Barley pan-transcriptome and reference transcript dataset (pan-BaRT)

Establishing a barley pan-transcriptome that will catalogue transcribed gene sequences and variants therein.

Genetic diversity is vital for adapting barley to new challenging environments and increasing yields. Sources of adaptation are found in our barley collections and are our route to understanding the role of central genes to valuable traits. Recently, 20 barley landraces, cultivars and a wild barley were selected as representatives of global barley diversity. These were sequenced to form the first barley pan-genome and pinpoint previously hidden genetic variation for genetic studies and breeding.

To extend the concept and value of the pan-genome, we are establishing a barley pan-transcriptome that will catalogue transcribed gene sequences and variants therein. Detecting changes in gene transcript expression has become routine in plants by using RNA-seq, a sequencing protocol that allows the assembly of all the transcribed sequences in a sample and allows us to distinguish changes in gene expression between samples. Rapid and accurate quantification of transcribed gene sequences from RNA-seq data can be achieved by using a reference transcript dataset (RTD). We have already developed RTDs for two barley varieties (Morex – BaRTv1.0 and Barke – BaRTv2.18) and these have been used to quantify expression across a range of barley sample tissues and stresses. For example, see our barley expression database (EoRNA) that displays gene and transcript abundance data on demand across over 800 RNA-seq samples from 22 different experiments.

But this does not capture all the variation in expression between barley cultivars!

Construction of a pan-transcriptome and cultivar specific transcriptomes to the 20 pan-genome varieties is underway to expand the range of barley gene transcripts and provide a comprehensive RTD that can be used against most barley cultivars, including contemporary elite lines and wild barely relatives. The barley pan-transcriptome will identify transcripts that are common to barley (“core”), transcripts which are shared by some cultivars only (“dispensable”) and transcripts that are unique to individual varieties and are highly regulated regarding tissue, developmental stage or environmental condition. The barley pan-RTD (pan-BaRT) will allow precise quantification and comparison of allelic variant expression across barley cultivars, enable the construction of regulatory genetic and epigenetic networks, support the development of proteomic resources for barley, promote gene-discovery, gene-editing and will be an essential tool in barley breeding programmes.

This is an international consortium effort with scientists from: Council for Agricultural Research and Economics (CREA), Italy; Institute of Experimental Botany of the Czech Academy of Sciences, Czech Republic; Helmholtz Zentrum München, Germany; Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Germany; Martin Luther University Halle-Wittenberg (MLU), Germany; Murdoch University, Australia; Okayama University, Japan; The James Hutton Institute, Scotland; The University of Adelaide, Australia; University of Dundee, Scotland; University of Minnesota, USA; University of Saskatchewan, Canada; Zhejiang University, China.