allowed addressing how the barley transcriptome varied between tissues [9], and how it responded to pathogens and to environmental cues such as vernalization and heat [10,11,12,13]. eQTL studies with these arrays further revealed a complex pattern of genomewide regulation of barley genes [14], and described how limited pleiotropy acted on gene expression in a tissue dependent manner [15]
To study genomic diversity in spring barley inbreds, we first selected 23 inbreds from a panel of 224 representing a broad range of origins [31] (Additional file 1: Table S1). mRNA was extracted from seedlings and leaves of all of these 23 inbreds, and from apex of a subset of six inbreds (Additional file 1: Table S1)
Summary
Barley is the world’s fourth most cultivated cereal and is an important crop model for genetic studies. The availability of a reference genome sequence facilitates the use of generation sequencing technologies for the discovery of novel sequence variants [6] This allowed e.g. to characterize most of the barley accessions of the German ex situ genebank using a genotyping by sequencing approach [7]. Genome wide quantification of gene expression has been accessible in barley since many years through the development of gene expression arrays [8] This technology allowed addressing how the barley transcriptome varied between tissues [9], and how it responded to pathogens and to environmental cues such as vernalization and heat [10,11,12,13]. With the release of a high quality reference sequence, resequencing technologies are successfully providing novel information on the barley genome and transcriptome that had remained inaccessible [16,17,18]
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