Epigenetic-mediated yield increases in Tomato

A fundamental goal in agriculture is achieving higher yields per acre, in conjunction with similar or lower inputs, for higher profitability and more sustainable use of resources. To achieve higher yields, plants need to be more energy efficient to complement the trend towards breeding and farming at higher plant densities. To date biotechnology has been very successful at weed and insect control products, but has not made much progress on developing more energy efficient plants due to the complex interactions of the many proteins and metabolic pathways involved. The large numbers of genes needed to improve complex traits affecting yield is beyond biotechnologies current capabilities. Our epigenetic technology provides a very different method to affect the expression of many genes in a useful and natural manner. Surprisingly, this epigenetic technology can be implemented without any changes in the DNA sequence of the plant.One of the fundamental biological processes increasing plant productivity is heterosis (increased yields from hybrid progeny relative to the yields of the parent plants), with hybrid corn as one of the most successful commercial examples. Although heterosis is phenotypically defined, its molecular basis is still debated and unproven. Our epigenetic technology phenotypically meets the definition of heterosis by increasing yields in progeny. Our working hypothesis is that epigenetics is an aspect of heterosis that has not been previously separable from genetics due to their concurrence on chromosomes. It is only with the ability to independently manipulate the epigenome in a biologically useful manner without changing DNA sequences that the role of the epigenome becomes apparent. Our proposal will advance our understanding of how epigenetics affects crop performance in field trials.Specifically in this proposal, we will develop improved methods for creating, identifying, and breeding epigenetic modifications for producing higher yielding tomato plants.The knowledge gained will advance our ability to manipulate the epigenome for increased yields in agriculture in multiple crops. A broad impact across multiple crops is supported by our findings of epigenetic-mediated yield increases in representative species in the Brassicaceae (mustards), Solanaceae [vegetables], Gramineae (cereals), and Leguminosae (beans), thereby providing examples in these important crops inboth dicotyledonous and monocotyledonous plant examples.Epigenetics is the collective physical status of chromosomes including their chromosomal proteins and their posttranslational modifications, structural RNA, and DNA methylation components that affect transcription and splicing. The term 'epigenetics' is often used to refer to cellular and developmental chromosomal events during a life cycle of an organism as well as transgenerational transmission of this 'non-DNA sequence' information, with DNA methylation being the most studied aspect. In this proposal we are focused on the transgenerational aspect of epigenetics and use the term 'epigenetics' in that context.A second feature of our epigenetic system is that it appears to require proceeding through one or more sexual reproduction steps. Meiosis appears to be a developmental stage at which epigenetic reprogramming occurs and at which decisions are made for which epigenetic modifications will be inherited.In particular, CHH methylation is partially removed and reprogramed via an elegant vegetative nucleus mechanism that transfers small RNAs from the vegetative cell to the sperm cell of the pollen to reestablish CHH methylation. CG and CHG methylation is predominantly maintained during meiosis and inherited in the progeny of plants.