16 ERA-CAPS Barley yield associated networks

Lead Research Organisation: University of Dundee
Department Name: School of Life Sciences

Abstract

Our goal is to identify and characterize novel barley genes that regulate yield, specifically those affecting seed, spike (the inflorescence) and tiller (seed bearing stems) traits. We have previously
generated exome capture sequence data from a geo-referenced collection of 192 two-row landraces, revealing over 1.6 million SNP alleles. Here we plan to phenotype this germplasm collection for yield-related parameters with particular focus on seed, spike, and productive tiller traits. We will assess the same traits, in the same way at each partners location. The uniqueness of our approach lies in our proposal to add layers of transcriptome sequence data (six trait related tissues per genotype) and to analyse how gene expression relates to trait development. In plants, the power of the approach has recently been demonstrated in brassicas under the banner of 'Associative Transcriptomics' to identify genes controlling seed compositional traits. However in yeast and mammalian model organisms, 'chains of causality' are now being identified that link SNPs to transcript abundance variation, to physiological transformation and ultimately risk of disease. We propose that by using multiple tissue types we will take this form of analysis beyond the state-of-the-art, allowing deleterious SNPs in expressed sequences, patterns of transcript abundance, and expression networks to unravel complex yield-related genetic trait interactions.
To enable accurate quantification of transcript read depth, we propose to develop a reference transcript dataset by using deep paired-end Illumina RNA-seq and PacBio ISO-seq data from the six tissues
from cv. Morex. We will use this to quantify transcript abundance from RNA-seq data collected from the same six tissues sampled across the population. RNA-seq derived SNP alleles will supplement the exome capture SNPs and both these data and transcript read depth variation will be used for analysis of the yield-related traits. Gene co-expression networks will be constructed using the reference transcript dataset from Morex and the RNA-seq data from the six tissues sampled from the landrace collection. Both datasets will be integrated to identify candidate genes for key regulators of yield-related traits. Functional characterization of candidate genes will be initiated by identifying deleterious alleles from TILLING populations available in each of the three partner labs. The project will provide global community resources including: a reference transcript dataset, additional SNPs derived from the landrace collection, and gene co-expression networks for exploring key regulatory genes and their relationship to yield-related traits. We will gain an understanding of GxE interactions for key traits. Our approach is only feasible now due to the imminent barley genome release and the unique assembled and characterised germplasm available to the consortium.

Technical Summary

We propose to both phenotype and perform RNA-seq on six tissues from each of a collection of 192 diverse and geo-referenced barley accessions that have already been exome capture sequenced and perform 'associative transcriptomics' and network analysis on the resulting data. By using multiple tissue types we will take this form of analysis beyond the state-of-the-art, allowing deleterious SNPs in expressed sequences, patterns of transcript abundance, and expression networks to unravel complex yield-related genetic trait interactions. We propose to develop a reference transcript dataset by using deep paired-end Illumina RNA-seq and PacBio ISO-seq data from the six tissues from cv. Morex to enable transcript level quantification of gene expression. RNA-seq derived SNP alleles will supplement the exome capture SNPs and both these data and transcript read depth variation will be used for analysis of the yield-related traits. Gene co-expression networks will be constructed using the reference transcript dataset from Morex and the RNA-seq data from the six sampled tissues. Phenotypic and molecular datasets will be integrated to identify candidate genes for key regulators of yield-related traits. Functional characterization of candidate genes will be initiated by identifying deleterious alleles from TILLING populations. The project will provide a reference transcript dataset, additional SNPs derived from the landrace collection, and gene co-expression networks for exploring key regulatory genes and their relationship to yield-related traits. We will gain an understanding of GxE interactions for key traits. Our approach is only feasible now due to release of the barley genome sequence and the unique characterised germplasm available to the consortium.

Planned Impact

Who will benefit from this research?
Barley is a dominant component of European agriculture and 70-80% of the crop provides a major source of calories for inclusion in animal feed. Based on the use of approximately 30% of the UK crop, barley underpins the multi-billion pound beer and whisky industries that are key pillars of the UK food and drink sector. Developing novel types of high yielding, high quality barley will ultimately provide support for and benefit commercial breeders, farmers, maltsters, feed compounders, and processors.

How will they benefit from this research?
The entire value chain, from breeder to retailer, will benefit from higher revenues from increased production and consumption of traditional products and the development of novel high value products. Farmers will benefit from being able to produce and sell improved varieties with no additional investment, for both conventional and high value products. Processors will benefit from a resilient supply chain and retailers from the increasing demand of barley derived products - including health conscious populations seeking healthy products without additives. Demand for high quality malted barley is already increasing in Asia and this commercial pull could encourage farmers to grow more malting barley allowing themselves, maltsters and distributors to realise increased profits from high value commodity exports.

What will be done to ensure that they have the opportunity to benefit from this research?
The conduit through which almost all genetic advances in crop production must pass to release their benefits to the broader community is the plant breeding / biotech sector. Translational activities from basic science to application are therefore crucial and we will maintain and develop these throughout the proposed program. The UK boasts one of the most efficient and successful commercial cereal breeding sectors in Europe and the applicants have long standing collaborations with the majority of the UK breeding companies. All applicants have strong links within the academic sector and each has a strong reputation and identity within the global community. A key distinguishing feature of this project is the international collaboration and the added-value through participation of IPK Gatersleben and the University of Minneapolis. Collectively, the PI's have has many years' experience in researching barley, and have the relevant expertise, track-record and motivation to ensure the project reaches a successful conclusion: while also carrying out excellent fundamental research on a globally important crop.

Publications

10 25 50
 
Title BaRT 
Description A database containing a reference set of transcripts expressed from the barley cultivar Morex. Used for rapid and accurate analysis of RNA-seq data 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Rapid and accurate analysis of RNA-seq data using alignment free methods 
URL https://ics.hutton.ac.uk/barleyrtd/index.html
 
Description Barley Pan Genome 
Organisation IPK Gatersleben
Country Germany 
Sector Private 
PI Contribution Provide a reference quality sequence of the cultivar Golden Promise
Collaborator Contribution Reference Quality sequences of other barley genotypes (consortium effort)
Impact No outcomes yet
Start Year 2017
 
Description Barley Yield associated Networks (BARN) 
Organisation IPK Gatersleben
Country Germany 
Sector Private 
PI Contribution BARN is an ERA CAPS collaborative award with three partners. We will provide a Reference Transcript dataset and RNA seq information from 2 tissues from 200 barley cultivars. We will jointly analyse the resulting data
Collaborator Contribution Each has common and specific tasks. The Reference Transcript dataset and RNA seq information will be used to interrogate expression in a further 2 tissues from 200 barley cultivars. We will also survey sequence all 200 lines and build cultivar specific RTD's to assist analysis. The partners will jointly analyse the resulting data
Impact Too early
Start Year 2018
 
Description Barley Yield associated Networks (BARN) 
Organisation University of Minnesota
Country United States 
Sector Academic/University 
PI Contribution BARN is an ERA CAPS collaborative award with three partners. We will provide a Reference Transcript dataset and RNA seq information from 2 tissues from 200 barley cultivars. We will jointly analyse the resulting data
Collaborator Contribution Each has common and specific tasks. The Reference Transcript dataset and RNA seq information will be used to interrogate expression in a further 2 tissues from 200 barley cultivars. We will also survey sequence all 200 lines and build cultivar specific RTD's to assist analysis. The partners will jointly analyse the resulting data
Impact Too early
Start Year 2018
 
Description SAB 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact BBSRC requested we establish a Science Advisory Board for our Barley Reference Transcript Database (RTD) project and we extended the remit of this SAB to cover a range of other related projects and to gather their expert feedback more widely. We received written feedback from Mario Caccammo and Philippa Borill at our first meeting last April. The SAB will meet again in April though we have extended its composition to include Ian Bancroft (who couldnt make the first meeting) and representation from the EBI (Bruno Contreras) and the barley Pan Genome Consortium (Nils Stein).
Year(s) Of Engagement Activity 2019