microRNAs involved in auxin signalling modulate male sterility under high-temperature stress in cotton (Gossypium hirsutum)

A review on strategies for crop improvement against drought stress through molecular insights

The demand for food goods is rising along with the world population growth, which is directly related to the yield of agricultural crops around the world. However, a number of environmental factors, including floods, salinity, moisture, and drought, have a detrimental effect on agricultural production around the world. Among all of these stresses, drought stress (DS) poses a constant threat to agricultural crops and is a significant impediment to global agricultural productivity. Its potency and severity are expected to increase in the future years. A variety of techniques have been used to generate drought-resistant plants in order to get around this restriction. Different crop plants exhibit specific traits that contribute to drought resistance (DR), such as early flowering, drought escape (DE), and leaf traits. We are highlighting numerous methods that can be used to overcome the effects of DS in this review. Agronomic methods, transgenic methods, the use of sufficient fertilizers, and molecular methods such as clustered regularly interspaced short palindromic repeats (CRISPRs)-associated nuclease 9 (Cas9), virus-induced gene silencing (VIGS), quantitative trait loci (QTL) mapping, microRNA (miRNA) technology, and OMICS-based approaches make up the majority of these techniques. CRISPR technology has rapidly become an increasingly popular choice among researchers exploring natural tolerance to abiotic stresses although, only a few plants have been produced so far using this technique. In order to address the difficulties imposed by DS, new plants utilizing the CRISPR technology must be developed.

Unraveling the genetic and molecular basis of heat stress in cotton

Human activities and climate change have resulted in frequent and intense weather fluctuations, leading to diverse abiotic stresses on crops which hampers greatly their metabolic activities. Heat stress, a prevalent abiotic factor, significantly influences cotton plant biological activities resulting in reducing yield and production. We must deepen our understanding of how plants respond to heat stress across various dimensions, encompassing genes, RNAs, proteins, metabolites for effective cotton breeding. Multi-omics methods, primarily genomics, transcriptomics, proteomics, metabolomics, and phenomics, proves instrumental in studying cotton's responses to abiotic stresses. Integrating genomics, transcriptomics, proteomics, and metabolomic is imperative for our better understanding regarding genetics and molecular basis of heat tolerance in cotton. The current review explores fundamental omics techniques, covering genomics, transcriptomics, proteomics, and metabolomics, to highlight the progress made in cotton omics research.

Enigmatic role of auxin response factors in plant growth and stress tolerance

Abiotic and biotic stresses globally constrain plant growth and impede the optimization of crop productivity. The phytohormone auxin is involved in nearly every aspect of plant development. Auxin acts as a chemical messenger that influences gene expression through a short nuclear pathway, mediated by a family of specific DNA-binding transcription factors known as Auxin Response Factors (ARFs). ARFs thus act as effectors of auxin response and translate chemical signals into the regulation of auxin responsive genes. Since the initial discovery of the first ARF in Arabidopsis, advancements in genetics, biochemistry, genomics, and structural biology have facilitated the development of models elucidating ARF action and their contributions to generating specific auxin responses. Yet, significant gaps persist in our understanding of ARF transcription factors despite these endeavors. Unraveling the functional roles of ARFs in regulating stress response, alongside elucidating their genetic and molecular mechanisms, is still in its nascent phase. Here, we review recent research outcomes on ARFs, detailing their involvement in regulating leaf, flower, and root organogenesis and development, as well as stress responses and their corresponding regulatory mechanisms: including gene expression patterns, functional characterization, transcriptional, post-transcriptional and post- translational regulation across diverse stress conditions. Furthermore, we delineate unresolved questions and forthcoming challenges in ARF research.

The roles of non-coding RNAs in male reproductive development and abiotic stress responses during this unique process in flowering plants

Successful male reproductive development is the guarantee for sexual reproduction of flowering plants. Male reproductive development is a complicated and multi-stage process that integrates physiological processes and adaptation and tolerance to a myriad of environmental stresses. This well-coordinated process is governed by genetic and epigenetic machineries. Non-coding RNAs (ncRNAs) play pleiotropic roles in the plant growth and development. The identification, characterization and functional analysis of ncRNAs and their target genes have opened a new avenue for comprehensively revealing the regulatory network of male reproductive development and its response to environmental stresses in plants. This review briefly addresses the types, origin, biogenesis and mechanisms of ncRNAs in plants, highlights important updates on the roles of ncRNAs in regulating male reproductive development and emphasizes the contribution of ncRNAs, especially miRNAs and lncRNAs, in responses to abiotic stresses during this unique process in flowering plants.

Transcription Factors and Their Regulatory Roles in the Male Gametophyte Development of Flowering Plants

Male gametophyte development in plants relies on the functions of numerous genes, whose expression is regulated by transcription factors (TFs), non-coding RNAs, hormones, and diverse environmental stresses. Several excellent reviews are available that address the genes and enzymes associated with male gametophyte development, especially pollen wall formation. Growing evidence from genetic studies, transcriptome analysis, and gene-by-gene studies suggests that TFs coordinate with epigenetic machinery to regulate the expression of these genes and enzymes for the sequential male gametophyte development. However, very little summarization has been performed to comprehensively review their intricate regulatory roles and discuss their downstream targets and upstream regulators in this unique process. In the present review, we highlight the research progress on the regulatory roles of TF families in the male gametophyte development of flowering plants. The transcriptional regulation, epigenetic control, and other regulators of TFs involved in male gametophyte development are also addressed.

Comprehensive non-coding RNA analysis reveals specific lncRNA/circRNA-miRNA-mRNA regulatory networks in the cotton response to drought stress

Root and leaf are essential organs of plants in sensing and responding to drought stress. However, comparative knowledge of non-coding RNAs (ncRNAs) of root and leaf tissues in the regulation of drought response in cotton is limited. Here, we used deep sequencing data of leaf and root tissues of drought-resistant and drought-sensitive cotton varieties for identifying miRNAs, lncRNAs and circRNAs. A total of 1531 differentially expressed (DE) ncRNAs was identified, including 77 DE miRNAs, 1393 DE lncRNAs and 61 DE circRNAs. The tissue-specific and variety-specific competing endogenous RNA (ceRNA) networks of DE lncRNA-miRNA-mRNA response to drought were constructed. Furthermore, the novel drought-responsive lncRNA 1 (DRL1), specifically and differentially expressed in root, was verified to positively affect phenotypes of cotton seedlings under drought stress, competitively binding to miR477b with GhNAC1 and GhSCL3. In addition, we also constructed another ceRNA network consisting of 18 DE circRNAs, 26 DE miRNAs and 368 DE mRNAs. Fourteen circRNA were characterized, and a novel molecular regulatory system of circ125- miR7484b/miR7450b was proposed under drought stress. Our findings revealed the specificity of ncRNA expression in tissue- and variety-specific patterns involved in the response to drought stress, and uncovered novel regulatory pathways and potentially effective molecules in genetic improvement for crop drought resistance.

Non-coding RNAs (ncRNAs) in plant: Master regulators for adapting to extreme temperature conditions

Unusual daily temperature fluctuations caused by climate change and climate variability adversely impact agricultural crop production. Since plants are immobile and constantly receive external environmental signals, such as extreme high (heat) and low (cold) temperatures, they have developed complex molecular regulatory mechanisms to cope with stressful situations to sustain their natural growth and development. Among these mechanisms, non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), small-interfering RNAs (siRNAs), and long-non-coding RNAs (lncRNAs), play a significant role in enhancing heat and cold stress tolerance. This review explores the pivotal findings related to miRNAs, siRNAs, and lncRNAs, elucidating how they functionally regulate plant adaptation to extreme temperatures. In addition, this review addresses the challenges associated with uncovering these non-coding RNAs and understanding their roles in orchestrating heat and cold tolerance in plants.

miRNAs and Their Target Genes Play a Critical Role in Response to Heat Stress in Cynodon dactylon (L.) Pers

Annual global temperature is increasing rapidly. Therefore, in the near future, plants will be exposed to severe heat stress. However, the potential of microRNAs-mediated molecular mechanism for modulating the expression of their target genes is unclear. To investigate the changes of miRNAs in thermo-tolerant plants, in this study, we first investigated the impact of four high temperature regimes including 35/30 °C, 40/35 °C, 45/40 °C, and 50/45 °C in a day/night cycle for 21 days on the physiological traits (total chlorophyll, relative water content and electrolyte leakage and total soluble protein), antioxidant enzymes activities (superoxide dismutase, ascorbic peroxidase, catalase and peroxidase), and osmolytes (total soluble carbohydrates and starch) in two bermudagrass accessions named Malayer and Gorgan. The results showed that more chlorophyll and the relative water content, lower ion leakage, more efficient protein and carbon metabolism and activation of defense proteins (such as antioxidant enzymes) in Gorgan accession, led to better maintained plant growth and activity during heat stress. In the next stage, to investigate the role of miRNAs and their target genes in response to heat stress in a thermo-tolerant plant, the impact of severe heat stress (45/40 °C) was evaluated on the expression of three miRNAs (miRNA159a, miRNA160a and miRNA164f) and their target genes (GAMYB, ARF17 and NAC1, respectively). All measurements were performed in leaves and roots simultaneously. Heat stress significantly induced the expression of three miRNAs in leaves of two accession, while having different effects on the expression of these miRNAs in roots. The results showed that a decrease in the expression of the transcription factor ARF17, no change in the expression of the transcription factor NAC1, and an increase in the expression of the transcription factor GAMYB in leaf and root tissues of Gorgan accession led to improved heat tolerance in it. These results also showed that the effect of miRNAs on the modulating expression of target mRNAs in leaves and roots is different under heat stress, and miRNAs and mRNAs show spatiotemporal expression. Therefore, the simultaneous analysis of miRNAs and mRNAs expressions in shoot and roots is needed to comprehensively understand miRNAs regulatory function under heat stress.

Auxin and abiotic stress responses

Plants are exposed to a variety of abiotic stresses; these stresses have profound effects on plant growth, survival, and productivity. Tolerance and adaptation to stress require sophisticated stress sensing, signaling, and various regulatory mechanisms. The plant hormone auxin is a key regulator of plant growth and development, playing pivotal roles in the integration of abiotic stress signals and control of downstream stress responses. In this review, we summarize and discuss recent advances in understanding the intersection of auxin and abiotic stress in plants, with a focus on temperature, salt, and drought stresses. We also explore the roles of auxin in stress tolerance and opportunities arising for agricultural applications.

Histone H3 lysine 27 trimethylation suppresses jasmonate biosynthesis and signaling to affect male fertility under high temperature in cotton

High-temperature (HT) stress causes male sterility in crops, thus decreasing yields. To explore the possible contribution of histone modifications to male fertility under HT conditions, we defined the histone methylation landscape for the marks histone H3 lysine 27 trimethylation (H3K27me3) and histone H3 lysine 4 trimethylation (H3K4me3) by chromatin immunoprecipitation sequencing (ChIP-seq) in two differing upland cotton (Gossypium hirsutum) varieties. We observed a global disruption in H3K4me3 and H3K27me3 modifications, especially H3K27me3, in cotton anthers subjected to HT. HT affected the bivalent H3K4me3-H3K27me3 modification more than either monovalent modification. We determined that removal of H3K27me3 at the promoters of jasmonate-related genes increased their expression, maintaining male fertility under HT in the HT-tolerant variety at the anther dehiscence stage. Modulating jasmonate homeostasis or signaling resulted in an anther indehiscence phenotype under HT. Chemical suppression of H3K27me3 deposition increased jasmonic acid contents and maintained male fertility under HT. In summary, our study provides new insights into the regulation of male fertility by histone modifications under HT and suggests a potential strategy for improving cotton HT tolerance.

Heat-responsive microRNAs participate in regulating the pollen fertility stability of CMS-D2 restorer line under high-temperature stress

Anther development and pollen fertility of cytoplasmic male sterility (CMS) conditioned by Gossypium harknessii cytoplasm (CMS-D2) restorer lines are susceptible to continuous high-temperature (HT) stress in summer, which seriously hinders the large-scale application of "three-line" hybrids in production. Here, integrated small RNA, transcriptome, degradome, and hormone profiling was performed to explore the roles of microRNAs (miRNAs) in regulating fertility stability in mature pollens of isonuclear alloplasmic near-isogenic restorer lines NH and SH under HT stress at two environments. A total of 211 known and 248 novel miRNAs were identified, of which 159 were differentially expressed miRNAs (DEMs). Additionally, 45 DEMs in 39 miRNA clusters (PmCs) were also identified, and most highly expressed miRNAs were significantly induced in SH under extreme HT, especially four MIR482 and six MIR6300 family miRNAs. PmC28 was located in the fine-mapped interval of the Rf1 gene and contained two DEMs, gra-miR482_L-2R + 2 and gma-miR2118a-3p_R + 1_1ss18TG. Transcriptome sequencing identified 6281 differentially expressed genes, of which heat shock protein (HSP)-related genes, such as HSP70, HSP22, HSP18.5-C, HSP18.2 and HSP17.3-B, presented significantly reduced expression levels in SH under HT stress. Through integrating multi-omics data, we constructed a comprehensive molecular network of miRNA-mRNA-gene-KEGG containing 35 pairs of miRNA/target genes involved in regulating the pollen development in response to HT, among which the mtr-miR167a_R + 1, tcc-miR167c and ghr-miR390a, tcc-miR396c_L-1 and ghr-MIR169b-p3_1ss6AG regulated the pollen fertility by influencing ARF8 responsible for the auxin signal transduction, ascorbate and aldarate metabolism, and the sugar and lipid metabolism and transport pathways, respectively. Further combination with hormone analysis revealed that HT-induced jasmonic acid signaling could activate the expression of downstream auxin synthesis-related genes and cause excessive auxin accumulation, followed by a cascade of auxin signal transduction, ultimately resulting in pollen abortion. The results provide a new understanding of how heat-responsive miRNAs regulate the stability of fertility restoration for CMS-D2 cotton under heat stress.

The roles of miR156 in abiotic and biotic stresses in plants

MicroRNAs (miRNAs), known as a kind of non-coding RNA, can negatively regulate its target genes. To date, the roles of various miRNAs in plant development and resistance to abiotic and biotic stresses have been widely explored. The present review summarized and discussed the functions of miR156 or miR156-SPL module in abiotic and biotic stresses, such as drought, salt, heat, cold stress, UV-B radiation, heavy mental hazards, nutritional starvation, as well as plant viruses, plant diseases, etc. Based on this, the regulation of miR156-involved stress tolerance was better understood, thus, it would be much easier for plant biologists to carry out suitable strategies to help plants suffer from unfavorable living environments.

Non-coding RNAs-mediated environmental surveillance determines male fertility in plants

Plants are continuously exposed to environmental stresses leading to significant yield losses. With the changing climatic conditions, the intensity and duration of these stresses are expected to increase, posing a severe threat to crop productivity worldwide. Male gametogenesis is one of the most sensitive developmental stages. Exposure to environmental stresses during this stage leads to male sterility and yield loss. Elucidating the underlying molecular mechanism of environment-affected male sterility is essential to address this challenge. High-throughput RNA sequencing studies, loss-of-function phenotypes of sRNA biogenesis genes and functional genomics studies with non-coding RNAs have started to unveil the roles of small RNAs, long non-coding RNAs and the complex regulatory interactions between them in regulating male fertility under different growth regimes. Here, we discuss the current understanding of the non-coding RNA-mediated environmental stress surveillance and regulation of male fertility in plants. The candidate ncRNAs emerging from these studies can be leveraged to generate environment-sensitive male sterile lines for hybrid breeding or mitigate the impact of climate change on male fertility, as the situation demands.

Potential candidate genes and pathways related to cytoplasmic male sterility in Dianthus spiculifolius as revealed by transcriptome analysis

KEY MESSAGE

We introduced the candidate gene DsHSP70 into Arabidopsis thaliana, resulting in male gametophyte sterility and abnormal degeneration of sepals and petals. Cytoplasmic male sterility (CMS) is a useful tool for hybrid production. However, the regulatory mechanism of CMS in Dianthus spiculifolius remains unclear. In this study, we investigated whether male-sterile line of D. spiculifolius has a malformed tapetum and fails to produce normal fertile pollen. RNA sequencing technology was used to compare the gene expression patterns of the D. spiculifolius male-sterile line and its male fertility maintainer line during anther development. A total of 12,365 differentially expressed genes (DEGs) were identified, among which 1765 were commonly expressed in the S1, S2 and S3 stages. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that these DEGs were mainly involved in oxidation-reduction processes, signal transduction and programmed cell death. Additionally, weighted correlation network analysis (WGCNA) showed that three modules may be related to male sterility. A putative regulatory pathway for the male sterility traits was constructed based on the reproductive development network. After introducing the candidate DsHSP70 gene into Arabidopsis thaliana, we found that overexpressing plants showed anther abortion and shorter filaments, and accompanied by abnormal degeneration of sepals and petals. In summary, our results identified potential candidate genes and pathways related to CMS in D. spiculifolius, providing new insights for further research on the mechanism of male sterility.

An insight into the roles of regulatory ncRNAs in plants: An abiotic stress and developmental perspective

Different environmental cues lead to changes in physiology, biochemistry and molecular status of plant's growth. Till date, various genes have been accounted for their role in regulating plant development and response to abiotic stress. Excluding genes that code for a functional protein in a cell, a large chunk of the eukaryotic transcriptome consists of non-coding RNAs (ncRNAs) which lack protein coding capacity but are still functional. Recent advancements in Next Generation Sequencing (NGS) technology have led to the unearthing of different types of small and large non-coding RNAs in plants. Non-coding RNAs are broadly categorised into housekeeping ncRNAs and regulatory ncRNAs which work at transcriptional, post-transcriptional and epigenetic levels. Diverse ncRNAs play different regulatory roles in nearly all biological processes including growth, development and response to changing environments. This response can be perceived and counteracted by plants using diverse evolutionarily conserved ncRNAs like miRNAs, siRNAs and lncRNAs to participate in complex molecular regimes by activating gene-ncRNA-mRNA regulatory modules to perform the downstream function. Here, we review the current understanding with a focus on recent advancements in the functional studies of the regulatory ncRNAs at the nexus of abiotic stresses and development. Also, the potential roles of ncRNAs in imparting abiotic stress tolerance and yield improvement in crop plants are also discussed with their future prospects.

Integrated transcriptome and proteome analysis reveals molecular responses of soybean anther under high-temperature stress

It is well documented that high temperature (HT) severely affects the development of soybean male reproductive organs. However, the molecular mechanism of thermo-tolerance in soybean remains unclear. To explore the candidate genes and regulatory mechanism of soybean response to HT stress and flower development, here, the anthers of two previously identified HT-tolerant (JD21) and HT-sensitive (HD14) varieties were analyzed by RNA-seq. In total, 219 (172 upregulated and 47 downregulated), 660 (405 upregulated and 255 downregulated), and 4,854 (2,662 upregulated and 2,192 downregulated) differentially expressed genes (DEGs) were identified between JD21 anthers treated with HT stress vs. JD21 anthers in the natural field conditions (TJA vs. CJA), HD14 anthers treated with HT stress vs. HD14 anthers in the natural field conditions (THA vs. CHA), and JD21 vs. HD14 anthers treated with HT stress (TJA vs. THA), respectively. The results showed that there were more DEGs upregulated in JD21; this might be the reason why JD21 was more HT-resistant than the HT-sensitive variety HD14. GO annotation and KEGG enriched analysis showed that many DEGs are mainly involved in defense response, response to biological stimuli, auxin-activated signaling pathway, plant hormone signal transduction, MAPK signaling pathway-plant, starch and sucrose metabolism, etc. The conjoint analysis of RNA-seq and previous iTRAQ results found that there were 1, 24, and 54 common DEGs/DAPs showing the same expression pattern and 1, 2, and 13 common DEGs/DAPs showing the opposite pattern between TJA vs. CJA, THA vs. CHA, and TJA vs. THA at the protein and gene level, respectively, among which HSPs, transcription factor, GSTU, and other DEGs/DAPs participated in the response to HT stress and flower development. Notably, the qRT-PCR analysis and physiological index change results coincided with the sequencing results of RNA-seq and iTRAQ. In conclusion, the HT-tolerant cultivar performed better under stress than the HT-sensitive cultivar through modulation of HSP family proteins and transcription factors, and by keeping key metabolic pathways such as plant hormone signal transduction normal. This study provided important data and some key candidate genes to better study the effect and molecular basis of HT on anther in soybean at a transcription and translation level.

High-temperature stress in crops: male sterility, yield loss and potential remedy approaches

Global food security is one of the utmost essential challenges in the 21st century in providing enough food for the growing population while coping with the already stressed environment. High temperature (HT) is one of the main factors affecting plant growth, development and reproduction and causes male sterility in plants. In male reproductive tissues, metabolic changes induced by HT involve carbohydrates, lipids, hormones, epigenetics and reactive oxygen species, leading to male sterility and ultimately reducing yield. Understanding the mechanism and genes involved in these pathways during the HT stress response will provide a new path to improve crops by using molecular breeding and biotechnological approaches. Moreover, this review provides insight into male sterility and integrates this with suggested strategies to enhance crop tolerance under HT stress conditions at the reproductive stage.

Genome-Wide Investigation of Apyrase (APY) Genes in Peanut (Arachis hypogaea L.) and Functional Characterization of a Pod-Abundant Expression Promoter AhAPY2-1p

Peanut (Arachis hypogaea L.) is an important food and feed crop worldwide and is affected by various biotic and abiotic stresses. The cellular ATP levels decrease significantly during stress as ATP molecules move to extracellular spaces, resulting in increased ROS production and cell apoptosis. Apyrases (APYs) are the nucleoside phosphatase (NPTs) superfamily members and play an important role in regulating cellular ATP levels under stress. We identified 17 APY homologs in A. hypogaea (AhAPYs), and their phylogenetic relationships, conserved motifs, putative miRNAs targeting different AhAPYs, cis-regulatory elements, etc., were studied in detail. The transcriptome expression data were used to observe the expression patterns in different tissues and under stress conditions. We found that the AhAPY2-1 gene showed abundant expression in the pericarp. As the pericarp is a key defense organ against environmental stress and promoters are the key elements regulating gene expression, we functionally characterized the AhAPY2-1 promoter for its possible use in future breeding programs. The functional characterization of AhAPY2-1P in transgenic Arabidopsis plants showed that it effectively regulated GUS gene expression in the pericarp. GUS expression was also detected in flowers of transgenic Arabidopsis plants. Overall, these results strongly suggest that APYs are an important future research subject for peanut and other crops, and AhPAY2-1P can be used to drive the resistance-related genes in a pericarp-specific manner to enhance the defensive abilities of the pericarp.

Plant non-coding RNAs function in pollen development and male sterility

Male sterility is classified as either cytoplasmic male sterility (CMS) or genic male sterility (GMS). Generally, CMS involves mitochondrial genomes interacting with the nuclear genome, while GMS is caused by nuclear genes alone. Male sterility is regulated by multilevel mechanisms in which non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and phased small interfering RNAs (phasiRNAs), which have been proven to be critical elements. The development of high-throughput sequencing technology offers new opportunities to evaluate the genetic mechanism of ncRNAs in plant male sterility. In this review, we summarize the critical ncRNAs that regulate gene expression in ways dependent on or independent of hormones, which involve the differentiation of the stamen primordia, degradation of the tapetum, formation of microspores, and the release of pollen. In addition, the key mechanisms of the miRNA-lncRNA-mRNA interaction networks mediating male sterility in plants are elaborated. We present a different perspective on exploring the ncRNA-mediated regulatory pathways that control CMS in plants and create male-sterile lines through hormones or genome editing. A refined understanding of the ncRNA regulatory mechanisms in plant male sterility for the development of new sterile lines would be conducive to improve hybridization breeding.

Genome-wide identification of germin-like proteins in peanut (Arachis hypogea L.) and expression analysis under different abiotic stresses

Peanut is an important food and feed crop, providing oil and protein nutrients. Germins and germin-like proteins (GLPs) are ubiquitously present in plants playing numerous roles in defense, growth and development, and different signaling pathways. However, the GLP members have not been comprehensively studied in peanut at the genome-wide scale. We carried out a genome-wide identification of the GLP genes in peanut genome. GLP members were identified comprehensively, and gene structure, genomic positions, motifs/domains distribution patterns, and phylogenetic history were studied in detail. Promoter Cis-elements, gene duplication, collinearity, miRNAs, protein-protein interactions, and expression were determined. A total of 84 GLPs (AhGLPs ) were found in the genome of cultivated peanut. These GLP genes were clustered into six groups. Segmental duplication events played a key role in the evolution of AhGLPs, and purifying selection pressure was underlying the duplication process. Most AhGLPs possessed a well-maintained gene structure and motif organization within the same group. The promoter regions of AhGLPs contained several key cis-elements responsive to 'phytohormones', 'growth and development', defense, and 'light induction'. Seven microRNAs (miRNAs) from six families were found targeting 25 AhGLPs. Gene Ontology (GO) enrichment analysis showed that AhGLPs are highly enriched in nutrient reservoir activity, aleurone grain, external encapsulating structure, multicellular organismal reproductive process, and response to acid chemicals, indicating their important biological roles. AhGLP14, AhGLP38, AhGLP54, and AhGLP76 were expressed in most tissues, while AhGLP26, AhGLP29, and AhGLP62 showed abundant expression in the pericarp. AhGLP7, AhGLP20, and AhGLP21, etc., showed specifically high expression in embryo, while AhGLP12, AhGLP18, AhGLP40, AhGLP78, and AhGLP82 were highly expressed under different hormones, water, and temperature stress. The qRT-PCR results were in accordance with the transcriptome expression data. In short, these findings provided a foundation for future functional investigations on the AhGLPs for peanut breeding programs.

Evolutionary Landscape of Tea Circular RNAs and Its Contribution to Chilling Tolerance of Tea Plant

Chilling stress threatens the yield and distribution pattern of global crops, including the tea plant (Camellia sinensis), one of the most important cash crops around the world. Circular RNA (circRNA) plays roles in regulating plant growth and biotic/abiotic stress responses. Understanding the evolutionary characteristics of circRNA and its feedbacks to chilling stress in the tea plant will help to elucidate the vital roles of circRNAs. In the current report, we systematically identified 2702 high-confidence circRNAs under chilling stress in the tea plant, and interestingly found that the generation of tea plant circRNAs was associated with the length of their flanking introns. Repetitive sequences annotation and DNA methylation analysis revealed that the longer flanking introns of circRNAs present more repetitive sequences and higher methylation levels, which suggested that repeat-elements-mediated DNA methylation might promote the circRNAs biogenesis in the tea plant. We further detected 250 differentially expressed circRNAs under chilling stress, which were functionally enriched in GO terms related to cold/stress responses. Constructing a circRNA-miRNA-mRNA interaction network discovered 139 differentially expressed circRNAs harboring potential miRNA binding sites, which further identified 14 circRNAs that might contribute to tea plant chilling responses. We further characterized a key circRNA, CSS-circFAB1, which was significantly induced under chilling stress. FISH and silencing experiments revealed that CSS-circFAB1 was potentially involved in chilling tolerance of the tea plant. Our study emphasizes the importance of circRNA and its preliminary role against low-temperature stress, providing new insights for tea plant cold tolerance breeding.

Responses of differential metabolites and pathways to high temperature in cucumber anther

Cucumber is one of the most important vegetable crops, which is widely planted all over the world. Cucumber always suffers from high-temperature stress in South China in summer. In this study, liquid chromatography-mass spectrometry (LC-MS) analysis was used to study the differential metabolites of cucumber anther between high-temperature (HT) stress and normal condition (CK). After HT, the pollen fertility was significantly reduced, and abnormal anther structures were observed by the paraffin section. In addition, the metabolomics analysis results showed that a total of 125 differential metabolites were identified after HT, consisting of 99 significantly upregulated and 26 significantly downregulated metabolites. Among these differential metabolites, a total of 26 related metabolic pathways were found, and four pathways showed significant differences, namely, porphyrin and chlorophyll metabolism; plant hormone signal transduction; amino sugar and nucleotide sugar metabolism; and glycine, serine, and threonine metabolism. In addition, pollen fertility was decreased by altering the metabolites of plant hormone signal transduction and amino acid and sugar metabolism pathway under HT. These results provide a comprehensive understanding of the metabolic changes in cucumber anther under HT.

Homology-based identification of candidate genes for male sterility editing in upland cotton (Gossypium hirsutum L.)

Upland cotton (Gossypium hirsutum L.) accounts for more than 90% of the world's cotton production, providing natural material for the textile and oilseed industries worldwide. One strategy for improving upland cotton yields is through increased adoption of hybrids; however, emasculation of cotton flowers is incredibly time-consuming and genetic sources of cotton male sterility are limited. Here we review the known biochemical modes of plant nuclear male sterility (NMS), often known as plant genetic male sterility (GMS), and characterized them into four groups: transcriptional regulation, splicing, fatty acid transport and processing, and sugar transport and processing. We have explored protein sequence homology from 30 GMS genes of three monocots (maize, rice, and wheat) and three dicots (Arabidopsis, soybean, and tomato). We have analyzed evolutionary relationships between monocot and dicot GMS genes to describe the relative similarity and relatedness of these genes identified. Five were lowly conserved to their source species, four unique to monocots, five unique to dicots, 14 highly conserved among all species, and two in the other category. Using this source, we have identified 23 potential candidate genes within the upland cotton genome for the development of new male sterile germplasm to be used in hybrid cotton breeding. Combining homology-based studies with genome editing may allow for the discovery and validation of GMS genes that previously had no diversity observed in cotton and may allow for development of a desirable male sterile mutant to be used in hybrid cotton production.

Non-coding RNAs fine-tune the balance between plant growth and abiotic stress tolerance

To survive in adverse environmental conditions, plants have evolved sophisticated genetic and epigenetic regulatory mechanisms to balance their growth and abiotic stress tolerance. An increasing number of non-coding RNAs (ncRNAs), including small RNAs (sRNAs) and long non-coding RNAs (lncRNAs) have been identified as essential regulators which enable plants to coordinate multiple aspects of growth and responses to environmental stresses through modulating the expression of target genes at both the transcriptional and posttranscriptional levels. In this review, we summarize recent advances in understanding ncRNAs-mediated prioritization towards plant growth or tolerance to abiotic stresses, especially to cold, heat, drought and salt stresses. We highlight the diverse roles of evolutionally conserved microRNAs (miRNAs) and small interfering RNAs (siRNAs), and the underlying phytohormone-based signaling crosstalk in regulating the balance between plant growth and abiotic stress tolerance. We also review current discoveries regarding the potential roles of ncRNAs in stress memory in plants, which offer their descendants the potential for better fitness. Future ncRNAs-based breeding strategies are proposed to optimize the balance between growth and stress tolerance to maximize crop yield under the changing climate.

The S-Gene YUC6 Pleiotropically Determines Male Mating Type and Pollen Size in Heterostylous Turnera (Passifloraceae): A Novel Neofunctionalization of the YUCCA Gene Family

In heterostylous, self-incompatible Turnera species, a member of the YUCCA gene family, YUC6, resides at the S-locus and has been hypothesized to determine the male mating type. YUCCA gene family members synthesize the auxin, indole-3-acetic acid, via a two-step process involving the TAA gene family. Consequently, it has been speculated that differences in auxin concentration in developing anthers are the biochemical basis underlying the male mating type. Here, we provide empirical evidence that supports this hypothesis. Using a transgenic knockdown approach, we show that YUC6 acts pleiotropically to control both the male physiological mating type and pollen size, but not the filament length dimorphism associated with heterostyly in Turnera. Using qPCR to assess YUC6 expression in different transgenic lines, we demonstrate that the level of YUC6 knockdown correlates with the degree of change observed in the male mating type. Further assessment of YUC6 expression through anther development, in the knockdown lines, suggests that the male mating type is irreversibly determined during a specific developmental window prior to microsporogenesis, which is consistent with the genetically sporophytic nature of this self-incompatibility system. These results represent the first gene controlling male mating type to be characterized in any species with heterostyly.

Integrated analysis of metabolome and transcriptome reveals the cytoplasmic effects of CMS-D2 on pollen fertility resulting from disrupted lipid metabolism

Using cytoplasmic male sterility of Gossypium harknesii (CMS-D2) is an economical and effective method to produce cotton hybrids. However, the detrimental cytoplasmic effects of CMS-D2 on pollen fertility and fiber yields greatly limit the further development of three-line hybrid cotton in China. In this study, an integrated non-targeted metabolomics and transcriptome analysis was performed on mature pollens of maintainer line NB, isonuclear alloplasmic near-isogenic restorer lines NH and SH under two environments. A total of 820 metabolites were obtained, of which lipids and lipid-like molecules were the most, followed by organic acids derivatives, phenylpropanoids, and polyketides. Transcriptome analysis revealed significantly more differentially expressed genes (DEGs) in SH versus NH both in Anyang and Jiujiang, and most of the DEGs were significantly upregulated. Further KEGG analysis showed that most DEGs were enriched in the biosynthesis of unsaturated fatty acids, phenylalanine metabolism, and phagosome. Based on the weighted gene co-expression network analysis, totally 74 hub genes were also identified, of which three transcription factors, i.e., WRKY22, WRKY53, and ARF18 were significantly upregulated in SH and may play a negative regulatory role in pollen development by directly or indirectly regulating the jasmonic acid synthesis and signal transduction. Moreover, we found that the negative effects of CMS-D2 cytoplasm on pollen fertility were mainly due to disturbed lipid metabolism, especially the metabolic balance of unsaturated fatty acids, ultimately resulting in the decline of pollen fertility. Meanwhile, in the presence of CMS-D2 sterile cytoplasm, the cytoplasmic-nucleus interaction effects generated a substantial quantity of flavonoids involved in the fertility restoration process. This study preliminarily clarified some of the reasons for the negative effects of CMS-D2 cytoplasm on pollen fertility, and our results will provide an important theoretical reference for further breeding and improvement of three-line hybrid cotton in the future.

Identification of miRNAs and Target Genes at Key Stages of Sexual Differentiation in Androdioecious Osmanthus fragrans

Androdioecy is the crucial transition state in the evolutionary direction of hermaphroditism to dioecy, however, the molecular mechanisms underlying the formation of this sex system remain unclear. While popular in China for its ornamental and cultural value, Osmanthus fragrans has an extremely rare androdioecy breeding system, meaning that there are both male and hermaphroditic plants in a population. To unravel the mechanisms underlying the formation of androdioecy, we performed small RNA sequencing studies on male and hermaphroditic O. fragrans. A total of 334 miRNAs were identified, of which 59 were differentially expressed. Functional categorization revealed that the target genes of differentially expressed miRNAs were mainly involved in the biological processes of reproductive development and the hormone signal transduction pathway. We speculated that the miRNA160, miRNA167, miRNA393 and miRNA396 families may influence the sex differentiation in O. fragrans. Overall, our study is the first exploration of miRNAs in the growth and development process of O. fragrans, and is also the first study of androdioecious plants from the miRNA sequencing perspective. The analysis of miRNAs and target genes that may be involved in the sex differentiation process lay a foundation for the ultimate discovery of the androdioecious molecular mechanism in O. fragrans.

Application of RNAi technology: a novel approach to navigate abiotic stresses

BACKGROUND

Due to the rising population globally, and the demand for food, it is critical to significantly increase crop production by 2050. However, climate change estimates show that droughts and heatwaves will become more prevalent in many parts of the world, posing a severe danger to food output.

METHODS

Selective breeding based on genetic diversity is falling short of meeting the expanding need for food and feed. However, the advent of modern plant genetic engineering, genome editing, and synthetic biology provides precise techniques for producing crops capable of sustaining yield under stress situations.

RESULTS

As a result, crop varieties with built-in genetic tolerance to environmental challenges are desperately needed. In the recent years, small RNA (sRNA) data has progressed to become one of the most effective approaches for the improvement of crops. So many sRNAs (18-30nt) have been found with the use of hi-tech bioinformatics and sequencing techniques which are involved in the regulation of sequence specific gene noncoding RNAs (short ncRNAs) i.e., microRNA (miRNA) and small interfering RNA (siRNA). Such research outcomes may advance our understanding of the genetic basis of adaptability of plants to various environmental challenges and the genetic variation of plant's tolerance to a number of abiotic stresses.

CONCLUSION

The review article highlights current trends and advances in sRNAs' critical role in responses of plants to drought, heat, cold, and salinity, and also the potential technology that identifies the abiotic stress-regulated sRNAs, and techniques for analyzing and validating the target genes.

miR164g-MsNAC022 acts as a novel module mediating drought response by transcriptional regulation of reactive oxygen species scavenging systems in apple

Under drought stress, reactive oxygen species (ROS) overaccumulate as a secondary stress that impairs plant performance and thus severely reduces crop yields. The mitigation of ROS levels under drought stress is therefore crucial for drought tolerance. MicroRNAs (miRNAs) are critical regulators of plant development and stress responses. However, the complex molecular regulatory mechanism by which they function during drought stress, especially in drought-triggered ROS scavenging, is not fully understood. Here, we report a newly identified drought-responsive miRNA, miR164g, in the wild apple species Malus sieversii and elucidate its role in apple drought tolerance. Our results showed that expression of miR164g is significantly inhibited under drought stress and it can specifically cleave transcripts of the transcription factor MsNAC022 in M. sieversii. The heterologous accumulation of miR164g in Arabidopsis thaliana results in enhanced sensitivity to drought stress, while overexpression of MsNAC022 in Arabidopsis and the cultivated apple line 'GL-3' (Malus domestica Borkh.) lead to enhanced tolerance to drought stress by raising the ROS scavenging enzymes activity and related genes expression levels, particularly PEROXIDASE (MsPOD). Furthermore, we showed that expression of MsPOD is activated by MsNAC022 in transient assays. Interestingly, Part1 (P1) region is the key region for the positive regulation of MsPOD promoter by MsNAC022, and the different POD expression patterns in M. sieversii and M. domestica is attributed to the specific fragments inserted in P1 region of M. sieversii. Our findings reveal the function of the miR164g-MsNAC022 module in mediating the drought response of M. sieversii and lay a foundation for breeding drought-tolerant apple cultivars.

Integrated Analysis of Microarray, Small RNA, and Degradome Datasets Uncovers the Role of MicroRNAs in Temperature-Sensitive Genic Male Sterility in Wheat

Temperature-sensitive genic male sterile (TGMS) line Beijing Sterility 366 (BS366) has been utilized in hybrid breeding for a long time, but the molecular mechanism underlying male sterility remains unclear. Expression arrays, small RNA, and degradome sequencing were used in this study to explore the potential role of miRNA in the cold-induced male sterility of BS366. Microspore observation showed defective cell plates in dyads and tetrads and shrunken microspores at the vacuolated stage. Differential regulation of Golgi vesicle transport, phragmoplast formation, sporopollenin biosynthesis, pollen exine formation, and lipid metabolism were observed between cold and control conditions. Pollen development was significantly represented in the 352 antagonistic miRNA-target pairs in the integrated analysis of miRNA and mRNA profiles. The specific cleavage of ARF17 and TIR1 by miR160 and miR393 were found in the cold-treated BS366 degradome, respectively. Thus, the cold-mediated miRNAs impaired cell plate formation through repression of Golgi vesicle transport and phragmoplast formation. The repressed expression of ARF17 and TIR1 impaired pollen exine formation. The results of this study will contribute to our understanding of the roles of miRNAs in male sterility in wheat.

Regulation of small RNA-mediated high temperature stress responses in crop plants

Small RNAs have emerged as key players of gene expression regulation. Several lines of evidences highlight their role in modulating high temperature stress responsiveness in plants. Throughout their life cycle, plants have to regulate their gene expression at various developmental phases, physiological changes, and in response to biotic or environmental stress. High temperature is one the most common abiotic stress for crop plants, that results in impaired morphology, physiology, and yield. However, plants have certain mechanisms that enable them to withstand such conditions by modulating the expression of stress-related genes. Small RNA (sRNA)-regulated gene expression is one such mechanism which is ubiquitous in all eukaryotes. The sRNAs mainly include micro RNAs (miRNAs) and small interfering RNAs (siRNAs). They are primarily associated with the gene silencing either through translation inhibition, mRNA degradation, or DNA methylation. During high temperature stress the increased or decreased level of miRNAs altered the protein accumulation of target transcripts and, therefore, regulate stress responses. Several reports are available in plants which are genetically engineered through expressing artificial miRNAs resulted in thermotolerance. sRNAs have also been reported to bring the epigenetic changes on chromatin region through RNA-dependent DNA methylation (RdDM). The present article draws a brief illustration of sRNA origin, their functional mechanisms, role in high temperature stress, and possible application for developing stress tolerant crop plants.

Epigenetic Regulation of Heat Stress in Plant Male Reproduction

In flowering plants, male reproductive development is highly susceptible to heat stress. In this mini-review, we summarized different anomalies in tapetum, microspores, and pollen grains during anther development under heat stress. We then discussed how epigenetic control, particularly DNA methylation, is employed to cope with heat stress in male reproduction. Further understanding of epigenetic mechanisms by which plants manage heat stress during male reproduction will provide new genetic engineering and molecular breeding tools for generating heat-resistant crops.

Response and tolerance mechanism of food crops under high temperature stress: a review

High temperature stress events are critical factors inhibiting crop yield. Meanwhile, world population is growing very rapidly and will be reached up to 9 billion by 2050. To feed increasing world population, it is challenging task to increase about 70% global food productions. Food crops have significant contribution toward global food demand and food security. However, consequences from increasing heat stress events are demolishing their abilities to survive and sustain yield when subjected to extreme high temperature stress. Therefore, there is dire need to better understand response and tolerance mechanism of food crops following exposure to heat stress. Here, we aimed to provide recent update on impact of high temperature stress on crop yield of food crops, pollination, pollinators, and novel strategies for improving tolerance of food crop under high temperature stress. Importantly, development of heat-resistant transgenic food crops can grant food security through transformation of superior genes into current germplasm, which are associated with various signaling pathways as well as epigenetic regulation in response to extreme high temperature stress.

MicroRNAs Are Involved in Regulating Plant Development and Stress Response through Fine-Tuning of TIR1/AFB-Dependent Auxin Signaling

Auxin, primarily indole-3-acetic acid (IAA), is a versatile signal molecule that regulates many aspects of plant growth, development, and stress response. Recently, microRNAs (miRNAs), a type of short non-coding RNA, have emerged as master regulators of the auxin response pathways by affecting auxin homeostasis and perception in plants. The combination of these miRNAs and the autoregulation of the auxin signaling pathways, as well as the interaction with other hormones, creates a regulatory network that controls the level of auxin perception and signal transduction to maintain signaling homeostasis. In this review, we will detail the miRNAs involved in auxin signaling to illustrate its in planta complex regulation.

miR160: An Indispensable Regulator in Plant

MicroRNAs (miRNA), recognized as crucial regulators of gene expression at the posttranscriptional level, have been found to be involved in the biological processes of plants. Some miRNAs are up- or down-regulated during plant development, stress response, and secondary metabolism. Over the past few years, it has been proved that miR160 is directly related to the developments of different tissues and organs in multifarious species, as well as plant-environment interactions. This review highlights the recent progress on the contributions of the miR160-ARF module to important traits of plants and the role of miR160-centered gene regulatory network in coordinating growth with endogenous and environmental factors. The manipulation of miR160-guided gene regulation may provide a new method to engineer plants with improved adaptability and yield.

Climate change regulated abiotic stress mechanisms in plants: a comprehensive review

Global climate change is identified as a major threat to survival of natural ecosystems. Climate change is a dynamic, multifaceted system of alterations in environmental conditions that affect abiotic and biotic components of the world. It results in alteration in environmental conditions such as heat waves, intensity of rainfall, CO₂ concentration and temperature that lead to rise in new pests, weeds and pathogens. Climate change is one of the major constraints limiting plant growth and development worldwide. It impairs growth, disturbs photosynthesis, and reduces physiological responses in plants. The variations in global climate have gained the attention of researchers worldwide, as these changes negatively affect the agriculture by reducing crop productivity and food security. With this background, this review focuses on the effects of elevated atmospheric CO₂ concentration, temperature, drought and salinity on the morphology, physiology and biochemistry of plants. Furthermore, this paper outlines an overview on the reactive oxygen species (ROS) production and their impact on the biochemical and molecular status of plants with increased climatic variations. Also additionally, different tolerance strategies adopted by plants to combat environmental adversities have been discussed.

Combined Stress Conditions in Melon Induce Non-additive Effects in the Core miRNA Regulatory Network

Climate change has been associated with a higher incidence of combined adverse environmental conditions that can promote a significant decrease in crop productivity. However, knowledge on how a combination of stresses might affect plant development is still scarce. MicroRNAs (miRNAs) have been proposed as potential targets for improving crop productivity. Here, we have combined deep-sequencing, computational characterization of responsive miRNAs and validation of their regulatory role in a comprehensive analysis of response of melon to several combinations of four stresses (cold, salinity, short day, and infection with a fungus). Twenty-two miRNA families responding to double and/or triple stresses were identified. The regulatory role of the differentially expressed miRNAs was validated by quantitative measurements of the expression of the corresponding target genes. A high proportion (ca. 60%) of these families (mainly highly conserved miRNAs targeting transcription factors) showed a non-additive response to multiple stresses in comparison with that observed under each one of the stresses individually. Among those miRNAs showing non-additive response to stress combinations, most interactions were negative, suggesting the existence of functional convergence in the miRNA-mediated response to combined stresses. Taken together, our results provide compelling pieces of evidence that the response to combined stresses cannot be easily predicted from the study individual stresses.

Nanopore-Based Comparative Transcriptome Analysis Reveals the Potential Mechanism of High-Temperature Tolerance in Cotton (Gossypium hirsutum L.)

Extreme high temperatures are threatening cotton production around the world due to the intensification of global warming. To cope with high-temperature stress, heat-tolerant cotton cultivars have been bred, but the heat-tolerant mechanism remains unclear. This study selected heat-tolerant (‘Xinluzao36′) and heat-sensitive (‘Che61-72′) cultivars of cotton treated with high-temperature stress as plant materials and performed comparative nanopore sequencing transcriptome analysis to reveal the potential heat-tolerant mechanism of cotton. Results showed that 120,605 nonredundant sequences were generated from the raw reads, and 78,601 genes were annotated. Differentially expressed gene (DEG) analysis showed that a total of 19,600 DEGs were screened; the DEGs involved in the ribosome, heat shock proteins, auxin and ethylene signaling transduction, and photosynthesis pathways may be attributed to the heat tolerance of the heat-tolerant cotton cultivar. This study also predicted a total of 5118 long non-coding RNAs (lncRNAs)and 24,462 corresponding target genes. Analysis of the target genes revealed that the expression of some ribosomal, heat shock, auxin and ethylene signaling transduction-related and photosynthetic proteins may be regulated by lncRNAs and further participate in the heat tolerance of cotton. This study deepens our understandings of the heat tolerance of cotton.

Small RNA sequencing reveals various microRNAs involved in piperine biosynthesis in black pepper (Piper nigrum L.)

Background

Black pepper (Piper nigrum L.), an important and long-cultivated spice crop, is native to South India and grown in the tropics. Piperine is the main pungent and bioactive alkaloid in the berries of black pepper, but the molecular mechanism for piperine biosynthesis has not been determined. MicroRNAs (miRNAs), which are classical endogenous noncoding small RNAs, play important roles in regulating secondary metabolism in many species, but less is known regarding black pepper or piperine biosynthesis.

Results

To dissect the functions of miRNAs in secondary metabolism especially in piperine biosynthesis, 110 known miRNAs, 18 novel miRNAs and 1007 individual targets were identified from different tissues of black pepper by small RNA sequencing. qRT-PCR and 5′-RLM-RACE experiments were conducted to validate the reliability of the sequencing data and predicted targets. We found 3 miRNAs along with their targets including miR166-4CL, miR396-PER and miR397-CCR modules that are involved in piperine biosynthesis.

Conclusion

MiRNA regulation of secondary metabolism is a common phenomenon in plants. Our study revealed new miRNAs that regulate piperine biosynthesis, which are special alkaloids in the piper genus, and they might be useful for future piperine genetic improvement of black pepper.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08154-4.

Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing

BACKGROUND

Novel strategies for improvement of ornamental plants and their properties relay on miRNA control of differential plant gene expression modulation. Still, in response to the same abiotic stresses, some conserved miRNA families show different expression patterns in different plant species. In parallel, the use of deep sequencing technologies reveals new levels of complexity of regulatory networks in plants through identification of new miRNAs.

METHODS AND RESULTS

Fritillaria imperialis plants were collected from their natural habitats in Koohrang, Chaharmahal va Bakhtiari, Iran. Several tissues including stamen, pistil, petal, sepal, leaf, stem, bulb and fruit were collected during three developmental stages (stem elongation, flower development and seed head stages). Using RNAseq and qRT-PCR approach, this research revealed 21 conserved miRNAs, matching 15 miRNA families, in Fritilaria imperialis.

CONCLUSIONS

The expression of seven conserved miRNAs (Fim-miR156b, Fim-miR159, Fim-miR166a-5p, Fim-miR169d-5p, Fim-miR171c, Fim-miR393 and Fim-miR396e-3p) was further investigated in different tissues and three developmental stages, suggesting different roles for these miRNAs during growth and development of crown imperial. Gained knowledge from this research can open the door to find efficient ways to secure crown imperial survival, preservation and utilization and if proven useful may be applied in other plant species as well.

A small RNA of miR2119b from soybean CMS line acts as a negative regulator of male fertility in transgenic Arabidopsis

The miR2119 is involved in the growth, development and abiotic stress response of some legumes, including Medicago truncatula, Phaseolus vulgaris and soybean (Glycine max (L.) Merr.). Our previous small RNA sequencing analysis showed that miR2119b was up-regulated in the flower buds of soybean cytoplasmic male sterile (CMS) line compared with its maintainer line, but the role and mechanism of miR2119b in the regulation of soybean male fertility are still unclear. In this study, the gma-miR2119b and its target gene alcohol dehydrogenase 1.3b (ADH1.3b) were characterized and found to be highly expressed in the flowers of soybean CMS line and its maintainer. Transgenic Arabidopsis plants overexpressing gma-miR2119b exhibit male fertility abnormalities, including pollen fertility and germination rate decreased. Enzyme activity detection found the ADH and catalase (CAT) enzyme activities in inflorescence of gma-miR2119b overexpressed plants were lower than those of wild-type. Bioinformatics and gene expression analysis showed that gma-miR2119b/GmADH1.3b module was responsive to high temperature (HT) stress during flowering. After HT stress, the gma-miR2119b overexpressed plants showed male sterility, including shorter filament, sterile pollen, indehiscent anther and non seed. Moreover, some key genes involved in HT response and reactive oxygen species (ROS) signal regulation pathway, including heat shock protein70, galactinol synthase 1 and CAT, showed down-regulated expression in transgenic plants under HT stress, suggesting that gma-miR2119b regulates male fertility via HT-ROS signaling pathway under HT stress. It was speculated that the gma-miR2119b acted as a negative regulator of male fertility in plants by regulating ADH1, HT-induced and ROS scavenging genes expression.

Long noncoding RNA lncRNA354 functions as a competing endogenous RNA of miR160b to regulate ARF genes in response to salt stress in upland cotton

Long non-coding RNAs (lncRNAs) play important roles in response to biotic and abiotic stress through acting as competing endogenous RNAs (ceRNAs) to decoy mature miRNAs. However, whether this mechanism is involved in cotton salt stress response remains unknown. We report the characterization of an endogenous lncRNA, lncRNA354, whose expression was reduced in salt-treated cotton and was localized at the nucleus and cytoplasm. Using endogenous target mimic (eTM) analysis, we predicted that lncRNA354 had a potential binding site for miR160b. Transient expression in tobacco demonstrated that lncRNA354 was a miR160b eTM and attenuated miR160b suppression of its target genes, including auxin response factors (ARFs). Silencing or overexpressing lncRNA354 affected the expression of miR160b and target ARFs. Silencing lncRNA354 and targets GhARF17/18 resulted in taller cotton plants and enhanced the resistant to salt stress. Overexpression of lncRNA354 and targets GhARF17/18 in Arabidopsis led to dwarf plants, decreased root dry weight and reduced salt tolerance. Our results show that the lncRNA354-miR160b effect on GhARF17/18 expression may modulate auxin signalling and thus affect growth. These results also shed new light on a mechanism of lncRNA-associated responses to salt stress.

Small RNAs: The Essential Regulators in Plant Thermotolerance

Small RNAs (sRNAs) are a class of non-coding RNAs that consist of 21-24 nucleotides. They have been extensively investigated as critical regulators in a variety of biological processes in plants. sRNAs include two major classes: microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis and functional pathways. Due to global warming, high-temperature stress has become one of the primary causes for crop loss worldwide. Recent studies have shown that sRNAs are involved in heat stress responses in plants and play essential roles in high-temperature acclimation. Genome-wide studies for heat-responsive sRNAs have been conducted in many plant species using high-throughput sequencing. The roles for these sRNAs in heat stress response were also unraveled subsequently in model plants and crops. Exploring how sRNAs regulate gene expression and their regulatory mechanisms will broaden our understanding of sRNAs in thermal stress responses of plant. Here, we highlight the roles of currently known miRNAs and siRNAs in heat stress responses and acclimation of plants. We also discuss the regulatory mechanisms of sRNAs and their targets that are responsive to heat stress, which will provide powerful molecular biological resources for engineering crops with improved thermotolerance.

Hydrogen Sulfide Alleviates Alkaline Salt Stress by Regulating the Expression of MicroRNAs in Malus hupehensis Rehd. Roots

Malus hupehensis Rehd. var. pingyiensis Jiang (Pingyi Tiancha, PYTC) is an excellent apple rootstock and ornamental tree, but its tolerance to salt stress is weak. Our previous study showed that hydrogen sulfide (H₂S) could alleviate damage in M. hupehensis roots under alkaline salt stress. However, the molecular mechanism of H₂S mitigation alkaline salt remains to be elucidated. MicroRNAs (miRNAs) play important regulatory roles in plant response to salt stress. Whether miRNAs are involved in the mitigation of alkaline salt stress mediated by H₂S remains unclear. In the present study, through the expression analysis of miRNAs and target gene response to H₂S and alkaline salt stress in M. hupehensis roots, 115 known miRNAs (belonging to 37 miRNA families) and 15 predicted novel miRNAs were identified. In addition, we identified and analyzed 175 miRNA target genes. We certified the expression levels of 15 miRNAs and nine corresponding target genes by real-time quantitative PCR (qRT-PCR). Interestingly, H₂S pretreatment could specifically induce the downregulation of mhp-miR408a expression, and upregulated mhp-miR477a and mhp-miR827. Moreover, root architecture was improved by regulating the expression of mhp-miR159c and mhp-miR169 and their target genes. These results suggest that the miRNA-mediated regulatory network participates in the process of H₂S-mitigated alkaline salt stress in M. hupehensis roots. This study provides a further understanding of miRNA regulation in the H₂S mitigation of alkaline salt stress in M. hupehensis roots.

A combination of genome-wide and transcriptome-wide association studies reveals genetic elements leading to male sterility during high temperature stress in cotton

Global warming has reduced the productivity of many field-grown crops, as the effects of high temperatures can lead to male sterility in such plants. Genetic regulation of the high temperature (HT) response in the major crop cotton is poorly understood. We determined the functionality and transcriptomes of the anthers of 218 cotton accessions grown under HT stress. By analyzing transcriptome divergence and implementing a genome-wide association study (GWAS), we identified three thermal tolerance associated loci which contained 75 protein coding genes and 27 long noncoding RNAs, and provided expression quantitative trait loci (eQTLs) for 13 132 transcripts. A transcriptome-wide association study (TWAS) confirmed six causal elements for the HT response (three genes overlapped with the GWAS results) which are involved in protein kinase activity. The most susceptible gene, GhHRK1, was confirmed to be a previously uncharacterized negative regulator of the HT response in both cotton and Arabidopsis. These functional variants provide a new understanding of the genetic basis for HT tolerance in male reproductive organs.

Temperature regulation of plant hormone signaling during stress and development

Global climate change has broad-ranging impacts on the natural environment and human civilization. Increasing average temperatures along with more frequent heat waves collectively have negative effects on cultivated crops in agricultural sectors and wild species in natural ecosystems. These aberrantly hot temperatures, together with cold stress, represent major abiotic stresses to plants. Molecular and physiological responses to high and low temperatures are intricately linked to the regulation of important plant hormones. In this review, we shall highlight our current understanding of how changing temperatures regulate plant hormone pathways during immunity, stress responses and development. This article will present an overview of known temperature-sensitive or temperature-reinforced molecular hubs in hormone biosynthesis, homeostasis, signaling and downstream responses. These include recent advances on temperature regulation at the genomic, transcriptional, post-transcriptional and post-translational levels - directly linking some plant hormone pathways to known thermosensing mechanisms. Where applicable, diverse plant species and various temperature ranges will be presented, along with emerging principles and themes. It is anticipated that a grand unifying synthesis of current and future fundamental outlooks on how fluctuating temperatures regulate important plant hormone signaling pathways can be leveraged towards forward-thinking solutions to develop climate-smart crops amidst our dynamically changing world.

Dynamic expression of miRNAs and functional analysis of target genes involved in the response to male sterility of the wheat line YS3038

Thermosensitive cytoplasmic male sterile (TCMS) lines play an important role in wheat breeding, heterosis utilization, and germplasm innovation. MicroRNAs (miRNAs) can regulate the expression level of target genes by inhibiting the translation of these genes. YS3038 is a wheat TCMS line. In this study, the fertility conversion mechanism of YS3038 was studied by examining the abortion characteristics of YS3038, the regulation pattern of miRNAs and the target genes of miRNAs in YS3038. MiRNA-seq was performed on three important stages of YS3038 under sterile and fertile conditions. Then, the clean reads were aligned with some databases to filter other ncRNAs and repeats. The known miRNAs and novel miRNAs were predicted by sequence comparison with known miRNAs from miRbase. Differential expression of miRNAs between different stages and between different fertile conditions was analyzed, and functional analysis of target genes with opposite expression patterns as those of the miRNAs was conducted. The Ubisch bodies and microspores of sterile anthers were covered with filamentous materials. The degradation of the tapetum cells, the chloroplast structure of endothecium cells, and the microspore structure were abnormal. Microspore development was hindered from the late uninucleate stage to the binucleate stage. Twenty, 52, and 68 differentially expressed miRNAs (DEmiRs) were identified at the early uninucleate, late uninucleate, and binucleate stages, respectively, and there were 0, 7, and 72 differentially expressed target genes (DETGs), respectively, at these three stages. At the binucleate stage, 29 DEmiRs had 41 target mRNAs in total, and the expression patterns of the 41 target mRNAs were opposite to those of the 29 miRNAs. Fifteen significantly enriched KEGG pathways were associated with the 41 target mRNAs. Leucine-rich repeat receptor-like kinases (LRR-RLKs) play important roles in plant developmental and physiological processes. Some studies have shown that the expression of LRR-RLKs is related to the differentiation of microsporocytes and tapetum cells and to male sterility. An LRR-RLK (TaeRPK) gene was silenced by the barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) method, and the seed setting rates of the TaeRPK-silenced plants (3.51%) were significantly lower than those of the negative control plants (88.78%) (P < 0.01). Thus, the TaeRPK gene is likely to be involved in the fertility conversion of YS3038.

MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops

Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20-24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.

GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton

The leaf is a crucial organ evolved with remarkable morphological diversity to maximize plant photosynthesis. The leaf shape is a key trait that affects photosynthesis, flowering rates, disease resistance and yield. Although many genes regulating leaf development have been identified in the past years, the precise regulatory architecture underlying the generation of diverse leaf shapes remains to be elucidated. We used cotton as a reference model to probe the genetic framework underlying divergent leaf forms. Comparative transcriptome analysis revealed that the GhARF16-1 and GhKNOX2-1 genes might be potential regulators of leaf shape. We functionally characterized the auxin-responsive factor ARF16-1 acting upstream of GhKNOX2-1 to determine leaf morphology in cotton. The transcription of GhARF16-1 was significantly higher in lobed-leaved cotton than in smooth-leaved cotton. Furthermore, the overexpression of GhARF16-1 led to the up-regulation of GhKNOX2-1 and resulted in more and deeper serrations in cotton leaves, similar to the leaf shape of cotton plants overexpressing GhKNOX2-1. We found that GhARF16-1 specifically bound to the promoter of GhKNOX2-1 to induce its expression. The heterologous expression of GhARF16-1 and GhKNOX2-1 in Arabidopsis led to lobed and curly leaves, and a genetic analysis revealed that GhKNOX2-1 is epistatic to GhARF16-1 in Arabidopsis, suggesting that the GhARF16-1 and GhKNOX2-1 interaction paradigm also functions to regulate leaf shape in Arabidopsis. To our knowledge, our results uncover a novel mechanism by which auxin, through the key component ARF16-1 and its downstream-activated gene KNOX2-1, determines leaf morphology in eudicots.