Unravelling the MicroRNA-Mediated Gene Regulation in Developing Pongamia Seeds by High-Throughput Small RNA Profiling

A critical review of Pongamia pinnata multiple applications: From land remediation and carbon sequestration to socioeconomic benefits

Pongamia pinnata (L.) Pierre (Pongamia) is a tree native to Southeast Asia. Recently, interest in Pongamia focused on its potential as a biofuel source as its seeds contain around 40% oil. However, Pongamia has multiple applications beyond biofuel production. It is a legume, can form symbiotic associations with mycorrhizal fungi, has been shown to be tolerant to drought, salinity, and heavy metals in soil, and has potential to mitigate climate change. Additionally, Pongamia oil has medicinal properties, can be used as biopesticide, insect repellent, to produce soap, and as a source of edible grade vegetable oil. The seed cake can be used as a source of bioenergy, food and feed protein, and organic fertiliser, and the flowers are a good source of pollen and nectar. Pongamia can also bring socio-economic benefits as its ability to restore degraded and contaminated land provides opportunities for local communities through novel valorisation pathways. These multiple applications have potential to form part of a circular bioeconomy in line with sustainable development goals. Although research on the multiple applications of Pongamia has grown considerably, knowledge gaps remain and these need to be addressed so that the full potential of Pongamia can be achieved. Further understanding of the mechanisms underlying its resilience to abiotic stresses, phytoremediation potential and biotic interactions should be a priority, and co-ordinated breeding efforts will be key. Here, we critically review the available literature on Pongamia and highlight gaps in knowledge in which future research should focus on to ensure that the full potential of this versatile tree can be achieved. We conclude that Pongamia can potentially form part of a circular bioeconomy and that harnessing the multiple applications of Pongamia in a holistic manner, with collaboration among key stakeholders, is crucial for the successful application of its benefits far beyond biofuel production.

MicroRNAs in Woody Plants

MicroRNAs (miRNAs) are small (∼21-nucleotides) non-coding RNAs found in plant and animals. MiRNAs function as critical post-transcriptional regulators of gene expression by binding to complementary sequences in their target mRNAs, leading to mRNA destabilization and translational inhibition. Plant miRNAs have some distinct characteristics compared to their animal counterparts, including greater evolutionary conservation and unique miRNA processing methods. The lifecycle of a plant begins with embryogenesis and progresses through seed germination, vegetative growth, reproductive growth, flowering and fruiting, and finally senescence and death. MiRNAs participate in the transformation of plant growth and development and directly monitor progression of these processes and the expression of certain morphological characteristics by regulating transcription factor genes involved in cell growth and differentiation. In woody plants, a large and rapidly increasing number of miRNAs have been identified, but their biological functions are largely unknown. In this review, we summarize the progress of miRNA research in woody plants to date. In particular, we discuss the potential roles of these miRNAs in growth, development, and biotic and abiotic stresses responses in woody plants.

Transcriptome and metabolite analysis related to branch development in two genotypes of Eucalyptus urophylla

Branching in long-lived plants can cause scarring at the base and affect wood density, which greatly inhibits wood yield and quality. Eucalyptus urophylla is one of the most important commercial forest tree species in South China, with diverse branch number and branch angles under different genetic backgrounds. However, the main elements and regulatory mechanisms associated with different branching traits in E. urophylla remain unclear. To identify the factors that may influence branching, the transcriptome and metabolome were performed on the shoot apex (SA), lateral shoot apex (LSA), and stem segment at the 5th axillary bud from the shoot apex (S1) in lines ZQUC14 (A) and LDUD26 (B), with A exhibiting a smaller Ba than B. A total of 307.3 million high-quality clean reads and nine hormones were identified from six libraries. Several differentially expressed regulatory factors were identified between the two genotypes of E. urophylla. The Kyoto Encyclopedia of Genes and Genomes pathways were enriched in plant hormone signal transduction, plant hormone biosynthesis and their transport pathways. Furthermore, gene expression pattern analysis identified genes that were significantly downregulated or upregulated in S1 relative to the SA and LSA segments, and the plant hormone signal transduction pathway was constructed to explain branching development. This study clarified the main plant hormones and genes underlying branch numbers and angles of E. urophylla, confirmed that ABA and SA could promote a larger branch angle and smaller branch number, while IAA has an opposite function. Numbers of key candidate genes involved in plant hormone signal transduction were found in the positive regulation of branch formation. These novel findings should aid molecular breeding of branching in Eucalyptus.

MicroRNA-mediated regulation of agronomically important seed traits: a treasure trove with shades of grey!

Seed development is an intricate process with multiple levels of regulation. MicroRNAs (miRNAs) have emerged as one of the crucial components of molecular networks underlying agronomically important seed traits in diverse plant species. In fact, loss of function of the genes regulating miRNA biogenesis also exhibits defects in seed development. A total of 21 different miRNAs have experimentally been shown to regulate seed size, nutritional content, vigor, and shattering, and have been reviewed here. The mechanism details of the associated regulatory cascades mediated through transcriptional regulators, phytohormones, basic metabolic machinery, and secondary siRNAs are elaborated. Co-localization of miRNAs and their target regions with seed-related QTLs provides new avenues for engineering these traits using conventional breeding programs or biotechnological interventions. While global analysis of miRNAs using small RNA sequencing studies are expanding the repertoire of candidate miRNAs, recent revelations on their inheritance, transport, and mechanism of action would be instrumental in designing better strategies for optimizing agronomically relevant seed traits.

Identification and molecular characterization of miRNAs and their target genes associated with seed development through small RNA sequencing in chickpea

Multiple studies have attempted to dissect the molecular mechanism underlying seed development in chickpea (Cicer arietinum L.). These studies highlight the need to focus on the role of miRNAs in regulating storage protein accumulation in seeds. Therefore, a total of 8,856,691 short-read sequences were generated from a small RNA library of developing chickpea seeds and were analyzed using miRDeep-P to identify 74 known and 26 novel miRNA sequences. Known miRNAs were classified into 22 miRNA families with miRNA156 family being most abundant. Of the 26 putative novel miRNAs identified, only 22 could be experimentally validated using stem loop end point PCR. Differential expression analyses led to the identification of known as well as novel miRNAs that could regulate various stages of chickpea seed development. In silico target prediction revealed several important target genes and transcription factors like SPL, mediator of RNA Polymerase II transcription subunit 12, aspartic proteinase and NACs, which were further validated by real-time PCR analysis. A comparative expression analysis in chickpea genotypes with contrasting seed protein content revealed one known (Car-miR156h) and two novel miRNA (Car-novmiR7 and Car-novmiR23) candidates to be highly expressed in the LPC (low protein content) chickpea genotypes, targets of which are known to regulate seed storage protein accumulation. Therefore, this study provides a useful resource in the form of miRNA and their targets which can be further utilized to understand and manipulate various regulatory mechanisms involved in seed development with the overall aim of improving yield and nutrition attributes in chickpea.

Protein and Proteome Atlas for Plants under Stresses: New Highlights and Ways for Integrated Omics in Post-Genomics Era

In the post-genomics era, integrative omics studies for biochemical, physiological, and molecular changes of plants in response to stress conditions play more crucial roles. Among them, atlas analysis of plants under different abiotic stresses, including salinity, drought, and toxic conditions, has become more important for uncovering the potential key genes and proteins in different plant tissues. High-quality genomic data and integrated analyses of transcriptomic, proteomic, metabolomics, and phenomic patterns provide a deeper understanding of how plants grow and survive under environmental stresses. This editorial mini-review aims to synthesize the 27 papers including two timely reviews that have contributed to this Special Issue, which focuses on concluding the recent progress in the Protein and Proteome Atlas in plants under different stresses. It covers various aspects of plant proteins ranging from agricultural proteomics, structure and function of proteins, novel techniques and approaches for gene and protein identification, protein quantification, proteomics for post-translational modifications (PTMs), and new insights into proteomics. The proteomics-based results in this issue will help the readers to gain novel insights for the understanding of complicated physiological processes in crops and other important plants in response to stressed conditions. Furthermore, these target genes and proteins that are important candidates for further functional validation in economic plants and crops can be studied.