Award details

FACCE ERA-NET+ GrassLandscape (Project Leader: Jean-Paul Sampoux, INRA, France)

Reference	BB/M018393/1
Principal Investigator / Supervisor	Dr Matthew Hegarty
Co-Investigators / Co-Supervisors
Institution	Aberystwyth University
Department	IBERS
Funding type	Research
Value (£)	245,697
Status	Completed
Type	Research Grant
Start date	01/12/2014
End date	31/07/2017
Duration	32 months

Abstract

Natural populations of perennial ryegrass have been extensively collected during the last three decades as potential genetic resources for breeding programmes and have been maintained as seed lots (accessions) in genebanks of plant breeding research institutes. Genebanks thus provide a straightforward access to a large number of natural populations of perennial ryegrass. We will establish a "genebank set" by choosing 500 accessions originating from sites that will cover the distributional range of perennial ryegrass. We will also set up a second diversity test, by performing a new in situ sampling of 50 populations across the same territory that will maximise environmental variations. Sampling will be performed by collecting tillers from 30 plants in each of the 50 populations. Geographical coordinates of collection sites of populations will be used to extract climatic data from climatic databases. Data for other environmental parameters possibly involved in the spatial distribution of adaptive diversity will also be collected, along with field performance data (including NIRS measures of forage traits). Plants will be genotyped using Restriction-Associated DNA (RAD) sequencing on an Illumina HiSeq2500 platform to obtain ~70,000 genome-wide SNP markers. Resequencing of several candidate genes putatively associated with environmental adaptation (i.e. vernalisation) will also be conducted. Associations between genotype and phenotype will be detected using developing models for changes in allele frequency within mixed swards.

Summary

Our project aims to implement an innovative methodological frame to screen the natural diversity of a grassland species in order to discover genetic variability involved in environmental adaptation, and more specifically in climatic adaptation (Sampoux et al., 2013). We will consider the use of results delivered by this approach to plan strategies to restore permanent grasslands degraded by climatic shifts and disruptions. Our project will focus on perennial ryegrass (Lolium perenne L.), which is a major grass species naturally distributed over the whole European continent as well as in Northern Africa and Near East (Humphreys et al., 2010). This species is a major component of many natural grassland communities. It is a resource capture strategy species (Martin et al., 2009) which is especially prevalent in grasslands grazed by cattle. It is also the main grass species sown in Europe to create temporary meadows and it has therefore received extensive breeding effort during the last four decades (Sampoux et al., 2011). Recent developments in a new area of ecological sciences (landscape genomics) have paved the way to the discovery of genomic markers of adaptive diversity from genome-wide genotyping data. They are based on the implementation of methods correlating genomic polymorphisms and environmental variations at sites of origin of genotypes combined with tests of signature of selection (Manel et al., 2010). We will implement this methodological frame to detect genomic markers of climatic adaptation in the natural diversity of perennial ryegrass. We will use a genotyping method based on massively parallel sequencing technology applied to a high number of populations obtained from genebanks of plant breeding research institutes or collected in situ across Europe. We will furthermore take advantage of know-how and facilities of plant breeding research institutes participating in the project to phenotype these populations in fields and in controlled environment to record agronomic and ecophysiological traits. These phenotypic data will be used to model associations between phenotypic variability and genomic polymorphisms. Association models between genomic polymorphisms and environmental variations will be used to map the spatial distribution of genomic markers linked to adaptive diversity in present climatic conditions and to foresee possible shifts in the spatial range fitting these markers in the context of several climate change scenarios based on the four Representative Concentration Pathways (RCP) of IPCC AR5 (Moss et al., 2010). On the basis of these results, we will define allelic profiles of perennial ryegrass expected to provide climatic adaptation at regional scale over Europe under the future climatic conditions foreseen by climate models. We will consider combining climatic adaptation and value for services (forage production and climate mitigation) by the recombination of alleles providing climatic adaptation and value for services. We will design several genetic pools mixing different natural populations for breeding regionally adapted populations to restore permanent grasslands degraded climatic disruptions. Breeding and releasing improved genetic material will be out of the scope of the project but will be discussed with stakeholders at the end of the project during ad hoc meetings for implementation in further collaborative projects.

Impact Summary

Our project will be among the first ones to implement the landscape genomics approach with a so extended protocol (a large set of populations covering the whole area of primary expansion of a species and a genomewide genotyping providing several tens thousands of genomic markers). It should then release results that will be worthwhile to publish in high impact journals of Ecology such as Trends in Ecology and Evolution, Ecology Letters, Molecular Ecology and Ecography. Results about shifts with climate change in the spatial distribution of perennial ryegrass adaptive diversity could be published in journals like Global Change Biology, Climatic Change, Agricultural and Forest Meteorology, and Regional Environmental Change. The outcomes of our project in the domain of conservation and use of genetic resources and in plant breeding, notably the added value of the landscape genomics approach in these fields, could published in journals like Theoretical and Applied Genetics, Molecular Breeding and Field Crops Research. Results in the scope of landscape genomics and molecular ecology could be communicated at international conferences such as the VIPCA conferences. Results regarding genetic resources and plant breeding could be communicated at conferences such as the Eucarpia conferences (especially those of the forage plants section and genetic resources section), the MBFT(molecular breeding of forage and turf) conferences and the European Grassland Federation conferences. Communication towards stakeholders will be a point of focus in our project. It will be the target of task 4.3 in WP 4. WP 4 will have the objective to map the spatial range fitting genomic markers of adaptive diversity in present climate and in several climate change scenarios. WP 4 will also aim to design genetic pools mixing natural populations bearing different climatic adaptations. These genetic pools will have to be submitted to a number of selection cycles to recombine allelic diversity for climatic adaptation and value for services. Selection in these genetic pools is intended to deliver improved populations for restoring permanent grasslands with genetic material adapted to future regional contexts of Europe (see Figure 1 in part "Expected impact of the project"). Our project will include the design of these genetic pools. However, the practical setup of these pools will be out of the scope of the project. This will have to be undertaken, as well as further breeding, in next projects beyond the end of this FACCE-JPI project. Such tasks involving extensive plant breeding logistics cannot be carried by the sole academic partners of the project and will have to be implemented in close collaboration with other stakeholders, including plant breeders, technical advisers and farmers. Our communication towards stakeholders will not only have the objective of transferring our findings, but also to prepare a practical followup including the setting up of pools and breeding in collaboration with stakeholders. We plan to implement our communication strategy towards stakeholders by the medium of professional societies. We will consider the grassland societies gathering professionals interested in grasslands (farmers, technical advisers, scientists, plant breeders). All these societies have their own regular conferences and web sites to disseminate information. The national grasslands societies that we can address are the British Grassland Society in the UK, the 'Arbeitsgemeinschaft Grünland und Futterbau' (AGGF), the 'Gesellschaft für Pflanzenzüchtung' (GPZ) and DLG - 'Fachzentrum Land- und Ernährungswirtschaft' in Germany and the 'Association Française pour la Production Fourragère' (AFPF) in France. National grassland societies from other countries could possibly be contacted. We will also communicate towards national plant breeder societies.

Committee	Not funded via Committee
Research Topics	Crop Science, Plant Science
Research Priority	X – Research Priority information not available
Research Initiative	ERA-NET on Climate Smart Agriculture (FACCE ERA-NET-plus) [2014]
Funding Scheme	X – not Funded via a specific Funding Scheme

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