Comparative Metabolomics Reveals Two Metabolic Modules Affecting Seed Germination in Rice (Oryza sativa)

The process of seed germination is crucial not only for the completion of the plant life cycle but also for agricultural production and food chemistry; however, the underlying metabolic regulation mechanism involved in this process is still far from being clearly revealed. In this study, one indica variety (Zhenshan 97, with rapid germination) and one japonica variety (Nipponbare, with slow germination) in rice were used for in-depth analysis of the metabolome at different germination stages (0, 3, 6, 9, 12, 24, 36, and 48 h after imbibition, HAI) and exploration of key metabolites/metabolic pathways. In total, 380 annotated metabolites were analyzed by using a high-performance liquid chromatography (HPLC)-based targeted method combined with a nontargeted metabolic profiling method. By using bioinformatics and statistical methods, the dynamic changes in metabolites during germination in the two varieties were compared. Through correlation analysis, coefficient of variation analysis and differential accumulation analysis, 74 candidate metabolites that may be closely related to seed germination were finally screened. Among these candidates, 29 members belong to the ornithine–asparagine–polyamine module and the shikimic acid–tyrosine–tryptamine–phenylalanine–flavonoid module. As the core member of the second module, shikimic acid’s function in the promotion of seed germination was confirmed by exogenous treatment. These results told that nitrogen flow and antioxidation/defense responses are potentially crucial for germinating seeds and seedlings. It deepens our understanding of the metabolic regulation mechanism of seed germination and points out the direction for our future research.

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.

Gibberellin in tomato: metabolism, signaling and role in drought responses

The growth-promoting hormone gibberellin (GA) regulates numerous developmental processes throughout the plant life cycle. It also affects plant response to biotic and abiotic stresses. GA metabolism and signaling in tomato (Solanum lycopersicum) have been studied in the last three decades and major components of the pathways were characterized. These include major biosynthesis and catabolism enzymes and signaling components, such as the three GA receptors GIBBERELLIN INSENSITIVE DWARF 1 (GID1) and DELLA protein PROCERA (PRO), the central response suppressor. The role of these components in tomato plant development and response to the environment have been investigated. Cultivated tomato, similar to many other crop plants, are susceptible to water deficiency. Numerous studies on tomato response to drought have been conducted, including the possible role of GA in tomato drought resistance. Most studies showed that reduced levels or activity of GA improves drought tolerance and drought avoidance. This review aims to provide an overview on GA biosynthesis and signaling in tomato, how drought affects these pathways and how changes in GA activity affect tomato plant response to water deficiency. It also presents the potential of using the GA pathway to generate drought-tolerant tomato plants with improved performance under both irrigation and water-limited conditions.

Here, there and everywhere – the importance of neutral lipids in plant growth and development

In plants, lipids serve as one of the major and vital cellular constituents. Neutral lipids reserves play an essential role in the plant life cycle by providing carbon and energy equivalents for periods of active metabolism. The most common form of lipid storage are triacylglycerols (TAGs) packed into specialized organelles called lipid droplets (LDs). They have been observed in diverse plant organs and tissues, like oil seeds or pollen grains. LDs consist of a core, composed mostly of TAGs, enclosed by a single layer of phospholipids that is decorated by a unique set of structural proteins. Moreover, the recent advances in exploration of LDs proteome revealed a plethora of diverse proteins interacting with LDs. This is likely the result of a highly dynamic nature of these organelles and their involvement in many diverse aspect of cellular metabolism, tightly synchronized with plant developmental programs and directly related to plant-environment interactions. In this review we summarize and discuss the current progress in understanding the role of LDs and their cargo during plants life cycle, with a special emphasis on developmental aspects.

Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes

Plant microbiomes play an important role in agricultural productivity, but there is still much to learn about their provenance, diversity, and organization. In order to study the role of vertical transmission in establishing the bacterial and fungal populations of juvenile plants, we used high-throughput sequencing to survey the microbiomes of seeds, spermospheres, rhizospheres, roots, and shoots of the monocot crops maize (B73), rice (Nipponbare), switchgrass (Alamo), Brachiaria decumbens, wheat, sugarcane, barley, and sorghum; the dicot crops tomato (Heinz 1706), coffee (Geisha), common bean (G19833), cassava, soybean, pea, and sunflower; and the model plants Arabidopsis thaliana (Columbia-0) and Brachypodium distachyon (Bd21). Unsterilized seeds were planted in either sterile sand or farm soil inside hermetically sealed jars, and after as much as 60 days of growth, DNA was extracted to allow for amplicon sequence-based profiling of the bacterial and fungal populations that developed. Seeds of most plants were dominated by Proteobacteria and Ascomycetes, with all containing operational taxonomic units (OTUs) belonging to Pantoea and Enterobacter. All spermospheres also contained DNA belonging to Pseudomonas, Bacillus, and Fusarium. Despite having only seeds as a source of inoculum, all plants grown on sterile sand in sealed jars nevertheless developed rhizospheres, endospheres, and phyllospheres dominated by shared Proteobacteria and diverse fungi. Compared to sterile sand-grown seedlings, growth on soil added new microbial diversity to the plant, especially to rhizospheres; however, all 63 seed-transmitted bacterial OTUs were still present, and the most abundant bacteria (Pantoea, Enterobacter, Pseudomonas, Klebsiella, and Massilia) were the same dominant seed-transmitted microbes observed in sterile sand-grown plants. While most plant mycobiome diversity was observed to come from soil, judging by read abundance, the dominant fungi (Fusarium and Alternaria) were also vertically transmitted. Seed-transmitted fungi and bacteria appear to make up the majority of juvenile crop plant microbial populations by abundance, and based on occupancy, there seems to be a pan-angiosperm seed-transmitted core bacterial microbiome. Further study of these seed-transmitted microbes will be important to understand their role in plant growth and health, as well as their fate during the plant life cycle and may lead to innovations for agricultural inoculant development.

Seed Science Research: Global Trends in Seed Biology and Technology

Seeds are the central components of the plant life cycle because the establishment of a new generation of plants depends on them [...]

Nitrate-regulated growth processes involve activation of gibberellin pathway

Nitrate, one of the main nitrogen (N) sources for crops, acts as a nutrient and key signaling molecule coordinating gene expression, metabolism and various growth processes throughout the plant life cycle. It is widely accepted that nitrate-triggered developmental programs cooperate with hormone synthesis and transport, to finely adapt plant architecture to N availability. Here, we report that nitrate, acting through its signaling pathway, promotes growth in Arabidopsis and wheat, in part by modulating the accumulation of gibberellin (GA)-regulated DELLA growth repressors. We show that nitrate reduces the abundance of DELLAs by increasing GA contents through activation of GA metabolism gene expression. Consistently, the growth restraint conferred by nitrate deficiency is partially rescued in global-DELLA mutant that lacks all DELLAs. At the cellular level, we show that nitrate enhances both cell proliferation and elongation in a DELLA-dependent and -independent manner, respectively. Our findings establish a connection between nitrate and GA signaling pathways that allow plants to adapt their growth to nitrate availability.

Studies on the phenology of some terrestrial orchids of Western Ghats, India

The present paper describes the distribution, natural habitat and phenology of some terrestrial orchids in Shimoga district, Karnataka. The phenophases viz., leafing, flowering, fruiting, fruit dehiscence are observed for 25 orchid taxa belonging to 13 genera in Shimoga district. They are Dienia ophrydis (J. Koenig) Seidenf., Disperis zeylanica Trimen., Epipogium roseum (D. Don) Lindl., Eulophia spectabilis (Dennst.) Suresh., Geodorum densiflorum (Lam.) Schltr., Habenaria crinifera Lindl., Habenaria elwesii Hook f., Habenaria furcifera Lindl., Habenaria grandifloriformis Blatt. & Mc Cann., Habenaria heyneana Lindl., Habenaria longicorniculata J. Graham., Habenaria multicaudata Sedgw., Habenaria plantaginea Lindl., Liparis deflexa Hook. f., Liparis odorata (Willd) Lindl., Malaxis versicolor (Lindl.) Abeyw., Nervilia concolor (Blume) Schltr. Nervilia crociformis (Zoll. & Moritzi) Seidenf., Nervilia infundibulifolia Blatt. & Mc Cann., Nervilia plicata (Andrews) Schltr., Pecteilis gigantea (Sm.) Raf.. Peristylus plantagineus (Lindl.), Peristylus spiralis A. Rich., Satyrium nepalense D. Don, Zeuxine longilabris (Lindl.) Trimen. Phenology is the timing of plant life cycle events. Regular field visits were carried to observe the different life events. Most of the terrestrial orchids complete their life cycle in April to September or October month. The present research gives additional phenological aspects of terrestrial orchids in Shimoga district. Vegetative phenology is important to understand the ecology and instinct history of a plant species and may help to develop the conservation strategies of endangered species.