Genotypic characterisation of oat ex situ germplasm collections
Lead Research Organisation:
ABERYSTWYTH UNIVERSITY
Abstract
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Technical Summary
unavailable
Planned Impact
unavailable
Organisations
- ABERYSTWYTH UNIVERSITY (Lead Research Organisation)
- Plant Breeding and Acclimatization Institute (Collaboration)
- Kazakh Research Institute of Agriculture and Crop Production (Collaboration)
- N. I. Vavilov All-Russian Institute of Plant Genetic Resources (Collaboration)
- Kahramanmaras University (Collaboration)
Publications
Maughan PJ
(2019)
Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species.
in BMC biology
Paczos-Grzeda E
(2018)
Characteristics of Resistance to Puccinia coronata f. sp. avenae in Avena fatua.
in Plant disease
| Description | Efficient use of sequencing approaches and open source software have been combined by our partner, Dr Martin Mascher, to greatly reduce the cost of creating reference genome assemblies for large and complex plant genomes such as oat (a hexaploid, with a genome size of 13Gb). Funding from this project has allowed assembly of scaffolds for the red oat, Avena byzantina, with an N50 of 1.5Mb, comparable to the quality achieved by the International Wheat Genome Consortium. Scaffolds represent a genetic interval in the order of 1-4cM, a range which is considered tight linkage for genetic markers generated by standard mapping procedures. Our assembly thus allows identification of candidate genes for key agronomic traits, allowing development of functional markers and trait dissection strategies to accelerate breeding. Knowledge of genome sequence also allows identification of oat specific genes and orthologues involved in critical processes such as control of flowering time. Sequences from a range of accessions have been 'captured' using baits designed by Canadian collaborators to recognise the majority of coding sequences, providing a detailed look at the diversity in wild relatives and in traditional and modern cultivars. Anchoring the variants and high throughput genotyping markers to the reference assembly is greatly increasing the value of existing genetic resources and will be used to identify genetic variation to be used in breeding new varieties for our DAC partners in Brazil, Morocco, Turkey, Caucasus countries and Kazakhstan. |
| Exploitation Route | Additional funding has been awarded to continue this work, by completing the reference genome to pseudomolecule level and by carrying out wider and more detailed diversity screens. The scale of the new project will provide greater power to screens which will identify critical variants to fine tune traits such as flowering time. A consortium of leading international groups from North America and Europe will support this work, which will focus on identifying agronomically interesting variation in germplasm from DAC relevant regions, notably Turkey, the Mediterranean basin and Central Asia. Data and genetic resources will be publically available and DAC partners will be involved in its application. |
| Sectors | Agriculture Food and Drink |
| Description | This work strengthened existing links between IBERS and oat growing regions in DAC countries. The ability to compare genetics of native and improved varieties will contribute to enhanced breeding to introduce increased productivity and quality as well as disease resistance to indigenous crops. |
| First Year Of Impact | 2017 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Societal Economic |
| Description | CAPES fellowship |
| Amount | R$Â 90,000 (BRL) |
| Organisation | Ministry of Education (Brazil) |
| Sector | Public |
| Country | Brazil |
| Start | 01/2019 |
| End | 12/2019 |
| 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 | 03/2019 |
| End | 08/2019 |
| Description | Oat domestication - understanding the origin of a European cereal |
| Amount | £548,306 (GBP) |
| Funding ID | BB/S008195/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2018 |
| End | 06/2021 |
| Description | Updated MORPHological dEscriptors for Avena Species (UMORPHEAS) |
| Amount | € 15,000 (EUR) |
| Organisation | The European Cooperative Programme for Plant Genetic Resources |
| Sector | Academic/University |
| Start | 03/2020 |
| End | 02/2022 |
| Title | Annotation pipeline for Avena genomes |
| Description | A curated coding gene database has been developed to allow rapid high quality annotation of Avena genome assemblies. The database was developed from the BBSRC funded Avena byzantina genome assembly using a GeMoMa pipeline dependent on IBERS Avena transcriptome resources and publically available heterologous cereal peptide predictions. The optimised pipeline run on the Welsh SuperComputing facility allowed annotation of the A. sativa hexaploid genome released in summer 2020 by PepsiCo to ~99% completeness within a week (BUSCO statistic, C:98.6% [S:3.8%,D:94.8%],F:0.7%,M:0.7%,n:1440, where 1253 gene annotations were present as three copies). |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Annotation and comparison of red and white oat accessions representing two major lineages of cultivated hexaploid oat (publications in prep). |
| 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 | Exome capture design for oats |
| Description | An exome capture array, targetting 70% of the gene complement, was designed by our partners at AAFC Ottawa, using a variety of transcriptome resources aligned to the IBERS Avena atlantica genome contigs. The Ottawa lab has captured genic sequences from a range of Avena species, both diploid and polyploid, and will use the data to clarify relationships between species. Genic sequences have been recovered for 24 IBERS hexaploid accessions, including NAM population parents and key wild or weedy oat relatives. The combined data will be used to refine the capture design, which may then be deployed to look in more detail at patterns of diversity and targets of selection during adaptation and domestication in panels of cultivars, landraces and wild relatives. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2017 |
| Provided To Others? | No |
| Impact | Funding is being sought for further application of the capture design. |
| Title | Renseq capture 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 | Diversity panel GbS |
| Description | A collection of diverse cultivar, landrace and wild relative accessions for oats, with associated genotyping-by-sequence (GbS) data, of relevance to DAC breeding programmes. The collection includes accessions provided by breeding programmes in Turkey, Kazakhstan and Morocco, and collected on joint expeditions in Georgia and Armenia with representatives of the respective national botanic gardens. The collection is regularly expanded and will be made publically available following completion of the data analysis. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | No |
| Impact | GbS data has helped identify lineages of wild oats likely to have provided the early progenitors of the two main types of cultivated oat (A. sativa or white oat, and A. byzantina or red oat). Landrace comparisons are identifying variation lost during modern breeding bottlenecks. The information is being used to select the most informative lines to be used for fundamental research (exome capture) and field trials in DAC sites (Turkey, Kazakhstan). |
| 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. |
| Description | IHAR, Polish National Research Institute, Radzików |
| Organisation | Plant Breeding and Acclimatization Institute |
| Country | Poland |
| Sector | Learned Society |
| PI Contribution | Preliminary genotyping and transcriptome sequencing is underway for two accessions of the tetraploid Avena macrostachya. The genome of one accession will be sequenced to allow construction of a high quality assembly, which will be annotated using the pipelines developed in earlier BBSRC funded projects. |
| Collaborator Contribution | The IHAR partners have created the leading international collection of Avena macrostachya resouces. A publication in 2020 provides the first comprehensive description of genetic diversity across the range of A. macrostachya populations, while earlier work included introgression of A. macrostachya germplasm into cultivated hexaploid oats. |
| Impact | Preliminary data only |
| Start Year | 2019 |
| Description | Kahramanmaras University, Turkey |
| Organisation | Kahramanmaras University |
| Country | Turkey |
| Sector | Academic/University |
| PI Contribution | Hosted Turkish visitor (Ziya Dumlupinar ) and are growing 780 Turkish landraces at IBERS for allele discovery and pre-breeding |
| Collaborator Contribution | Provided the germplasm for this exchange |
| Impact | - |
| Start Year | 2013 |
| Description | Kazakh Research Institute of Agriculture and Crop Production |
| Organisation | Kazakh Research Institute of Agriculture and Crop Production |
| Country | Kazakhstan |
| Sector | Academic/University |
| PI Contribution | hosted PhD student for 3 months for training in genotyping and for UK field trial of Kazakh material; participated in MSc workshop, Almaty and lecturing. |
| Collaborator Contribution | Hosted IBERS researcher (Tim Langdon) in Kazakhstan. Sharing of Kazakh oat germplasm |
| Impact | - |
| Start Year | 2014 |
| Description | Vavilov Institute |
| Organisation | N. I. Vavilov All-Russian Institute of Plant Genetic Resources |
| Country | Russian Federation |
| Sector | Public |
| PI Contribution | We have good sequence resources and a wide range of germplasm from public genebanks and institute collections, plus bioinformatics and genomics expertise. |
| Collaborator Contribution | Our partners have a unique and extensive genebank collected over many years and added to by recent collections, which is particularly relevant for studies of domestication and adaptation to the ecogeographic conditions of Northern Europe. The head of the department is a world leading expert in Avena taxonomy and is able to provide invaluable advice about species diversity and distribution. |
| Impact | Selection of diversity panel material, sharing of genetic resources. Not multi-disciplinary |
| Start Year | 2019 |
| Description | Oat disease resistance workshop |
| 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 Aberystwyth to discuss application of developing genomics resources to discovery and exploitation of genetic resistance to fungal diseases of oat such as rust and mildew. International experts from Australia and Poland attended, and future collaborations were planned. |
| Year(s) Of Engagement Activity | 2018 |
| 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 | ScanOat meeting |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Discussion of IBERS interaction with newly established Swedish ScanOat research centre, specifically genomics research and dihaploid production. ScanOat have expressed support for genomics research at IBERS (BBSRC RM application) and spin-out company Crop Tailor are seeking to collaborate with IBERS, Senova and Saaten Union/Nordsaat on further development of dihaploid production. |
| Year(s) Of Engagement Activity | 2017 |