Oat domestication - understanding the origin of a European cereal

Lead Research Organisation: Aberystwyth University
Department Name: IBERS

Abstract

Oats can claim to be the only 'European' cereal. Previous work indicated that its closest wild relatives are found around Turkey near sites where wheat and barley were first domesticated, but archaeological evidence points to first use as a crop only late in the development of agriculture and then in Central Europe, rather than in its original environment. A plausible explanation for this transfer is that a population of the wild relative (Avena sterilis), which colonises broken ground, had become adapted to life as an agricultural weed. The new weed (A. fatua) is less able to spread in the wild but is very successful at colonising tilled fields of cereals such as barley. A. fatua could have spread across Europe with those crops and then become a crop in its own right in hard times where others failed. Indeed, oats have traditionally been grown on poor ground and at the end of rotations when soil fertility is low, a possible legacy of this secondary domestication. At some stage completely non-shattering oats would have been selected for easier grain harvest and storage, and greater pressure would have been applied for full domestication (loss of awns, larger grain size and so on).
A complication for this model is that oats appear to have been domesticated twice. Most cultivars now resemble 'white' oats (A. sativa), sown in the spring and most closely related to wild populations in central Turkey. However, around the Mediterranean, traditional landraces are often 'red' oats (A. byzantina), sown in autumn and most closely related to wild populations in south western Turkey. Modern breeding programmes are largely based on crosses between these two types, and the UK's unique winter oat cultivars may be particularly dependent on A. byzantina traits. We have a strong interest in understanding the origin of both red and white oats, and the role of A. fatua. This is not only driven by curiosity about the development of agriculture but also by the need to add new variation to the modern crop. Each domestication step has created genetic bottlenecks where potentially valuable germplasm has been lost. Better understanding of these bottlenecks, and of natural variation in wild populations, will help find useful variation to incorporate into breeding programmes.
Genotyping-by-sequence (GbS) is a recent high throughput method to reveal genetic variation across entire genomes. It samples short sequences adjacent to specific restriction enzyme sites, and does not require prior knowledge of which variants are present. Hundreds of samples may be processed, making it ideal for diversity screens. We have panels of over 500 weedy, wild and landrace accessions already screened by GbS. Unfortunately, the oat genome is almost as large and complex as that of wheat, and no reference is yet available to associate GbS tags with neighbouring genes. Even when the first references become available (expected in 2018), they will have been derived from modern cultivars which may differ from the ancestral stocks we are studying. In this project we will bridge the gap between GbS and genome references to assess gene variation either directly or by improving the references available. In the first step we will use a newly developed sequencing approach to cut the cost of building a red oat reference. In the second we will work with a German barley expert who developed exome capture, a method that samples and sequences only targeted gene regions, and with a Canadian partner who has created an exome capture for oats, based in part on our genome data. We will use an improved design to recover comprehensive collections of gene sequences from 220 key GbS panel accessions. Finally we will obtain sequence from progenitors that will allow comparisons of gene content and order with modern cultivars, and will enhance analysis of exome and GbS data. Working with a Polish partner who has created hybrid populations, we will identify key genes underpinning domestication.

Technical Summary

The project will establish a reliable reference genome for Avena byzantina, one of the two major lineages of cultivated oats, and will use exome capture to identify the most significant changes in genetic diversity that have occurred during the development of modern elite cultivars from wild hexaploids. Capture panels will include wild, weedy, landrace and early cultivar accessions. The data will clarify the origins of the two cultivated oat lineages (A. sativa ss and A. byzantina) and the role of the weed species A. fatua in the emergence of the oat crop in late Neolithic Europe. Resequencing of A. sterilis and A. fatua accessions will provide a full spectrum of gene content across the primary gene pool available for oat breeding.

We will work as part of an international consortium which will provide an exceptional combination of in-kind expertise and resources. An open source bioinformatics pipeline will be used to reduce the cost of assembling the complex (13Gb) hexaploid Avena genome, and increase the accessibility of pan-genome approaches for minor crops. Our exome capture panel is intended to complement work carried out in other public good programmes, and will inform strategies to recover the most valuable germplasm for use in current oat breeding programmes, while characterisation of the secondary domestication process(es) will be of interest to other temperate cereal programmes seeking to improve resilience in modern highly inbred crops.

Planned Impact

Oats have played a significant role in British agriculture for hundreds of years, and are traditionally grown on poorer land or at the end of rotations. As such they have also traditionally been seen as a low value crop. However, it is now widely appreciated that they may form a beneficial component of human diets, having positive effects on satiety, so reducing calorie intake, and providing significant intake of fibre including beta-glucans, which improve gut health and contribute to a lowering of blood cholesterol. Health claims have been approved by the FDA and EFSA and are widely promoted by producers. As a consequence the proportion of oats grown for milling and human use has increased greatly in recent years, and now forms the main use of the crop. This has also contributed to a significant reversal in the decline of the crop that had inevitably followed the loss of animal feed markets wth the introduction of mechanisation in the last century.

There is now an urgent need to revitalise oat breeding as the crop is struggling to maintain production even in the face of this increasing demand for profitable human consumption as food or in cosmetics. It is widely grown across Europe, although frequently on more traditional farms or by older generations of farmers, leading to fears that major producers such as Spain or Poland will abandon oats rather than adapt to more efficient methods. Loss of expertise and infrastructure such as mills is then difficult to reverse, as is being found in North America. Oats are a valuable part of rotations, however, with much unrealised potential both for human and animal use, and the UK leads the way in reversing the historic decline in oat production. The outputs from this proposal would contribute to the critical mass of research needed to introduce methods such as genomic selection into oat breeding, and to accelerate the (re-)introduction of unused variation from the very large numbers of landraces preserved in genebanks. We therefore believe that the project will have long term beneficial impacts (ie through improvements in new variety production) that will include more diverse and lower input agriculture, more sustainable animal feed production as oats substitute imported components and healthier functional foods as beneficial components become additional breeding targets.
 
Description We have constructed a reference genome for one of the two lineages of domesticated oat, Avena byzantina (red oat) in collaboration with Dr Martin Mascher (IPK, Gatersleben). The assembly has been annotated to a high standard (99.3% of BUSCO genes are present and complete, with a further 0.3% present as fragments; 95% of the BUSCO genes are present in multiple copies as expected for a hexaploid). Initial assembly created contigs with an N50 of 1.5Mb. This is a size range roughly equivalent to 1-2cM on a genetic map, allowing markers linked to traits by QTL mapping to be associated with candidate genes. Contigs have been aligned against the most recent oat consensus map which reflects the organisation of the white oat genome, and key genes which differentiate the two lineages are being identified. This will shed light on the processes which have diverged in winter and spring habits. Domestication genes, such as that responsible for loss of grain shattering, are being identified in collaboration with Dr Edyta Paczos-Greda (Lublin). An exome capture design has been made by Nimblegen based on our annotated genes. It targets 140Mb of coding sequence and is being used to reveal sequence diversity in cultivated and wild hexaploid germplasm. A further capture design targets NB-ARC and RLCK gene families which have been found to be responsible for the majority of disease resistance variants in other crops.
Exploitation Route The reference genome adds significant value to existing oat maps and genotyping approaches, enabling identification of candidate genes and improving phenotype prediction.Specifically, the comparison between red and white oat genomes and genes will help dissect the processes responsible for winter and spring growth habits, which will benefit breeding programmes for the UK (predominantly winter) crop in particular. The allele discovery and genetic diversity screens being carried out with the exome captures will provide germplasm and data for prebreeding and elite crop improvement. The improved assembly and annotation resources developed here will support the emerging oat pan-genome project, and be of interest for other complex plant genome researchers.
Sectors Agriculture, Food and Drink

 
Description International Exchanges 2019 Cost Share
Amount £7,300 (GBP)
Funding ID IEC\R2\192164 
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 12/2019 
End 10/2021
 
Description OECD co-operative research programme
Amount $25,000 (CAD)
Organisation Organisation for Economic Co-operation and Development OECD 
Sector Public
Country France
Start 04/2019 
End 08/2019
 
Title Exome capture design for hexaploid oats 
Description A Nimblegen bait design was made targetting 140Mb of coding sequence as annotated from the IBERS Avena byzantina genome assembly. The A. byzantina sequences were supplemented with the most divergent coding sequences identified in transcriptome and preliminary exome capture databases for the IBERS NAM population parents and a small number of additional hexaploid accessions (including A. fatua and A. sterilis). 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? No  
Impact Validation underway, March 2020. 
 
Title Nested Association Mapping (NAM) population for spring oats 
Description Fourteen diverse hexaploid cultivars were crossed with the widely used European spring oat cultivar Firth. 650 lines were derived by single seed descent and advanced generations (F8 on) grown for three years at Aberystwyth and one year in Lublin, Poland (collaboration with Dr Edyta Paczos-Grzeda). RNAseq of developing grain was carried out for all parents. Seed and DNA were saved for the F4 generation of all lines, allowing lines heterozygous for alleles of interest to be identified and used to produce HIFs (contrasting alleles in near identical genetic backgrounds). Exome capture with the Ottawa diploid-based design was carried out on all parents, with skim sequencing and FISHIS libraries of the common parent.. 
Type Of Material Biological samples 
Year Produced 2018 
Provided To Others? Yes  
Impact A consensus map is being created. Candidate gene mapping has identified a candidate for the N1 (naked) gene (collaboration with the Tinker lab, Ottawa). 
 
Title Renseq cature for hexaploid oats 
Description A Resistance gene ENrichment SEQence (Renseq) capture design has been made by Nimblegen based on sequences derived from the IBERS Avena byzantina genome assembly. These sequences include NB-ARC and RLCK gene families. 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? No  
Impact Validation to be carried out in summer 2020. 
 
Title Hexaploid oat coding gene annotation 
Description Coding genes of Avena byzantina have been annotated using an initial MAKER pipeline and heterologous peptide information, followed by a number of refinement steps. BUSCO completeness measurements (v.3) are 99.3% complete, 0.3% fragmented, 95% complete and duplicated. Over 80% of BUSCO genes are present as three or more complete copies. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? No  
Impact A Nimblegen design targetting 140Mb of exon sequence has been produced, as well as a second design targetting NB-ARC and RLCK disease resistance gene families. 
 
Title Hexaploid oat reference genome 
Description A reference genome is being constructed for the hexaploid red oat (A. byzantina) in collaboration with Dr Martin Mascher, IPK, Gatersleben. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact The reference genome is being used to anchor high throughput genetic markers (genotyping-by-sequence) associated with important agronomic traits to sequence scaffolds, which allows the identification of likely candidate genes for further validation. Target genes under analysis (March 2019) include those responsible for grain shattering, naked grain, flowering time, grain beta-glucan content and plant height. 
 
Title Hexaploid oat transcriptomes 
Description RNAseq (Illumina) for six Avena byzantina tissues to support annotation of the A. byzantina reference genome. Additional data from two A. sterilis, two A. fatua and seventeen A. sativa accessions has been generated. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? No  
Impact Annotation of the A. byzantina genome is of a very high quality (BUSCO completeness of 99.7%) 
 
Description BYU 
Organisation Brigham Young University
Country United States 
Sector Academic/University 
PI Contribution Access to diploid and hexaploid reference genome data, transcriptome and mapping population data
Collaborator Contribution Access to diploid reference genome data, genome analyses
Impact Pseudomolecule scale assembly of AA and CC diploid Avena genomes (BYU), assembly of hexaploid oat reference genome (IBERS).
Start Year 2017
 
Description IPK 
Organisation IPK Gatersleben
Country Germany 
Sector Private 
PI Contribution Genetic and physical resources needed to support genomics programme - mapping populations, initial genotyping and selection of key accessions, genomic DNA and specific tissue RNA isolation, resource management.
Collaborator Contribution Genome assembly expertise, including modelling of most efficient sequencing strategies, implementation of bioinformatic pipelines, provision of specialised computing facilities and data analysis
Impact Assembly of a reference genome for red oat, Avena byzantina.
Start Year 2017
 
Description Morden 
Organisation Agriculture and Agri-Food Canada
Country Canada 
Sector Public 
PI Contribution Access to genomic and transcriptomic data
Collaborator Contribution Genetic resources and expertise
Impact OECD fellowship awarded to Canadian RA for 4 month research visit Consortium for RenSeq development
Start Year 2017
 
Description Ottawa 
Organisation Agriculture and Agri-Food Canada
Department Ottawa Research and Development Centre
Country Canada 
Sector Public 
PI Contribution IBERS has assembled and annotated a red oat (Avena byzantina) reference genome.
Collaborator Contribution AAFC Ottawa has designed an exome capture based on the IBERS diploid zipper and additional resources, which has been used to recover coding sequences from white oat (Avena sativa) cultivars and various wild or weedy accessions.
Impact Project meeting in Toronto, 2019 Pan-genome consortium meeting, San Diego 2020
Start Year 2017
 
Description University of Life Sciences, Lublin 
Organisation University of Life Sciences in Lublin
Country Poland 
Sector Academic/University 
PI Contribution Bioinformatics support and access to genomics databases
Collaborator Contribution Population and genetic marker development, field trials and phenotyping of cultivated and hybrid oats.
Impact ERA-CAPS full proposal invited (Avenex, exome capture and targeted resequencing of oats). Identification of candidate genes for key agronomic traits (height, disease resistance), awaiting validation. Training and exchange of support staff. Collaboration with international consortium for hexaploid oat genome sequencing, assembly and annotation.
Start Year 2016
 
Description Oat genomics workshop 2019 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A meeting was held in Toronto to discuss the current state of oat genomics projects and related collaborations. Seven groups from UK, US, Canada, Germany and Sweden took part. Plans were confirmed for the recently funded UK programme, and preparations made for a significant Canadian funding application.
Year(s) Of Engagement Activity 2019
 
Description Pan-oat consortium meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A meeting was held in San Diego following the Oat Workshop at the 2020 PAG conference in January 2020 to establish a pan-genome sequencing consortium for oat. Several dozen conference attendees were present. Dr Martin Mascher outlined the existing consortium and invited additional participation. Discussions of strategy and funding followed.
Year(s) Of Engagement Activity 2020
 
Description Speaker, PAG Oat workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited speaker at PAG, Oat workshop. PAG is the largest international agri-genomics conference and the workshop in 2020 was a focal point to attract participants in a pan-genome sequencing consortium for oat (grant holder organsised a follow-on breakfast meeting for subsequent detailed discussion).
Year(s) Of Engagement Activity 2020