Reprogramming of Histone H3 Lysine Methylation During Plant Sexual Reproduction

Plants undergo extensive reprogramming of chromatin status during sexual reproduction, a process vital to cell specification and pluri- or totipotency establishment. As a crucial way to regulate chromatin organization and transcriptional activity, histone modification can be reprogrammed during sporogenesis, gametogenesis, and embryogenesis in flowering plants. In this review, we first introduce enzymes required for writing, recognizing, and removing methylation marks on lysine residues in histone H3 tails, and describe their differential expression patterns in reproductive tissues, then we summarize their functions in the reprogramming of H3 lysine methylation and the corresponding chromatin re-organization during sexual reproduction in Arabidopsis, and finally we discuss the molecular significance of histone reprogramming in maintaining the pluri- or totipotency of gametes and the zygote, and in establishing novel cell fates throughout the plant life cycle. Despite rapid achievements in understanding the molecular mechanism and function of the reprogramming of chromatin status in plant development, the research in this area still remains a challenge. Technological breakthroughs in cell-specific epigenomic profiling in the future will ultimately provide a solution for this challenge.

Controlling transgene flow from engineered crops to unintended hosts by molecular approaches.

For most transgenic crops, the purported ecological risk from transgenic-host hybridization and introgression to unintended host species is negligible. Nonetheless, there remains a risk-associated focus on the potential for gene flow in the governance and regulation of crop biotechnology. Because of uncertainties in the large world of biology as well as regulatory certainties (regulations will likely not diminish), researchers and stakeholders have a great interest in eliminating or substantially decreasing gene flow from transgenic crops. To that end, numerous approaches have been investigated for limiting transgene flow via hybridization and introgression to unintended hosts. While such bioconfinement may be accomplished by ecological and management strategies as discussed elsewhere in this book, this chapter focuses on mitigating unintended gene flow from engineered crops by way of genetic engineering itself. The chapter will mainly discuss the manipulation of relatively simple means to alter plant sexual reproduction and plant growth and development to control transgene flow, with the desired outcome being the prevention of transgenes from moving and/or introgression into free-living unintended hosts. These approaches include: (i) decreasing or delaying flowering; (ii) eliminating pollen production via male sterility or selective male sterility; (iii) removing transgenes from pollen or eggs by gene use restriction technologies; and (iv) kill switches. Emerging synthetic biology approaches that may be used for transgene bioconfinement are explored. Taken together, the same molecular biology strategies that are used to improve crops can also help assure their biosafety.

Sugar and Hormone Dynamics and the Expression Profiles of SUT/SUC and SWEET Sugar Transporters during Flower Development in Petunia axillaris

Flowering is the first committed step of plant sexual reproduction. While the developing flower is a strong sink requiring large quantity of sugars from photosynthetic source tissues, this process is under-temper-spatially controlled via hormone signaling pathway and nutrient availability. Sugar transporters SUT/SUC and SWEET mediate sugars movement across membranes and play a significant role in various physiological processes, including reproductive organ development. In Petunia axillaris, a model ornamental plant, 5 SUT/SUC and 36 SWEET genes are identified in the current version of the genome. Analysis of their gene structure and chromosomal locations reveal that SWEET family is moderately expanded. Most of the transporter genes are abundantly expressed in the flower than in other organs. During the five flower developmental stages, transcript levels of PaSUT1, PaSUT3, PaSWEET13c, PaSWEET9a, PaSWEET1d, PaSWEET5a and PaSWEET14a increase with the maturation of the flower and reach their maximum in the fully open flowers. PaSWEET9c, the nectar-specific PhNEC1 orthologous, is expressed in matured and fully opened flowers. Moreover, determination of sugar concentrations and phytohormone dynamics in flowers at the five developmental stages shows that glucose is the predominant form of sugar in young flowers at the early stage but depletes at the later stage, whereas sucrose accumulates only in maturated flowers prior to the corolla opening. On the other hand, GA3 content and to a less extent IAA and zeatin decreases with the flower development; however, JA, SA and ABA display a remarkable peak at mid- or later flower developmental stage.

Plant Sexual Reproduction: Perhaps the current plant two-sex model should be replaced with three- and four-sex models?

The current plant two-sex model makes the assumption that there are only two sexual reproductive states: male and female. However, the application of this model to the plant alternation of generations requires the subtle redefinition of several common terms related to sexual reproduction, which also seems to obscure aspects of one or the other plant generation: For instance, the homosporous sporophytic plant is treated as being “asexual,” and the gametophytes of angiosperms treated like mere gametes. In contrast, the proposal is made that the sporophytes of homosporous plants are indeed sexual reproductive organisms, as are the gametophytes of heterosporous plants. This view requires the expansion of the number of sexual reproductive states we accept for plants, therefore a three-sex model for homosporous plants and a four-sex model for heterosporous plants are described and then contrasted with the current two-sex model. These new models allow the use of sexual reproductive terms in a manner largely similar to that seen in animals, and may better accommodate the plant alternation of generations life cycle than does the current plant two-sex model. These new three-sex and four-sex models may also help stimulate new lines of research, and examples of how they might alter our view of the flower, and may lead to new perspectives in terms of sexual determination, are presented. Thus it is suggested that plants have more than merely two sexual reproductive states, and that recognition of this may promote our study and understanding of plants.

MCRiceRepGP: a framework for identification of sexual reproduction associated coding and lincRNA genes in rice

Sexual reproduction in plants underpins global food production and evolution. It is a complex process, requiring intricate signalling pathways integrating a multitude of internal and external cues. However, key players and especially non-coding genes controlling plant sexual reproduction remain elusive. We report the development of MCRiceRepGP a novel machine learning framework, which integrates genomic, transcriptomic, homology and available phenotypic evidence and employs multi-criteria decision analysis and machine learning to predict coding and non-coding genes involved in rice sexual reproduction.The rice genome was re-annotated using deep sequencing transcriptomic data from reproduction-associated tissues/cell types identifying novel putative protein coding genes, transcript isoforms and long intergenic non-coding RNAs (lincRNAs). MCRiceRepGP was used for genome-wide discovery of sexual reproduction associated genes in rice; 2,275 protein-coding and 748 lincRNA genes were predicted to be involved in sexual reproduction. The annotation performed and the genes identified, especially the ones for which mutant lines with phenotypes are available provide a valuable resource. The analysis of genes identified gives insights into the genetic architecture of plant sexual reproduction. MCRiceRepGP can be used in combination with other genome-wide studies, like GWAS, giving more confidence that the genes identified are associated with the biological process of interest. As more data, especially about mutant plant phenotypes will become available, the power of MCRiceRepGP with grow providing researchers with a tool to identify candidate genes for future experiments. MCRiceRepGP is available as a web application (http://mcgplannotator.com/MCRiceRepGP/)Significance statementRice is a staple food crop plant for over half of the world’s population and sexual reproduction resulting in grain formation is a key process underpinning global food security. Despite considerable research efforts, much remains to be learned about the molecular mechanisms involved in rice sexual reproduction. We have developed MCRiceRepGP, a novel framework which allows prediction of sexual reproduction associated genes using multi-omics data, multicriteria decision analysis and machine learning. The genes identified and the methodology developed will become a significant resource for the plant research community.