Final Report Summary - TRIBE (Transgressive Inheritance in plant Breeding and Evolution)
New varieties of plant and animal are produced by hybridization of closely related varieties or species. This process generates hybrid varieties that are better than the parents with "transgressive" traits that are outside the parental range. Transgressive segregation in hybrids may involve complementation of genetic differences between the two parents, heterozygous advantage, genetic rearrangements and, from our recent work, epigenetic effects associated with RNA silencing.
In this project have investigated these effects using tomato for which there are genome sequence data and well characterised genetic resources based on hybrids between cultivated tomato and its wild relatives. In one part of the project we mapped the genome and epigenome of F2-F4 generation hybrids between S. lycopersicum and its wild relative S. pennelli and, in parallel, we looked at the expression of all genes including those producing small silencing RNAs. We have identified transgressive changes in gene expression in these lines and ongoing analysis is exploring the extent to which they link to epigenetic and genetic changes.
The analysis of data generation in TRIBE will provide the first systematic analysis of genomes, their expression and epigenetic modifications in the four post-hybridization generations. This information will be informative about the nature and extent of genome rearrangements and epigenetic modifications following hybridization and the ways that they link to transgressive changes in gene expression. It will generate information that will be central to the understanding of hybrids in the evolution of plants and the exploitation of hybrids in breeding of crops.
Epigenetic changes are often associated with gene silencing in which the production of RNA and protein is reduced at specific loci. In some instances, however, this silencing is not simply a passive effect: the silenced allele can transfer its epigenetically silent state to an active allele in a process known as paramutation. In subsequent generations of hybrid plants a secondary paramutation process results in this newly silenced allele transferring its silent state to another active allele. Most previous work on paramutation has been on maize but we have now shown that this process is triggered by interspecific crosses of tomato and, prompted by this discovery, we are now investigating the mechanism of paramutation. Our findings indicate that this process is more widespread than previously thought and that it may play a significant role in the evolution of natural populations and in crop plant breeding.
TRIBE has also set up approaches to be used in conventional plant breeding involving that exploit hidden heritability due to epigenetic rather than genetic marks. These approaches may involve epigenetic marks that are either added to or removed from the crop plant genomes and that affect agronomic traits.
At the level of basic research the TRIBE project has allowed us to approach the relationship between genetic features of the genome and epigenetic marks. Like most genomes there are distinct regions of epigenetically silenced heterochromatin in tomato that are separate from the euchromatin domains that are gene-rich and with only sparse evidence of epigenetic marks. We have found, however, that the analysis of euchromatin is more informative about epigenetics than the heterochromatin. Using this approach we have identified several novel genetic determinants of different types of epigenetic mark.
Our interest in the epigenetics of hybrids necessarily required the analysis of regulatory RNA in tomato including micro (mi)RNA. A by product of this analysis is the discovery of miRNA-mediated negative regulation of innate immunity in plants and that can be manipulated to enhance the quantitative disease resistance against a broad spectrum of pathogens. We have follow on funding to continue this interesting line of research.
The ultimate outcome of TRIBE has been a test of the hypothesis that hybridization is important in evolution because it allows not only the formation of new combinations of genes: it is also a process that induces new heritable variation via epigenetic and RNA silencing based mechanisms. We have generated new information about evolutionary mechanisms that can be integrated into our understanding of the tree of life.
In this project have investigated these effects using tomato for which there are genome sequence data and well characterised genetic resources based on hybrids between cultivated tomato and its wild relatives. In one part of the project we mapped the genome and epigenome of F2-F4 generation hybrids between S. lycopersicum and its wild relative S. pennelli and, in parallel, we looked at the expression of all genes including those producing small silencing RNAs. We have identified transgressive changes in gene expression in these lines and ongoing analysis is exploring the extent to which they link to epigenetic and genetic changes.
The analysis of data generation in TRIBE will provide the first systematic analysis of genomes, their expression and epigenetic modifications in the four post-hybridization generations. This information will be informative about the nature and extent of genome rearrangements and epigenetic modifications following hybridization and the ways that they link to transgressive changes in gene expression. It will generate information that will be central to the understanding of hybrids in the evolution of plants and the exploitation of hybrids in breeding of crops.
Epigenetic changes are often associated with gene silencing in which the production of RNA and protein is reduced at specific loci. In some instances, however, this silencing is not simply a passive effect: the silenced allele can transfer its epigenetically silent state to an active allele in a process known as paramutation. In subsequent generations of hybrid plants a secondary paramutation process results in this newly silenced allele transferring its silent state to another active allele. Most previous work on paramutation has been on maize but we have now shown that this process is triggered by interspecific crosses of tomato and, prompted by this discovery, we are now investigating the mechanism of paramutation. Our findings indicate that this process is more widespread than previously thought and that it may play a significant role in the evolution of natural populations and in crop plant breeding.
TRIBE has also set up approaches to be used in conventional plant breeding involving that exploit hidden heritability due to epigenetic rather than genetic marks. These approaches may involve epigenetic marks that are either added to or removed from the crop plant genomes and that affect agronomic traits.
At the level of basic research the TRIBE project has allowed us to approach the relationship between genetic features of the genome and epigenetic marks. Like most genomes there are distinct regions of epigenetically silenced heterochromatin in tomato that are separate from the euchromatin domains that are gene-rich and with only sparse evidence of epigenetic marks. We have found, however, that the analysis of euchromatin is more informative about epigenetics than the heterochromatin. Using this approach we have identified several novel genetic determinants of different types of epigenetic mark.
Our interest in the epigenetics of hybrids necessarily required the analysis of regulatory RNA in tomato including micro (mi)RNA. A by product of this analysis is the discovery of miRNA-mediated negative regulation of innate immunity in plants and that can be manipulated to enhance the quantitative disease resistance against a broad spectrum of pathogens. We have follow on funding to continue this interesting line of research.
The ultimate outcome of TRIBE has been a test of the hypothesis that hybridization is important in evolution because it allows not only the formation of new combinations of genes: it is also a process that induces new heritable variation via epigenetic and RNA silencing based mechanisms. We have generated new information about evolutionary mechanisms that can be integrated into our understanding of the tree of life.