MicroRNA prediction and its function in regulating drought-related genes in cowpea

Changes in epigenetic features in legumes under abiotic stresses

Legume crops are rich in nutritional value for human and livestock consumption. With global climate change, developing stress-resilient crops is crucial for ensuring global food security. Because of their nitrogen-fixing ability, legumes are also important for sustainable agriculture. Various abiotic stresses, such as salt, drought, and elevated temperatures, are known to adversely affect legume production. The responses of plants to abiotic stresses involve complicated cellular processes including stress hormone signaling, metabolic adjustments, and transcriptional regulations. Epigenetic mechanisms play a key role in regulating gene expressions at both transcriptional and posttranscriptional levels. Increasing evidence suggests the importance of epigenetic regulations of abiotic stress responses in legumes, and recent investigations have extended the scope to the epigenomic level using next-generation sequencing technologies. In this review, the current knowledge on the involvement of epigenetic features, including DNA methylation, histone modification, and noncoding RNAs, in abiotic stress responses in legumes is summarized and discussed. Since most of the available information focuses on a single aspect of these epigenetic features, integrative analyses involving omics data in multiple layers are needed for a better understanding of the dynamic chromatin statuses and their roles in transcriptional regulation. The inheritability of epigenetic modifications should also be assessed in future studies for their applications in improving stress tolerance in legumes through the stable epigenetic optimization of gene expressions.

Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting Indica Rice Cultivars under Reproductive-Stage Drought

Recurrent occurrence of drought stress in varying intensity has become a common phenomenon in the present era of global climate change, which not only causes severe yield losses but also challenges the cultivation of rice. This raises serious concerns for sustainable food production and global food security. The root of a plant is primarily responsible to perceive drought stress and acquire sufficient water for the survival/optimal growth of the plant under extreme climatic conditions. Earlier studies reported the involvement/important roles of microRNAs (miRNAs) in plants' responses to environmental/abiotic stresses. A number (738) of miRNAs is known to be expressed in different tissues under varying environmental conditions in rice, but our understanding of the role, mode of action, and target genes of the miRNAs are still elusive. Using contrasting rice [IR-64 (reproductive-stage drought sensitive) and N-22 (drought-tolerant)] cultivars, imposed with terminal (reproductive-stage) drought stress, we demonstrate differential expression of 270 known and 91 novel miRNAs in roots of the contrasting rice cultivars in response to the stress. Among the known miRNAs, osamiR812, osamiR166, osamiR156, osamiR167, and osamiR396 were the most differentially expressed miRNAs between the rice cultivars. In the root of N-22, 18 known and 12 novel miRNAs were observed to be exclusively expressed, while only two known (zero novels) miRNAs were exclusively expressed in the roots of IR-64. The majority of the target gene(s) of the miRNAs were drought-responsive transcription factors playing important roles in flower, grain development, auxin signaling, root development, and phytohormone-crosstalk. The novel miRNAs identified in this study may serve as good candidates for the genetic improvement of rice for terminal drought stress towards developing climate-smart rice for sustainable food production.

Epigenomics in stress tolerance of plants under the climate change

BACKGROUND

Climate change has had a tremendous impact on the environment in general as well as agricultural crops grown in these situations as time passed. Agricultural production of crops is less suited and of lower quality due to disturbances in plant metabolism brought on by sensitivity to environmental stresses, which are brought on by climate change. Abiotic stressors that are specific to climate change, including as drought, extremes in temperature, increasing CO₂, waterlogging from heavy rain, metal toxicity, and pH changes, are known to negatively affect an array of species. Plants adapt to these challenges by undergoing genome-wide epigenetic changes, which are frequently accompanied by differences in transcriptional gene expression. The sum of a cell's biochemical modifications to its nuclear DNA, post-translational modifications to histones, and variations in the synthesis of non-coding RNAs is called an epigenome. These modifications frequently lead to variations in gene expression that occur without any alteration in the underlying base sequence.

EPIGENETIC MECHANISMS AND MARKS

The methylation of homologous loci by three different modifications-genomic (DNA methylation), chromatin (histone modifications), and RNA-directed DNA methylation (RdDM)-could be regarded as epigenetic mechanisms that control the regulation of differential gene expression. Stresses from the environment cause chromatin remodelling, which enables plant cells to adjust their expression patterns temporarily or permanently. EPIGENOMICS' CONSEQUENCES FOR GENOME STABILITY AND GENE EXPRESSION: DNA methylation affects gene expression in response to abiotic stressors by blocking or suppressing transcription. Environmental stimuli cause changes in DNA methylation levels, either upward in the case of hypermethylation or downward in the case of hypomethylation. The type of stress response that occurs as a result also affects the degree of DNA methylation alterations. Stress is also influenced by DRM2 and CMT3 methylating CNN, CNG, and CG. Both plant development and stress reactions depend on histone changes. Gene up-regulation is associated with histone tail phosphorylation, ubiquitination, and acetylation, while gene down-regulation is associated with de-acetylation and biotinylation. Plants undergo a variety of dynamic changes to histone tails in response to abiotic stressors. The relevance of these transcripts against stress is highlighted by the accumulation of numerous additional antisense transcripts, a source of siRNAs, caused by abiotic stresses. The study highlights the finding that plants can be protected from a range of abiotic stresses by epigenetic mechanisms such DNA methylation, histone modification, and RNA-directed DNA methylation. TRANSGENERATIONAL INHERITANCE AND SOURCES OF EPIGENETIC VARIATION: Stress results in the formation of epialleles, which are either transient or enduring epigenetic stress memory in plants. After the stress is gone, the stable memory is kept for the duration of the plant's remaining developmental cycles or passed on to the next generations, leading to plant evolution and adaptability. The bulk of epigenetic changes brought on by stress are temporary and return to normal after the stress has passed. Some of the modifications, however, might be long-lasting and transmitted across mitotic or even meiotic cell divisions. Epialleles often have genetic or non-genetic causes. Epialleles can arise spontaneously due to improper methylation state maintenance, short RNA off-target effects, or other non-genetic causes. Developmental or environmental variables that influence the stability of epigenetic states or direct chromatin modifications may also be non-genetic drivers of epigenetic variation. Transposon insertions that change local chromatin and structural rearrangements, such copy number changes that are genetically related or unrelated, are two genetic sources of epialleles.

EPIGENOMICS IN CROP IMPROVEMENT

To include epigenetics into crop breeding, it is necessary to create epigenetic variation as well as to identify and evaluate epialleles. Epigenome editing or epi-genomic selection may be required for epiallele creation and identification. In order to combat the challenges given by changing environments, these epigenetic mechanisms have generated novel epialleles that can be exploited to develop new crop types that are more climate-resilient. Numerous techniques can be used to alter the epigenome generally or at specific target loci in order to induce the epigenetic alterations necessary for crop development. Technologies like CRISPR/Cas9 and dCas, which have recently advanced, have opened up new avenues for the study of epigenetics. Epialleles could be employed in epigenomics-assisted breeding in addition to sequence-based markers for crop breeding.

CONCLUSIONS AND FUTURE PROSPECTUS

A few of the exciting questions that still need to be resolved in the area of heritable epigenetic variation include a better understanding of the epigenetic foundation of characteristics, the stability and heritability of epialleles, and the sources of epigenetic variation in crops. Investigating long intergenic non-coding RNAs (lincRNAs) as an epigenetic process might open up a new path to understanding crop plant's ability to withstand abiotic stress. For many of these technologies and approaches to be more applicable and deployable at a lower cost, technological breakthroughs will also be necessary. Breeders will probably need to pay closer attention to crop epialleles and how they can affect future responses to climate changes. The development of epialleles suitable for particular environmental circumstances may be made possible by creating targeted epigenetic changes in pertinent genes and by comprehending the molecular underpinnings of trans generational epigenetic inheritance. More research on a wider variety of plant species is required in order to fully comprehend the mechanisms that produce and stabilise epigenetic variation in crops. In addition to a collaborative and multidisciplinary effort by researchers in many fields of plant science, this will require a greater integration of the epigenomic data gathered in many crops. Before it may be applied generally, more study is required.

Genome-Wide Identification, Quantification, and Validation of Differentially Expressed miRNAs in Eggplant (Solanum melongena L.) Based on Their Response to Ralstonia solanacearum Infection

MicroRNAs (miRNAs), a type of short noncoding RNA molecule (21-23 nucleotides), mediate repressive gene regulation through RNA silencing at the posttranscriptional level and play an important role in the defense response to abiotic and biotic stresses. miRNAs of the plant system have been studied in model crops for their diverse regulatory role while less is known about their significance in other plants whose genome and transcriptome data are scarce in the database, including eggplant (Solanum melongena L.). In the present study, a next-generation sequencing platform was used for the sequencing of miRNA, and real-time quantitative PCR for miRNAs was used to validate the gene expression patterns of miRNAs in Solanum melongena plantlets infected with the bacterial wilt-causing pathogen Ralstonia solanacearum (R. solanacearum). Sequence analyses showed the presence of 375 miRNAs belonging to 29 conserved families. The miR414 is highly conserved miRNA across the plant system while miR5658 and miR5021 were found exclusively in Arabidopsis thaliana surprisingly, these miRNAs were found in eggplants too. The most abundant families were miR5658 and miR414. Ppt-miR414, hvu-miR444b, stu-miR8020, and sly miR5303 were upregulated in Pusa purple long (PPL) (susceptible) at 48 h postinfection, followed by a decline after 96 h postinfection. A similar trend was obtained in ath-miR414, stu-mir5303h, alymiR847-5p, far-miR1134, ath-miR5021, ath-miR5658, osa-miR2873c, lja-miR7530, stu-miR7997c, and gra-miR8741 but at very low levels after infection in the susceptible variety, indicating their negative role in the suppression of host immunity. On the other hand, osa-miR2873c was found to be slightly increased after 96 hpi from 48 hpi. Most of the miRNAs under study showed relatively lower expression in the resistant variety Arka Nidhi after infection than in the susceptible variety. These results shed light on a deeper regulatory role of miRNAs and their targets in regulation of the plant response to bacterial infection. The present experiment and their results suggested that the higher expression of miRNA leads to a decline in host mRNA and thus shows susceptibility.

Epigenomics as Potential Tools for Enhancing Magnitude of Breeding Approaches for Developing Climate Resilient Chickpea

Epigenomics has become a significant research interest at a time when rapid environmental changes are occurring. Epigenetic mechanisms mainly result from systems like DNA methylation, histone modification, and RNA interference. Epigenetic mechanisms are gaining importance in classical genetics, developmental biology, molecular biology, cancer biology, epidemiology, and evolution. Epigenetic mechanisms play important role in the action and interaction of plant genes during development, and also have an impact on classical plant breeding programs, inclusive of novel variation, single plant heritability, hybrid vigor, plant-environment interactions, stress tolerance, and performance stability. The epigenetics and epigenomics may be significant for crop adaptability and pliability to ambient alterations, directing to the creation of stout climate-resilient elegant crop cultivars. In this review, we have summarized recent progress made in understanding the epigenetic mechanisms in plant responses to biotic and abiotic stresses and have also tried to provide the ways for the efficient utilization of epigenomic mechanisms in developing climate-resilient crop cultivars, especially in chickpea, and other legume crops.

Integrative small RNA and transcriptome analysis provides insight into key role of miR408 towards drought tolerance response in cowpea

Drought stress response studies and overexpression of vun-miR408 proved it to be essential for abiotic stress tolerance in cowpea. Small RNA and transcriptome sequencing of an elite high-yielding drought-tolerant Indian cowpea cultivar, Pusa Komal revealed a differential expression of 198 highly conserved, 21 legume-specific, 14 less-conserved, and 10 novel drought-responsive microRNAs (miRNAs) along with 3391 (up-regulated) and 3799 (down-regulated) genes, respectively, in the leaf and root libraries. Among the differentially expressed miRNAs, vun-miR408-3p, showed an up-regulation of 3.53-log₂-fold change under drought stress. Furthermore, laccase 12 (LAC 12) was identified as the potential target of vun-miR408-3p using 5' RNA ligase-mediated rapid amplification of cDNA ends. The stable transgenic cowpea lines overexpressing artificial vun-miR408-3p (OX-amiR408) displayed enhanced drought and salinity tolerance as compared to the wild-type plants. An average increase of 30.17% in chlorophyll, 26.57% in proline, and 27.62% in relative water content along with lesser cellular H₂O₂ level was observed in the transgenic lines in comparison with the wild-type plants under drought stress. Additionally, the scanning electron microscopic study revealed a decrease in the stomatal aperture and an increase in the trichome density in the transgenic lines. The expression levels of laccase 3 and laccase 12, the potential targets of miR408, related to lipid catabolic processes showed a significant reduction in the wild-type plants under drought stress and the transgenic lines, indicating the regulation of lignin content as a plausibly essential trait related to the drought tolerance in cowpea. Taken together, this study primarily focused on identification of drought-responsive miRNAs and genes in cowpea, and functional validation of role of miR408 towards drought stress response in cowpea.

Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development

Noncoding RNAs, including microRNAs (miRNAs), small interference RNAs (siRNAs), circular RNA (circRNA), and long noncoding RNAs (lncRNAs), control gene expression at the transcription, post-transcription, and translation levels. Apart from protein-coding genes, accumulating evidence supports ncRNAs playing a critical role in shaping plant growth and development and biotic and abiotic stress responses in various species, including legume crops. Noncoding RNAs (ncRNAs) interact with DNA, RNA, and proteins, modulating their target genes. However, the regulatory mechanisms controlling these cellular processes are not well understood. Here, we discuss the features of various ncRNAs, including their emerging role in contributing to biotic/abiotic stress response and plant growth and development, in addition to the molecular mechanisms involved, focusing on legume crops. Unravelling the underlying molecular mechanisms and functional implications of ncRNAs will enhance our understanding of the coordinated regulation of plant defences against various biotic and abiotic stresses and for key growth and development processes to better design various legume crops for global food security.

Whole Aegilops tauschii Transcriptome Investigation Revealed Nine Novel miRNAs Involved in Stress Response

Background:

Aegilops tauschii is a wild relative of bread wheat. This species has been reported as the donor of bread wheat D genome. There are also several reports that mentioned the importance of Ae. tauschii in biotic and abiotic stress tolerance. On the other hands, miRNAs have been reported as the essential regulatory elements in stress response.

Objective:

Therefore, it is important to discover novel miRNAs involved in stress tolerance in this species. The aim of the current study was to predict novel miRNAs in Ae. tauschii and also uncover their potential role in stress response.

Methods:

For this purpose, ESTs, TSAs, and miRBase databases were obtained and used to predict new miRNAs.

Results:

Our results discovered nine novel stem-loop miRNAs. These predicted miRNAs could be introduced as the new members of previously identified miRNA families in Ae. tauschii, including miR156, miR168, miR169, and miR319. The result indicating that miR397 and miR530 are novel families in this species. Furthermore, several novel stem-loop miRNAs predicted for T. aestivum showed remarkable similarities to novel Ae. tauschii stem-loops.

Conclusion:

Our results demonstrated that predicted novel miRNAs could play a significant role in stress response.

Epigenetics: possible applications in climate-smart crop breeding

To better adapt transiently or lastingly to stimuli from the surrounding environment, the chromatin states in plant cells vary to allow the cells to fine-tune their transcriptional profiles. Modifications of chromatin states involve a wide range of post-transcriptional histone modifications, histone variants, DNA methylation, and activity of non-coding RNAs, which can epigenetically determine specific transcriptional outputs. Recent advances in the area of '-omics' of major crops have facilitated identification of epigenetic marks and their effect on plant response to environmental stresses. As most epigenetic mechanisms are known from studies in model plants, we summarize in this review recent epigenetic studies that may be important for improvement of crop adaptation and resilience to environmental changes, ultimately leading to the generation of stable climate-smart crops. This has paved the way for exploitation of epigenetic variation in crop breeding.

sRNAome and transcriptome analysis provide insight into chilling response of cowpea pods

Cowpea is an important horticultural crop in tropical and subtropical areas of Asia, Africa, and Latin America, as well as parts of southern Europe and Central and South America. Chilling injury is a common physiological hazard of cowpea in cold chain logistics which reduce the cowpea pods nutritional quality and product value. However, the molecular mechanism involved in chilling injury remains unclear in cowpea pods. RNA-Seq and sRNA-Seq technologies were employed to decipher the miRNAs and mRNAs expression profiles and their regulatory networks in cowpea pods involved in chilling stress. Differentially expressed miRNAs and mRNA profiles were obtained based on cluster analysis, miRNAs and target genes were found to show coherent relationships in the regulatory networks of chilling injury. Furthermore, we found that numerous miRNAs and nat-siRNAs' targets were predicted to be key enzymes involved in the redox reactions such as POD, CAT, AO and LOX, energy metabolism such as ATPase, FAD and NAD related enzymes and different transcription factors such as WRKY, bHLH, MYB, ERF and NAC which play important roles in chilling injury.

Cowpea and abiotic stresses: identification of reference genes for transcriptional profiling by qPCR

BACKGROUND

Due to cowpea ability to fix nitrogen in poor soils and relative tolerance to drought and salt stresses, efforts have been directed to identifying genes and pathways that confer stress tolerance in this species. Real-time quantitative PCR (qPCR) has been widely used as the most reliable method to measure gene expression, due to its high accuracy and specificity. In the present study, nine candidate reference genes were rigorously tested for their application in normalization of qPCR data onto roots of four distinct cowpea accessions under two abiotic stresses: root dehydration and salt (NaCl, 100 mM). In addition, the regulation of four target transcripts, under the same referred conditions was also scrutinized.

RESULTS

geNorm, NormFinder, BestKeeper, and ΔCt method results indicated a set of three statistically validated RGs for each stress condition: (I) root dehydration (actin, ubiquitin-conjugating enzyme E2 variant 1D, and a Phaseolus vulgaris unknown gene-UNK), and (II) salt (ubiquitin-conjugating enzyme E2 variant 1D, F-box protein, and UNK). The expression profile of the target transcripts suggests that flavonoids are important players in the cowpea response to the abiotic stresses analyzed, since chalcone isomerase and chalcone synthase were up-regulated in the tolerant and sensitive accessions. A lipid transfer protein also participates in the cowpea tolerance mechanisms to root dehydration and salt stress. The referred transcript was up-regulated in the two tolerant accessions and presented no differential expression in the sensitive counterparts. Chitinase B, in turn, generally related to plant defense, was an important target transcript under salt stress, being up-regulated at the tolerant, and down-regulated in the sensitive accession.

CONCLUSIONS

Reference genes suitable for qPCR analyses in cowpea under root dehydration and salt stress were identified. This action will lead to a more accurate and reliable analysis of gene expression on this species. Additionally, the results obtained in this study may guide future research on gene expression in cowpea under other abiotic stress types that impose osmotic imbalance. The target genes analyzed, in turn, deserve functional evaluation due to their transcriptional regulation under stresses and biotechnological potential.

Variation in relative water content, proline accumulation and stress gene expression in two cowpea landraces under drought

Many landraces of cowpea [Vigna unguiculata (L.) Walp.] are adapted to particular geographical and climatic conditions. Here we describe two landraces grown respectively in arid and temperate areas of Algeria and assess their physiological and molecular responses to drought stress. As expected, when deprived of water cowpea plants lose water over time with a gradual reduction in transpiration rate. The landraces differed in their relative water content (RWC) and whole plant transpiration rate. The landrace from Menia, an arid area, retained more water in adult leaves. Both landraces responded to drought stress at the molecular level by increasing expression of stress-related genes in aerial parts, including proline metabolism genes. Expression of gene(s) encoding proline synthesis enzyme P5CS was up regulated and gene expression of ProDH, a proline catabolism enzyme, was down regulated. Relatively low amounts of proline accumulated in adult leaves with slight differences between the two landraces. During drought stress the most apical part of plants stayed relatively turgid with a high RWC compared to distal parts that wilted. Expression of key stress genes was higher and more proline accumulated at the apex than in distal leaves indicating that cowpea has a non-uniform stress response at the whole plant level. Our study reveals a developmental control of water stress through preferential proline accumulation in the upper tier of the cowpea plant. We also conclude that cowpea landraces display physiological adaptations to water stress suited to the arid and temperate climates in which they are cultivated.

Cowpea: a legume crop for a challenging environment

Cowpea is a grain legume native from Africa and is a primary source of protein for millions of people in sub-Saharan Africa and other parts of the developing world. The main important characteristics of this crop include a good protein quality with a high nutritional value, its nitrogen-fixing ability, and an ability to be more drought- and heat-tolerant than most of its legume relatives. In a research perspective, studies of cowpea are relatively scarce, despite its relevance to agriculture in the developing world and its resilience to stress. The present review provides an overview of different aspects of cowpea, with a special emphasis on the molecular markers for assessing genetic diversity, as well as on biochemical and transcriptomic data with respect to evaluating cowpea drought stress tolerance. The integration of both datasets will be useful for the improvement of cowpea because research on drought stress tolerance is of major interest for this crop in a challenging environment. © 2017 Society of Chemical Industry.

MicroRNAs associated with drought response in the pulse crop common bean (Phaseolus vulgaris L.)

Drought stress significantly reduces common bean yields. Recently, some drought-related miRNAs were found in various plants. However, reports of miRNAs involved in drought stress in common bean are limited. Here, we obtained four sRNA samples from drought-tolerant and -sensitive cultivars of common bean that experienced with or without drought treatment. A total of 49 novel miRNAs and 120 known miRNAs were detected. Under drought treatment, 9 and 7 known miRNAs were down and up-regulated, respectively, and 5 and 3 of the novel miRNAs were increased and decreased, respectively. Among these miRNAs, four miRNAs shared the same pattern of expression between Long 22-0579 and Naihua. Target genes of these miRNAs included transcription factors, protein kinases, and nuclear transcription factors. Finally, we verified all of the differentially expressed miRNAs by RT-qPCR, and we identified 16 miRNAs that are potentially associated with the drought stress response. These miRNAs and target genes will be useful in future basic studies and in applied studies investigating how miRNA regulation can be used to enhance drought resistance in plant species.

In-silico based identification and functional analyses of miRNAs and their targets in Cowpea (Vigna unguiculata L.)

Cowpea (Vigna unguiculata L.) is an important leguminous plant and a good diet due to presence of carbohydrate and high protein contents. Currently, only few cowpea microRNAs (miRNAs) are reported. This study is intended to identify and functionally analyze new miRNAs and their targets in cowpea. An in-silico based homology search approach was applied and a total of 46 new miRNAs belonging to 45 families were identified and functionally annotated from the cowpea expressed sequence tags (ESTs). All these potential miRNAs are reported here for the first time in cowpea. The 46 new miRNAs were also observed with stable hairpin structures with minimum free energy, ranging from -10 to -132 kcal mol^-1 with an average of -40 kcal mol^-1. The length of new cowpea miRNAs are ranged from 18 to 26 nt with an average of 21 nt. The cowpea miRNA-vun-mir4414, is found as pre-miRNA cluster for the first time in cowpea. Furthermore, a set of 138 protein targets were also identified for these newly identified 46 cowpea miRNAs. These targets have significant role in various biological processes, like metabolism, transcription regulation as transcription factor, cell transport, signal transduction, growth & development and structural proteins. These findings are the significant basis to utilize and manage this important leguminous plant-cowpea for better nutritional properties and tolerance for biotic and abiotic stresses.

Identification of Drought-Responsive MicroRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing

Alfalfa, an important forage legume, is an ideal crop for sustainable agriculture and a potential crop for bioenergy resources. Drought, one of the most common environmental stresses, substantially affects plant growth, development, and productivity. MicroRNAs (miRNAs) are newly discovered gene expression regulators that have been linked to several plant stress responses. To elucidate the role of miRNAs in drought stress regulation of alfalfa, a high-throughput sequencing approach was used to analyze 12 small RNA libraries comprising of four samples, each with three biological replicates. From the 12 libraries, we identified 348 known miRNAs belonging to 80 miRNA families, and 281 novel miRNAs, using Mireap software. Eighteen known miRNAs in roots and 12 known miRNAs in leaves were screened as drought-responsive miRNAs. With the exception of miR319d and miR157a which were upregulated under drought stress, the expression pattern of drought-responsive miRNAs was different between roots and leaves in alfalfa. This is the first study that has identified miR3512, miR3630, miR5213, miR5294, miR5368 and miR6173 as drought-responsive miRNAs. Target transcripts of drought-responsive miRNAs were computationally predicted. All 447 target genes for the known miRNAs were predicted using an online tool. This study provides a significant insight on understanding drought-responsive mechanisms of alfalfa.

Functional Roles of microRNAs in Agronomically Important Plants-Potential as Targets for Crop Improvement and Protection

MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses toward environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic-or abiotic origin.

Identification and characterization of durum wheat microRNAs in leaf and root tissues

MicroRNAs are a class of post-transcriptional regulators of plant developmental and physiological processes and responses to environmental stresses. Here, we present the study regarding the annotation and characterization of MIR genes conducted in durum wheat. We characterized the miRNAome of leaf and root tissues at tillering stage under two environmental conditions: irrigated with 100% (control) and 55% of evapotranspiration (early water stress). In total, 90 microRNAs were identified, of which 32 were classified as putative novel and species-specific miRNAs. In addition, seven microRNA homeologous groups were identified in each of the two genomes of the tetraploid durum wheat. Differential expression analysis highlighted a total of 45 microRNAs significantly differentially regulated in the pairwise comparisons leaf versus root. The miRNA families, miR530, miR395, miR393, miR5168, miR396 and miR166, miR171, miR319, and miR167, were the most expressed in leaves in comparison to roots. Putative microRNA targets were predicted for both five and three prime sequences derived from the stem-loop of the MIR gene. Gene ontology analysis showed significant overrepresented gene categories in microRNA targets belonging to transcription factors, phenylpropanoids, oxydases, and lipid binding-protein. This work represents one of the first genome wide characterization of MIR genes in durum wheat, identifying leaf and root tissue-specific microRNAs. This genomic identification of microRNAs together with the analysis of their expression profiles is a well-accepted starting point leading to a better comprehension of the role of MIR genes in the genus Triticum.

Cowpea (Vigna unguiculata L. Walp.) Metabolomics: Osmoprotection as a Physiological Strategy for Drought Stress Resistance and Improved Yield

Plants usually tolerate drought by producing organic solutes, which can either act as compatible osmolytes for maintaining turgor, or radical scavengers for protecting cellular functions. However, these two properties of organic solutes are often indistinguishable during stress progression. This study looked at individualizing properties of osmotic adjustment vs. osmoprotection in plants, using cowpea as the model species. Two cultivars were grown in well-watered soil, drought conditions, or drought followed by rewatering through fruit formation. Osmoadaptation was investigated in leaves and roots using photosynthetic traits, water homoeostasis, inorganic ions, and primary and secondary metabolites. Multifactorial analyses indicated allocation of high quantities of amino acids, sugars, and proanthocyanidins into roots, presumably linked to their role in growth and initial stress perception. Physiological and metabolic changes developed in parallel and drought/recovery responses showed a progressive acclimation of the cowpea plant to stress. Of the 88 metabolites studied, proline, galactinol, and a quercetin derivative responded the most to drought as highlighted by multivariate analyses, and their correlations with yield indicated beneficial effects. These metabolites accumulated differently in roots, but similarly in leaves, suggesting a more conservative strategy to cope with drought in the aerial parts. Changes in these compounds roughly reflected energy investment in protective mechanisms, although the ability of plants to adjust osmotically through inorganic ions uptake could not be discounted.