The implications of natural genetic variation in flax for crop development.

Lead Research Organisation: Durham University
Department Name: Biosciences

Abstract

This project is allied to the agriculture and food security sector via genetic improvement of crops. The project will investigate cultivated flax L. usitatissimum, a globally important crop with many end-uses including an annual global production 2305 Ktonnes of linseed oil and 303 Ktonnes of linen fibre (data from 2013, http://faostat.fao.org/) and Linum bienne, the wild progenitor of cultivated flax. The UK is Europe's leading linseed producer generating 51 ktonnes in 2013. Therefore, this project will contribute to industrial strategy aims to improve UK living standards and economic growth by generating new knowledge and increasing productivity. The approach taken will be through science, research and innovation and developing specialist quantitative and computing skills.
The specific challenge addressed will be improving flax yields through better understanding of the relationship between performance and genetic variation in this crop and its wild relatives. Previous research shows that flax experiences inbreeding depression that limits productivity because controlled crosses lead to a boost in yield in new hybrids. Wild flax harbours considerable natural genetic variation that flax lost during domestication. Therefore, the study of a new European wild flax collection will allow us to test a greater range of inbreeding and genomic responses to inbreeding than would be possible in the crop alone. We will apply controlled crossing studied to directly test the transferability of beneficial natural genetic variation in wild samples into cultivars for agricultural impact.
Aims: This project will measure and compare samples of cultivated and wild flax that vary in their history of genetic inbreeding to test the impact of inbreeding on components of fitness. This fundamental aspect of evolution is thought to drive the maintenance of outcrossing breeding systems and the huge biodiversity of life. This project will contribute to BBSRC's research priority of sustainably enhancing agricultural production via genetic improvement of crops. The CASE partner, RBGE, is an internationally important organization responsible for the conservation and study of plant and fungal biodiversity. This project will feed into the core scientific activities of RBGE to generate baseline botanical data, to document and conserve plant biodiversity, and better understand evolutionary processes in plants.
Methodology: Cultivated and wild flax samples have been collected from a wide transect from north to south Europe. Progenies of these samples will be grown in the glasshouse. Controlled pollination experiments will be performed to generate new seed representing self and outcross progeny. DNA will be sampled and Restriction Amplified DNA (RADseq) genotyping performed for 1000s of single nucleotide polymorphisms (SNPs). Analysis of the sequence data will provide genetically-based measures of outcrossing rate and inbreeding depression across the genome. Inbred and outcrossed controlled-cross individuals will then be grown together and performance and fitness traits (biomass, number of seeds) measured. Sample collection information will be combined with genetic and phenotypic data to be archived in the herbarium collection at RBGE according to internationally agreed standards for plant collections. Associated digital records at RBGE will also be developed to facilitate access and use of these data.
Individual-level patterns of heterozygosity across the genome will be combined with performance data and tested for associations with fitness. Genetic association mapping will be performed to identify genomic regions that contain genetic variation contributing to expression of inbreeding depression and particular performance traits.

Publications

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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/R506321/1 01/10/2017 30/09/2021
2072216 Studentship BB/R506321/1 01/08/2018 31/07/2022 Horasman Habeahan
 
Description A modification of DNA extraction protocol for Linum bienne were developed with new addition in order to strengthen the protocol for Linum species. a new RAD sequence library were developed from these DNA extraction, ready to be analysed further to examine differences in breeding strategies within our population.

Research into how our flax population from different part of Europe are affected under different local adaptations were also undertaken. This allows us to pinpoint and physically examine the fitness of certain local population in our flax collection, allowing us to examine differences between population and local adaptations. There were observed differences under different treatments. Research papers are currently being written on how flax populations are differing across their local latitude. This work is in progress and in partnership with our research partner at Portsmouth University. Due to Covid-19 restrictions and other circumstances surrounding it, we are still being held on the publication of this paper.

Development of whole genome for the wild flax species were also undertaken. This will make it easier for future research involving wild flax. This is useful for development into further flax research. Flax fibres are used to make linen while its seeds are important for the production of lin-seed oil and industrial resins. This makes it a significant player in terms of agriculture while also being part of a wider genus. This features makes flax interesting from both agricultural and evolutionary point of view. Whole genome sequences have been available for cultivars, however, novel wild genomes are only just now being wholly sequenced. This will make it easier to study their wild relatives which may have a genetic advantage that could be introduced into cultivars. Due to Covid-19 circumstances, whole genome work are being disturbed as we are unable to visit our CASE partner at the Royal botanic garden of Edinburgh.

Work to examine pollens viability under different environment were developed. Microscopy techniques are currently being developed to phenotypically examine the sexual viability of each of our population. This would mean a species specific technique for uses of microscopy on future Linum studies.
Exploitation Route Uses of better protocols could be used to produce better results by other researchers.

Whole genome sequence of wild flax are useful to do further genetic work on wild flax.

Phenotypic investigation into the effect of local adaptations within our flax populations might be of interest to further environmental studies involving wild relative of plants.
Sectors Agriculture, Food and Drink,Environment

 
Title Whole Genome sequencing of Wild Flax 
Description We realised that whole genome sequences were available for cultivated flax but not for their wild relatives. Our study would very much be inclusive of the wild flax. With the lack of whole genome sequences for the wild flax as a species, it would then make sense for us to gain genomic sequences. A couple of genomic plants were chosen and were sequenced. We are still at the process of analysis. New techniques, using Oxford Nanopore technologies are also being developed by our group for the purposes of whole genome sequencing of these wild flax. 
Type Of Material Data handling & control 
Year Produced 2019 
Provided To Others? No  
Impact Research involving wild flax as a species should be made easier with the availability of its whole genome. 
 
Description CASE Partnersip 
Organisation Royal Botanic Garden Edinburgh (RBGE)
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution a 3 months placement with potential to do research at the institution for our research purposes.
Collaborator Contribution Funding and CASE Partnership
Impact This collaboration isn't multi-disciplinary. Engagement with the Botanic Garden. Collaboration on laboratory procedures and learning of new techniques for whole genome sequencing of our species of interest. Specialist
Start Year 2018
 
Description Portsmouth Research Collaboration 
Organisation University of Portsmouth
Country United Kingdom 
Sector Academic/University 
PI Contribution Collaboration of research materials from both Durham and Portsmouth universities were done. This allows both collaborators to benefit from a wider set of collected samples as well as future research that can be done together.
Collaborator Contribution Significant sample addition into our flax collections means the quality of our research output are better.
Impact Current ongoing work towards the phenotypic exploration of our collections.
Start Year 2018
 
Description Ecological Genetics SIG: 63rd Annual meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact A Participation in poster presentations in the Ecological Genetics Group annual conference. The 63rd Annual meeting took place at the University of Cambridge where ecological genetic researchers from across the country and beyond come together to present their research and awards. This is part of the British Ecological Society event.
Year(s) Of Engagement Activity 2019
 
Description Public engagement at Durham Botanic Garden 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact A public engagement event with the Botanical Garden of Edinburgh in order for the Department of Biosciences to engage publicly.

The garden gives us a few plots to work with whereby we can showcase our research 'live' to the members of the public as they walk through to botanic garden. These includes school trips and other university members. The plots were used as a "garden" environmental control for our research as well as showcase.

The engagement provided our group with the opportunity to present our work to the wider public and specifically those that may be interested in plants in general. Since our research is plant based and finding out about breeding strategies of plants under different environments, this public engagement was very much of interest to us.

This engagement lasted for more than a year, pre COVID-19 circumstances. We were able to put up posters and a few descriptions which would directly explain what we were doing in the garden plots as well as the research that is taking place inside the laboratory in the department of Biosciences at Durham University.

Our direct presence at the garden plots also gives us the chance to engage with the public directly. These have lead onto conversations and further curiosity of those members of the general public.
Year(s) Of Engagement Activity 2018,2019