Comparative population genomics of red clover domestication and improvement

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The aim of this project is to characterise the genetic diversity in natural and breeding populations to identify genome wide changes during breeding of red clover. We wish to investigate to what extent artificial selection has affected the genome including genic and non-genic regions, and whether this has resulted in a reduction in diversity and increase in rare alleles. We propose the following programme to test this. Firstly, we will use RAD marker polymorphisms from an existing mapping family to improve alignment of the red clover genome assembly to a genetic map. Secondly, we will use a 600 genotype strong panel of ecotypes with mostly prostrate growth habit together with erect elite breeding material to analyse the genetic diversity by RAD marker sequencing. Phenotypic, chemical analyses and ecogeographical information of the diversity panel will allow us to obtain information on how haplotype structure correlates with phenotype and environmental gradients likely to impact on environmental adaptations. Nucleotide diversity and locus by locus genetic differentiation will reveal genomic regions under selection. We will also generate mapping families segregating for growth habit, thus enabling us to associate and map more accurately the target traits relating to a prostrate and erect phenotype. The goal is to identify the genes responsible for most of the genetic variation in this key domestication trait. This project will generate information on the genetic basis of a fundamental trait, provide insight into selection during recent domestication and inform the forage legume breeding programme. We will also re-sequence the five pollen donors in the new mapping family. This, the RAD marker data and the reference assembly will give us valuable information about genome-wide linkage disequilibrium, levels of heterozygosity, SNP density and patterns of polymorphisms in coding and non-coding sequence.

The delivery of the proposed objectives is focused on current needs for which suitable tools and skilled researchers are lacking or not fully developed. The objectives will also directly contribute solutions in areas of research relevant to the BBSRC's scientific priorities in food security and integrate established methods in genetics with emerging multidisciplinary research areas such as genomics and bioinformatics.
This programme will generate new opportunities for collaborative work between TGAC and IBERS and will also extend to other R&D groups in industry and academic institutions. We will communicate our results of fundamental aspects of domestication traits in forage crops through peer reviewed publications, and at national and international conferences. This work will significantly improve the draft red clover genome, which will be one of the first for a temperate forage crop. It will thus have general interest beyond the immediate circle of colleagues interested in red clover. We will disseminate the data using TGAC computing resources and by depositing the raw sequences and assemblies in long-term repositories established at the EMBL-EBI. One of the main stakeholders is Germinal Holdings Ltd who funds a significant part of IBERS breeding programme. This work is aligned closely with the initial stages of the new red clover breeding programme. The generation of large numbers of SNP marker polymorphisms will bring with it the potential to use genomics-based prediction of selection candidates. Accelerated breeding cycles lead to a faster route from breeding material to new varieties. The current programme of genetic improvement in red clover has the potential to lead to significant increases in seed sales, of which Germinal Holdings have 18% currently in the UK. New varieties with better persistence and disease resistance also open up significant opportunities for export to the European market, as well as North America and New Zealand.

The proposed work will directly impact the local community with the generation of new jobs and potential funding opportunities. The collaboration between IBERS and TGAC has strengthened the position of these Institutes in hosting specific expertise in advanced breeding for forage legumes. This will create new opportunities around the development of applications in genomics and bioinformatics, which will translate into job opportunities. It is widely recognised that the shortage of expertise and skills in biomathematics and informatics in the UK and across the world is a major risk for future development in life sciences, in this context this proposal will attract talented staff to work with IBERS and TGAC. Finally, the ecotype collection we use here consists partly of natural populations that were collected from locations in Eastern Europe in the period from the early 1990's to the early 2000's. Many of these habitats are now under severe threat, which means that some of the accessions we work with may no longer exist naturally. Our work thus represents the best way of utilising this unique resource, and preserving the diversity.

This collaboration will contribute to reinforce the UK's leadership in translating the development of genetic and genomic resources from fundamental science to applications with a potential impact on the local and national economy. The development of a more sustainable agriculture is a key aspect of the UK strategy and this is aligned with the objectives in the recently published Agri-tech Strategy. A consequence of the implementation of this proposal is to position IBERS and TGAC as international leaders in biotechnology specifically in the area of forage legumes. This will deliver impact to a broad range of stakeholders emphasising the key role that the Institutes will play in enabling researchers to develop cutting-edge science in the coming years, and ensure that the genomics resources will be translated to research and breeding programmes.