HvST1: A novel suppressor of recombination in barley

Lead Research Organisation: The James Hutton Institute
Department Name: Cell & Molecular Sciences

Abstract

Genetic recombination is the major driver for the creation of new varieties, but in barley and other large genome cereals, the number of recombination events is limited and mainly located towards the ends of the chromosomes. An ability to increase and/or modulate recombination in these crops would potentially accelerate the improvement of commercially important traits with minimum costs to breeders. Recent works have highlighted several mutations in genes such as FANCM, RECQ4, and HEI10, that increase recombination in Arabidopsis. Taking advantage of the new barley genomic resources, a large collection of meiotic mutants and super resolution microscopy, I have found differences between Arabidopsis and barley (as well as wheat), suggesting that large genome plants have a different level of control over recombination events, perhaps due to their size and complex genome organisation. I recently identified a novel E3 ubiquitin ligase that I called STICKY TELOMERES 1 (HvST1) that in homozygous mutants exhibits disturbed meiosis but also, and somewhat surprisingly, a dramatic increase in effective recombination of around 50% in all chromosomes. I have identified orthologues of HvST1 in wheat, rice and Brachypodium but not in Arabidopsis, suggesting that a potentially novel recombination pathway or component pathway exists in the cereals. In this proposal, I combine a range of experimental approaches that focus on investigating and characterising the role of this novel E3 ubiquitin ligase in meiosis. This research will help elucidate the first known mechanism controlling recombination by a novel ubiquitin pathway in barley and promises to reveal a new way to modulate recombination in large genome crops.

Technical Summary

By characterizing a number of independent barley DESYNAPTIC mutants, I have observed both profound and subtle differences in the modulation of crossing over in large genome crops when compared to the model plant Arabidopsis. One of these desynaptic mutants carries a recessive mutation in a novel E3 ubiquitin ligase that I called STICKY TELOMERES 1 (HvST1). HvST1 mutants have disturbed meiosis, ut retain some level of fertility. Surprisingly, HvST1 mutants have a dramatic increase in effective recombination of around 50% in all chromosomes. Phylogenetic analysis revealed that HvST1 was grass-specific, suggesting that a potentially novel recombination pathway or component pathway exists in barley and other cereals. Most of the studies on the control of meiosis by E3 RING ligase (HvST1 gene family) have been conducted in mammals and there is no comparative plant study that we can use to propose the precise role or function of HvST1 in meiosis. In this proposal I propose to combine cytological and proteomic approaches to investigate and characterise the role of this novel E3 ubiquitin ligase during meiosis. In the first part, I will establish an accurate timing of events during meiosis in the HvST1 mutant to understand when crossovers are regulated by conducting a time course analysis with a combination of meiosis specific antibodies and EDU. In the second part, I will use a different combination of antibodies, 3D imaging and mass spectrometry to deepen our understanding of the organization of the chromatin in presence or absence of HvST1. Finally, I will probe the network of proteins that interact with, or are targets of, HvST1 using a co-IP/mass spec approach. At the end of this project I will have a fuller picture of the mode of action of HvST1. Any HvST1 network proteins could potentially be used to explore the possibility of using chemicals/drugs to modulate recombination in a practical setting without the need to use induced mutations.

Planned Impact

Who will benefit from this research?
Barley is the 4th most important cultivated cereal in the world (146 million tons in 2013, FAOSTAT) and is used for animal feed, human consumption and the production of fermented beverages. The UK is in the top 10 of global barley producers with more than 6 million tons in 2016 (FAOSTAT 2016). Around 30% of the UK crop is malted supporting the brewing and distilling industries. The research proposed here will ultimately benefit all who live and work in the UK through direct tax return of £3.7Bn to the exchequer from the whisky sector alone. Increasing crop yield and quality underpins the profitability of these industries and is pivotally dependent upon the development and release of new plant varieties suited to end user demands. Plant breeding depends upon combining valuable traits by creating novel combinations of alleles produced by recombination while maintaining pre-existing and beneficial gene complexes assembled over time during the generation of the elite cultivated gene pool. In barley and other large genome crops, a large portion of the chromosomes rarely recombine. This means that 20-30% of the genes that are almost inaccessible for breeders, hence slowing down the creation of new and resilient crops that are more tolerant pathogens or environmental stress. The outputs of this project will potentially lead to the development of new strategies to modulate recombination that would enable the creation of new varieties, sustainably enhancing agricultural production.
How they will benefit from this research?
The natural mutation found in HvST1, increases recombination in all the barley chromosomes by more than 50%. The Hvst1 mutant is spontaneous and could be used directly in pre-breeding programs to increase gene diversity in the regions with increased recombination. However, because this is newly identified, we don't know what other processes may be affected in the absence of HvST1 function that could be detrimenal to e.g. plant development. This proposal aims to address this issue by exploring the role of HvST1 during meiosis. Hvst1 is a (severe) knockout mutation and it may be more appropriate for application to identify hypomorphic alleles that exert a similar effect on recombination but reduce any associated side effects (e.g reduced fertility). At the end of this project, I should know when HvST1 is functioning during meiosis (objective 1) and what are its proteins partners are (objective 3). By establishing the network of proteins with which HvST1 interacts I will be in a strong position to explore potential direct or indirect inhibitors of HvST1 complex function and their potential use in practically managing recombination in a plant breeding setting. Barley genomic resources are now easily accessible and the closely conserved synteny between barley and the more complex wheat genome (global production of 690 million tonnes in 2013, FAOSTAT) makes barley a good model for fundamental studies of large genome cereal crops. Understand what is happening in barley will facilitate the transfer knowledge to other crops.
What will be done to ensure that they have the opportunity to benefit from this research?
If supported, this project will form part of the International Barley Hub (IBH), a centre of excellence linking fundamental, translational and industry-focussed research with innovation, to both deliver immediate impact and ensure the long-term sustainability of the UK and International barley supply and value chains. The IBH is backed by a £40M investment as part of the Tay Cities deal. I have a long-lasting interactions with breeding companies, and worked closely with KWS on various projects (EU-COMREC, Innovate-UK DRRUM). I will explore the potential of translating any applied value associated with HvST1 along similar lines, initially in barley, and subsequently in wheat.

Publications

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