Epigenetic variation in early and late flowering plants of the rubber-producing Russian dandelion Taraxacum koksaghyz provides insights into the regulation of flowering time.

The Russian dandelion (Taraxacum koksaghyz) grows in temperate zones and produces large amounts of poly(cis-1,4-isoprene) in its roots, making it an attractive alternative source of natural rubber. Most T. koksaghyz plants require vernalization to trigger flower development, whereas early flowering varieties that have lost their vernalization dependence are more suitable for breeding and domestication. To provide insight into the regulation of flowering time in T. koksaghyz, we induced epigenetic variation by in vitro cultivation and applied epigenomic and transcriptomic analysis to the resulting early flowering plants and late flowering controls, allowing us to identify differences in methylation patterns and gene expression that correlated with flowering. This led to the identification of candidate genes homologous to vernalization and photoperiodism response genes in other plants, as well as epigenetic modifications that may contribute to the control of flower development. Some of the candidate genes were homologous to known floral regulators, including those that directly or indirectly regulate the major flowering control gene FT. Our atlas of genes can be used as a starting point to investigate mechanisms that control flowering time in T. koksaghyz in greater detail and to develop new breeding varieties that are more suited to domestication.

Overexpression of a pseudo-etiolated-in-light-like protein in Taraxacum koksaghyz leads to a pale green phenotype and enables transcriptome-based network analysis of photomorphogenesis and isoprenoid biosynthesis.

Introduction: Plant growth and greening in response to light require the synthesis of photosynthetic pigments such as chlorophylls and carotenoids, which are derived from isoprenoid precursors. In Arabidopsis, the pseudo-etiolated-in-light phenotype is caused by the overexpression of repressor of photosynthetic genes 2 (RPGE2), which regulates chlorophyll synthesis and photosynthetic genes. Methods: We investigated a homologous protein in the Russian dandelion (Taraxacum koksaghyz) to determine its influence on the rich isoprenoid network in this species, using a combination of in silico analysis, gene overexpression, transcriptomics and metabolic profiling. Results: Homology-based screening revealed a gene designated pseudo-etiolated-in-light-like (TkPEL-like), and in silico analysis identified a light-responsive G-box element in its promoter. TkPEL-like overexpression in dandelion plants and other systems reduced the levels of chlorophylls and carotenoids, but this was ameliorated by the mutation of one or both conserved cysteine residues. Comparative transcriptomics in dandelions overexpressing TkPEL-like showed that genes responsible for the synthesis of isoprenoid precursors and chlorophyll were downregulated, probably explaining the observed pale green leaf phenotype. In contrast, genes responsible for carotenoid synthesis were upregulated, possibly in response to feedback signaling. The evaluation of additional differentially expressed genes revealed interactions between pathways. Discussion: We propose that TkPEL-like negatively regulates chlorophyll- and photosynthesis-related genes in a light-dependent manner, which appears to be conserved across species. Our data will inform future studies addressing the regulation of leaf isoprenoid biosynthesis and photomorphogenesis and could be used in future breeding strategies to optimize selected plant isoprenoid profiles and generate suitable plant-based production platforms.

Microscopic and Transcriptomic Analysis of Pollination Processes in Self-Incompatible Taraxacum koksaghyz.

The transition of the Russian dandelion Taraxacum koksaghyz (Asteraceae) to a profitable, alternative crop producing natural rubber and inulin requires the optimization of several agronomic traits, cultivation conditions and harvesting procedures to improve the yield. However, efficient breeding is hindered by the obligatory sexual outcrossing of this species. Several other asters have been investigated to determine the mechanism of self-incompatibility, but the underlying molecular basis remains unclear. We therefore investigated the self-pollination and cross-pollination of two compatible T. koksaghyz varieties (TkMS2 and TkMS3) by microscopy and transcriptomic analysis to shed light on the pollination process. Self-pollination showed typical sporophytic self-incompatibility characteristics, with the rare pollen swelling at the pollen tube apex. In contrast, cross-pollination was characterized by pollen germination and penetration of the stigma by the growing pollen tubes. RNA-Seq was used to profile gene expression in the floret tissue during self-pollination and cross-pollination, and the differentially expressed genes were identified. This revealed three candidates for the early regulation of pollination in T. koksaghyz, which can be used to examine self-incompatibility mechanisms in more detail and to facilitate breeding programs.

Comparative Transcriptome Analysis in Taraxacum koksaghyz to Identify Genes that Determine Root Volume and Root Length.

The Russian dandelion (Taraxacum koksaghyz, family Asteraceae) produces large amounts of natural rubber in the laticifers of its roots. This species has been proposed as an alternative source of natural rubber to augment or partly replace the rubber tree (Hevea brasiliensis) but domestication would require genetic improvement to increase rubber yields and agronomic optimization to facilitate harvesting and processing. Optimization has focused thus far on the size and shape of the roots, the primary storage organ for natural rubber and inulin. However, the corresponding genetic factors are poorly understood. Here we describe the comparative transcriptomic analysis of root tissues from T. koksaghyz plant sets featuring different root sizes and shapes, aiming to identify differentially expressed genes correlating with root length or root diameter in the upper root and root tip. The resulting datasets revealed multiple candidate genes for each trait and root part, including a glucan endo-1,3-ß-d-glucosidase, an allene oxide synthase 3, and a TIFY10A/JAZ1 homolog. These three genes were tested by qRT-PCR in outdoor-grown plants with diverse root morphology, and the expression of two genes correlated with the appropriate root morphotype, confirming the effectiveness of our method. We evaluated the candidate genes to gain insight into their potential functions in root development. Such candidate genes could be suitable for marker-assisted breeding programs in the future.

Comparative proteome and metabolome analyses of latex-exuding and non-exuding Taraxacum koksaghyz roots provide insights into laticifer biology.

Taraxacum koksaghyz has been identified as one of the most promising alternative rubber crops. Its high-quality rubber is produced in the latex of laticifers, a specialized cell type that is organized in a network of elongated tubules throughout the entire plant body. In order to gain insights into the physiological role(s) of latex and hence laticifer biology, we examine the effects of barnase-induced latex RNA degradation on the metabolite and protein compositions in the roots. We established high-quality datasets that enabled precise discrimination between cellular and physiological processes in laticifers and non-laticifer cell types of roots at different vegetative stages. We identified numerous latex-specific proteins, including a perilipin-like protein that has not been studied in plants yet. The barnase-expressing plants revealed a phenotype that did not exude latex, which may provide a valuable genetic basis for future studies of plant-environment interactions concerning latex and also help to clarify the evolution and arbitrary distribution of latex throughout the plant kingdom. The overview of temporal changes in composition and protein abundance provided by our data opens the way for a deeper understanding of the molecular interactions, reactions, and network relationships that underlie the different metabolic pathways in the roots of this potential rubber crop.