Legume genetic resources and transcriptome dynamics under abiotic stress conditions

Strigolactones as promising biomolecule for oxidative stress management: A comprehensive review

Strigolactones, which are a group of plant hormones, have emerged as promising biomolecules for effectively managing oxidative stress in plants. Oxidative stress occurs when the production of reactive oxygen species (ROS) exceeds the plant's ability to detoxify or scavenge these harmful molecules. An elevation in reactive oxygen species (ROS) levels often occurs in response to a range of stressors in plants. These stressors encompass both biotic factors, such as fungal, viral, or nematode attacks, as well as abiotic challenges like intense light exposure, drought, salinity, and pathogenic assaults. This ROS surge can ultimately lead to cellular harm and damage. One of the key ways in which strigolactones help mitigate oxidative stress is by stimulating the synthesis and accumulation of antioxidants. These antioxidants act as scavengers of ROS, neutralizing their harmful effects. Additionally, strigolactones also regulate stomatal closure, which reduces water loss and helps alleviate oxidative stress during conditions of drought stress or water deficiencies. By understanding and harnessing the capabilities of strigolactones, it becomes possible to enhance crop productivity and enable plants to withstand environmental stresses in the face of a changing climate. This comprehensive review provides an in-depth exploration of the various roles of strigolactones in plant growth, development, and response to various stresses, with a specific emphasis on their involvement in managing oxidative stress. Strigolactones also play a critical role in detoxifying ROS while regulating the expression of genes related to antioxidant defense pathways, striking a balance between ROS detoxification and production.

The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)

MicroRNAs (miRNAs) are 21-24 nt small RNAs (sRNAs) that negatively regulate protein-coding genes and/or trigger phased small-interfering RNA (phasiRNA) production. Two thousand nine hundred miRNA families, of which ∼40 are deeply conserved, have been identified in ∼80 different plant species genomes. miRNA functions in response to abiotic stresses is less understood than their roles in development. Only seven peanut MIRNA families are documented in miRBase, yet a reference genome assembly is now published and over 480 plant-like MIRNA loci were predicted in the diploid peanut progenitor Arachis duranensis genome. We explored by computational analysis of a leaf sRNA library and publicly available sRNA, degradome, and transcriptome datasets the miRNA and phasiRNA space associated with drought and heat stresses in peanut. We characterized 33 novel candidate and 33 ancient conserved families of MIRNAs and present degradome evidence for their cleavage activities on mRNA targets, including several noncanonical targets and novel phasiRNA-producing noncoding and mRNA loci with validated novel targets such as miR1509 targeting serine/threonine-protein phosphatase7 and miRc20 and ahy-miR3514 targeting penta-tricopeptide repeats (PPRs), in contradistinction to other claims of miR1509/173/7122 superfamily miRNAs indirectly targeting PPRs via TAS-like noncoding RNA loci. We characterized the inverse correlations of significantly differentially expressed drought- and heat-regulated miRNAs, assayed by sRNA blots or transcriptome datasets, with target mRNA expressions in the same datasets. Meta-analysis of an expression atlas and over representation of miRNA target genes in co-expression networks suggest that miRNAs have functions in unique aspects of peanut gynophore development. Genome-wide MIRNA annotation of the published allopolyploid peanut genome can facilitate molecular breeding of value-added traits.

Improving phosphorus acquisition efficiency through modification of root growth responses to phosphate starvation in legumes

Phosphorus (P) is one of the essential macronutrients for plant growth and development, and it is an integral part of the major organic components, including nucleic acids, proteins and phospholipids. Although total P is abundant in most soils, a large amount of P is not easily absorbed by plants. Inorganic phosphate (Pi) is the plant-available P, which is generally immobile and of low availability in soils. Hence, Pi starvation is a major constraint limiting plant growth and productivity. Enhancing plant P efficiency can be achieved by improving P acquisition efficiency (PAE) through modification of morpho-physiological and biochemical alteration in root traits that enable greater acquisition of external Pi from soils. Major advances have been made to dissect the mechanisms underlying plant adaptation to P deficiency, especially for legumes, which are considered important dietary sources for humans and livestock. This review aims to describe how legume root growth responds to Pi starvation, such as changes in the growth of primary root, lateral roots, root hairs and cluster roots. In particular, it summarizes the various strategies of legumes to confront P deficiency by regulating root traits that contribute towards improving PAE. Within these complex responses, a large number of Pi starvation-induced (PSI) genes and regulators involved in the developmental and biochemical alteration of root traits are highlighted. The involvement of key functional genes and regulators in remodeling root traits provides new opportunities for developing legume varieties with maximum PAE needed for regenerative agriculture.

Selenium Regulates Antioxidant, Photosynthesis, and Cell Permeability in Plants under Various Abiotic Stresses: A Review

Plant growth is affected by various abiotic stresses, including water, temperature, light, salt, and heavy metals. Selenium (Se) is not an essential nutrient for plants but plays important roles in alleviating the abiotic stresses suffered by plants. This article summarizes the Se uptake and metabolic processes in plants and the functions of Se in response to water, temperature, light, salt, and heavy metal stresses in plants. Se promotes the uptake of beneficial substances, maintains the stability of plasma membranes, and enhances the activity of various antioxidant enzymes, thus alleviating adverse effects in plants under abiotic stresses. Future research directions on the relationship between Se and abiotic stresses in plants are proposed. This article will further deepen our understanding of the relationship between Se and plants.

Seed management using NGS technology to rapidly eliminate a deleterious allele from rice breeder seeds

Spontaneous mutations are stochastic phenomena that occur in every population. However, deleterious mutated allele present in seeds distributed to farmers must be detected and removed. Here, we eliminated undesirable mutations from the parent population in one generation through a strategy based on next-generation sequencing (NGS). This study dealt with a spontaneous albino mutant in the 'Hinohikari' rice variety grown at the Miyazaki Comprehensive Agricultural Experiment Station, Japan. The incidence of albinism in the population was 1.36%. NGS analysis revealed the genomic basis for differences between green and albino phenotypes. Every albino plant had a C insertion in the Snow-White Leaf1 (SWL1) gene on chromosome 4 causing a frameshift mutation. Selfing plants heterozygous for the mutant allele, swl1-R332P, resulted in a 3:1 green/albino ratio, confirming that a single recessive gene controls albinism. Ultrastructural leaf features in the swl1-R332P mutants displayed deformed chlorophyll-associated organelles in albino plants that were similar to those of previously described swl1 mutants. Detection of the causative gene and its confirmation using heterozygous progenies were completed within a year. The NGS technique outlined here facilitates rapid identification of spontaneous mutations that can occur in breeder seeds.

Salt stress resilience in plants mediated through osmolyte accumulation and its crosstalk mechanism with phytohormones

Salinity stress is one of the significant abiotic stresses that influence critical metabolic processes in the plant. Salinity stress limits plant growth and development by adversely affecting various physiological and biochemical processes. Enhanced generation of reactive oxygen species (ROS) induced via salinity stress subsequently alters macromolecules such as lipids, proteins, and nucleic acids, and thus constrains crop productivity. Due to which, a decreasing trend in cultivable land and a rising world population raises a question of global food security. In response to salt stress signals, plants adapt defensive mechanisms by orchestrating the synthesis, signaling, and regulation of various osmolytes and phytohormones. Under salinity stress, osmolytes have been investigated to stabilize the osmotic differences between the surrounding of cells and cytosol. They also help in the regulation of protein folding to facilitate protein functioning and stress signaling. Phytohormones play critical roles in eliciting a salinity stress adaptation response in plants. These responses enable the plants to acclimatize to adverse soil conditions. Phytohormones and osmolytes are helpful in minimizing salinity stress-related detrimental effects on plants. These phytohormones modulate the level of osmolytes through alteration in the gene expression pattern of key biosynthetic enzymes and antioxidative enzymes along with their role as signaling molecules. Thus, it becomes vital to understand the roles of these phytohormones on osmolyte accumulation and regulation to conclude the adaptive roles played by plants to avoid salinity stress.

miR3633a-GA3ox2 Module Conducts Grape Seed-Embryo Abortion in Response to Gibberellin

Seedlessness is one of the important quality and economic traits favored by grapevine consumers, which are mainly affected by phytohormones, especially gibberellin (GA). GA is widely utilized in seedless berry production and could effectively induce grape seed embryo abortion. However, the molecular mechanism underlying this process, like the role of RNA silencing in the biosynthesis pathway of GA remains elusive. Here, Gibberellin 3-β dioxygenase2 (GA3ox2) as the last key enzyme in GA biosynthesis was predicated as a potential target gene for miR3633a, and two of them were identified as a GA response in grape berries. We also analyzed the promoter regions of genes encoding GA biosynthesis and found the hormone-responsive elements to regulate grape growth and development. The cleavage interaction between VvmiR3633a and VvGA3ox2 was validated by RLM-RACE and the transient co-transformation technique in tobacco in vivo. Interestingly, during GA-induced grape seed embryo abortion, exogenous GA promoted the expression of VvmiR3633a, thereby mainly repressing the level of VvGA3ox2 in seed embryos. We also observed a negative correlation between down-regulated VvGA20ox2/VvGA3ox2 and up-regulated VvGA2ox3/VvGA2ox1, of which GA inactivation was greater than GA synthesis, inhibited active GA content, accompanied by the reduction of VvSOD and VvCAT expression levels and enzymatic activities. These series of changes might be the main causes of grape seed embryo abortion. In conclusion, we have preliminarily drawn a schematic mode of GA-mediated VvmiR3633a and related genes regulatory network during grape seed abortion induced by exogenous GA. Our findings provide novel insights into the GA-responsive roles of the VvmiR3633a-VvGA3ox2 module in the modulation of grape seed-embryo abortion, which has implications for the molecular breeding of high-quality seedless grape berries.

Comparative Transcriptomic Analysis of Root and Leaf Transcript Profiles Reveals the Coordinated Mechanisms in Response to Salinity Stress in Common Vetch

Owing to its strong environmental suitability to adverse abiotic stress conditions, common vetch (Vicia sativa) is grown worldwide for both forage and green manure purposes and is an important protein source for human consumption and livestock feed. The germination of common vetch seeds and growth of seedlings are severely affected by salinity stress, and the response of common vetch to salinity stress at the molecular level is still poorly understood. In this study, we report the first comparative transcriptomic analysis of the leaves and roots of common vetch under salinity stress. A total of 6361 differentially expressed genes were identified in leaves and roots. In the roots, the stress response was dominated by genes involved in peroxidase activity. However, the genes in leaves focused mainly on Ca²⁺ transport. Overexpression of six salinity-inducible transcription factors in yeast further confirmed their biological functions in the salinity stress response. Our study provides the most comprehensive transcriptomic analysis of common vetch leaf and root responses to salinity stress. Our findings broaden the knowledge of the common and distinct intrinsic molecular mechanisms within the leaves and roots of common vetch and could help to develop common vetch cultivars with high salinity tolerance.

Transcriptome Analysis Reveals Molecular Mechanisms under Salt Stress in Leaves of Foxtail Millet (Setaria italica L.)

Foxtail millet (Setaria italica L.) is an important cereal for managing future water scarcity and ensuring food security, due to its strong drought and salt stress resistance owing to its developed root system. However, the molecular responses of foxtail millet leaves to salt stress are largely unknown. In this study, seeds of 104 foxtail millet accessions were subjected to 0.17 mol·L^-1 NaCl stress during germination, and various germination-related parameters were analyzed to derive 5 salt-sensitive accessions and 13 salt-tolerant accessions. Hong Gu 2000 and Pu Huang Yu were the most salt-tolerant and salt-sensitive accessions, respectively. To determine the mechanism of the salt stress response, transcriptomic differences between the control and salt-treated groups were investigated. We obtained 2019 and 736 differentially expressed genes under salt stress in the salt-sensitive and salt-tolerant accessions, respectively. The transcription factor families bHLH, WRKY, AP2/ERF, and MYB-MYC were found to play critical roles in foxtail millet's response to salt stress. Additionally, the down-regulation of ribosomal protein-related genes causes stunted growth in the salt-sensitive accessions. The salt-tolerant accession alleviates salt stress by increasing energy production. Our findings provide novel insights into the molecular mechanism of foxtail millet's response to salt stress.

Chickpea Biofortification for Cytokinin Dehydrogenase via Genome Editing to Enhance Abiotic-Biotic Stress Tolerance and Food Security

Globally more than two billion people suffer from micronutrient malnutrition (also known as "hidden hunger"). Further, the pregnant women and children in developing nations are mainly affected by micronutrient deficiencies. One of the most important factors is food insecurity which can be mitigated by improving the nutritional values through biofortification using selective breeding and genetic enhancement techniques. Chickpea is the second most important legume with numerous economic and nutraceutical properties. Therefore, chickpea production needs to be increased from the current level. However, various kind of biotic and abiotic stresses hamper global chickpea production. The emerging popular targets for biofortification in agronomic crops include targeting cytokinin dehydrogenase (CKX). The CKXs play essential roles in both physiological and developmental processes and directly impact several agronomic parameters i.e., growth, development, and yield. Manipulation of CKX genes using genome editing tools in several crop plants reveal that CKXs are involved in regulation yield, shoot and root growth, and minerals nutrition. Therefore, CKXs have become popular targets for yield improvement, their overexpression and mutants can be directly correlated with the increased yield and tolerance to various stresses. Here, we provide detailed information on the different roles of CKX genes in chickpea. In the end, we discuss the utilization of genome editing tool clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) to engineer CKX genes that can facilitate trait improvement. Overall, recent advancements in CKX and their role in plant growth, stresses and nutrient accumulation are highlighted, which could be used for chickpea improvement.

Analysis of miRNAs responsive to long-term calcium deficiency in tef (Eragrostis tef (Zucc.) Trotter)

MicroRNAs (miRNAs) play an important role in growth, development, stress resilience, and epigenetic modifications of plants. However, the effect of calcium (Ca²⁺) deficiency on miRNA expression in the orphan crop tef (Eragrostis tef) remains unknown. In this study, we analyzed expression of miRNAs in roots and shoots of tef in response to Ca²⁺ treatment. miRNA-seq followed by bioinformatic analysis allowed us to identify a large number of small RNAs (sRNAs) ranging from 17 to 35 nt in length. A total of 1380 miRNAs were identified in tef experiencing long-term Ca²⁺ deficiency while 1495 miRNAs were detected in control plants. Among the miRNAs identified in this study, 161 miRNAs were similar with those previously characterized in other plant species and 348 miRNAs were novel, while the remaining miRNAs were uncharacterized. Putative target genes and their functions were predicted for all the known and novel miRNAs that we identified. Based on gene ontology (GO) analysis, the predicted target genes are known to have various biological and molecular functions including calcium uptake and transport. Pairwise comparison of differentially expressed miRNAs revealed that some miRNAs were specifically enriched in roots or shoots of low Ca²⁺-treated plants. Further characterization of the miRNAs and their targets identified in this study may help in understanding Ca²⁺ deficiency responses in tef and related orphan crops.

Molecular Regulation of Cotton Fiber Development: A Review

Cotton (Gossypium spp.) is an economically important natural fiber crop. The quality of cotton fiber has a substantial effect on the quality of cotton textiles. The identification of cotton fiber development-related genes and exploration of their biological functions will not only enhance our understanding of the elongation and developmental mechanisms of cotton fibers but also provide insights that could aid the cultivation of new cotton varieties with improved fiber quality. Cotton fibers are single cells that have been differentiated from the ovule epidermis and serve as a model system for research on single-cell differentiation, growth, and fiber production. Genes and fiber formation mechanisms are examined in this review to shed new light on how important phytohormones, transcription factors, proteins, and genes linked to fiber development work together. Plant hormones, which occur in low quantities, play a critically important role in regulating cotton fiber development. Here, we review recent research that has greatly contributed to our understanding of the roles of different phytohormones in fiber development and regulation. We discuss the mechanisms by which phytohormones regulate the initiation and elongation of fiber cells in cotton, as well as the identification of genes involved in hormone biosynthetic and signaling pathways that regulate the initiation, elongation, and development of cotton fibers.

De novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (Vigna aconitifolia) (Jacq.) Marechal

BACKGROUND

The underutilized species Vigna aconitifolia (Moth Bean) is an important legume crop cultivated in semi-arid conditions and is valued for its seeds for their high protein content. It is also a popular green manure cover crop that offers many agronomic benefits including nitrogen fixation and soil nutrients. Despite its economic potential, genomic resources for this crop are scarce and there is limited knowledge on the developmental process of this plant at a molecular level. In the present communication, we have studied the molecular mechanisms that regulate plant development in V. aconitifolia, with a special focus on flower and seed development. We believe that this study will greatly enrich the genomic resources for this plant in form of differentially expressed genes, transcription factors, and genic molecular markers.

RESULTS

We have performed the de novo transcriptome assembly using six types of tissues from various developmental stages of Vigna aconitifolia (var. RMO-435), namely, leaves, roots, flowers, pods, and seed tissue in the early and late stages of development, using the Illumina NextSeq platform. We assembled the transcriptome to get 150938 unigenes with an average length of 937.78 bp. About 79.9% of these unigenes were annotated in public databases and 12839 of those unigenes showed a significant match in the KEGG database. Most of the unigenes displayed significant differential expression in the late stages of seed development as compared with leaves. We annotated 74082 unigenes as transcription factors and identified 12096 simple sequence repeats (SSRs) in the genic regions of V.aconitifolia. Digital expression analysis revealed specific gene activities in different tissues which were validated using Real-time PCR analysis.

CONCLUSIONS

The Vigna aconitifolia transcriptomic resources generated in this study provide foundational resources for gene discovery with respect to various developmental stages. This study provides the first comprehensive analysis revealing the genes involved in molecular as well as metabolic pathways that regulate seed development and may be responsible for the unique nutritive values of moth bean seeds. Hence, this study would serve as a foundation for characterization of candidate genes which would not only provide novel insights into understanding seed development but also provide resources for improved moth bean and related species genetic enhancement.

Comparative Proteomics Combined with Morphophysiological Analysis Revealed Chilling Response Patterns in Two Contrasting Maize Genotypes

Maize yield is significantly influenced by low temperature, particularly chilling stress at the maize seedling stage. Various physiological approaches have been established to resist chilling stress; however, the detailed proteins change patterns underlying the maize chilling stress response at the seedling stage remain unknown, preventing the development of breeding-based methods to resist chilling stress in maize. Thus, we performed comprehensive physiological, comparative proteomics and specific phytohormone abscisic acid (ABA) assay on different maize inbred lines (tolerant-line KR701 and sensitive-line hei8834) at different seedling stages (the first leaf stage and third leaf stage) under chilling stress. The results revealed several signalling proteins and pathways in response to chilling stress at the maize seedling stage. Meanwhile, we found ABA pathway was important for chilling resistance of tolerant-line KR701 at the first leaf stage. Related chilling-responsive proteins were further catalogued and analysed, providing a resource for further investigation and maize breeding.

Unravelling the treasure trove of drought-responsive genes in wild-type peanut through transcriptomics and physiological analyses of root

Peanut is one of the most valuable legumes, grown mainly in arid and semi-arid regions, where its production may be hindered by the lack of water. Therefore, breeding drought tolerant varieties is of great importance for peanut breeding programs around the world. Unlike cultivated peanuts, wild peanuts have greater genetic diversity and are an important source of alleles conferring tolerance/resistance to abiotic and biotic stresses. To decipher the transcriptome changes under drought stress, transcriptomics of roots of highly tolerant Arachis duranensis (ADU) and moderately susceptible A. stenosperma (AST) genotypes were performed. Transcriptome analysis revealed an aggregate of 1465 differentially expressed genes (DEGs), and among the identified DEGs, there were 366 single nucleotide polymorphisms (SNPs). Gene ontology and Mapman analyses revealed that the ADU genotype had a higher number of transcripts related to DNA methylation or demethylation, phytohormone signal transduction and flavonoid production, transcription factors, and responses to ethylene. The transcriptome analysis was endorsed by qRT-PCR, which showed a strong correlation value (R² = 0.96). Physio-biochemical analysis showed that the drought-tolerant plants produced more osmolytes, ROS phagocytes, and sugars, but less MDA, thus attenuating the effects of drought stress. In addition, three SNPs of the gene encoding transcription factor NFAY (Aradu.YE2F8), expansin alpha (Aradu.78HGD), and cytokinin dehydrogenase 1-like (Aradu.U999X) exhibited polymorphism in selected different genotypes. Such SNPs could be useful for the selection of drought-tolerant genotypes.

Phytogenic Selenium Nanoparticles Elicited the Physiological, Biochemical, and Antioxidant Defense System Amelioration of Huanglongbing-Infected ‘Kinnow’ Mandarin Plants

Citrus greening or huanglongbing (HLB) is commonly known as yellow dragon disease and affects citrus production worldwide. Therefore, it has a significant impact on and deleterious effects in the agro-industrial sector. Significant efforts have been made to combat this disease and mitigate its destructive impact on citrus production, but still, there is no effective biocompatible treatment available to control HLB disorder. This study is considered the first biocompatible approach to evaluate the potential of phytogenic selenium nanoparticles (SeNPs) to improve the health of HLB-infected ‘Kinnow’ mandarin plants. Polymerase chain reactions (PCRs) with specific primers were used to detect HLB disease in ‘Kinnow’ mandarin plants, and PCR products were sequenced to identify Candidatus Liberibacter asiaticus (CLas), and accession numbers for CLas1 and CLas2, MZ851933 and MZ851934, respectively, were obtained. SeNPs were synthesized by using Allium sativum L. clove extract as a reducing, capping, and stabilizing agent and various techniques such as UV-visible spectrophotometry, energy dispersive X-rays, scanning electron microscopy (SEM), Fourier transformed infrared spectroscopy (FTIR), and X-ray diffraction analysis (XRD) were used to confirm the biogenesis of SeNPs. Different concentrations of SeNPs (25, 50, 75, and 100 mg L⁻¹) were exogenously applied to HLB-infected ‘Kinnow’ mandarin plants and obtained spectacular results. The obtained results from the current study proved that 75 mg L⁻¹ of SeNPs was most effective to improve the chlorophyll, carotenoids, relative water content (RWC), membrane stability index (MSI), total soluble sugar (TSS), superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), total flavonoid content (TFC), and total phenolic content (TPC) and significant decrease was observed in hydrogen peroxide (H₂O₂), malondialdehyde (MDA), and proline (PRO) contents of HLB-infected ‘Kinnow’ mandarin plants as compared to untreated diseased citrus plants. In conclusion, these results allow us to synthesize the SeNPs formulation as a promising management strategy to treat the HLB disease in citrus plants.

Fab Advances in Fabaceae for Abiotic Stress Resilience: From 'Omics' to Artificial Intelligence

Legumes are a better source of proteins and are richer in diverse micronutrients over the nutritional profile of widely consumed cereals. However, when exposed to a diverse range of abiotic stresses, their overall productivity and quality are hugely impacted. Our limited understanding of genetic determinants and novel variants associated with the abiotic stress response in food legume crops restricts its amelioration. Therefore, it is imperative to understand different molecular approaches in food legume crops that can be utilized in crop improvement programs to minimize the economic loss. 'Omics'-based molecular breeding provides better opportunities over conventional breeding for diversifying the natural germplasm together with improving yield and quality parameters. Due to molecular advancements, the technique is now equipped with novel 'omics' approaches such as ionomics, epigenomics, fluxomics, RNomics, glycomics, glycoproteomics, phosphoproteomics, lipidomics, regulomics, and secretomics. Pan-omics-which utilizes the molecular bases of the stress response to identify genes (genomics), mRNAs (transcriptomics), proteins (proteomics), and biomolecules (metabolomics) associated with stress regulation-has been widely used for abiotic stress amelioration in food legume crops. Integration of pan-omics with novel omics approaches will fast-track legume breeding programs. Moreover, artificial intelligence (AI)-based algorithms can be utilized for simulating crop yield under changing environments, which can help in predicting the genetic gain beforehand. Application of machine learning (ML) in quantitative trait loci (QTL) mining will further help in determining the genetic determinants of abiotic stress tolerance in pulses.

Maladaptation of U.S. corn and soybeans to a changing climate

We quantify long-run adaptation of U.S. corn and soybean yields to changes in temperature and precipitation over 1951-2017. Results show that although the two crops became more heat- and drought-tolerant, their productivity under normal temperature and precipitation conditions decreased. Over 1951-2017, heat- and drought-tolerance increased corn and soybean yields by 33% and 20%, whereas maladaptation to normal conditions reduced yields by 41% and 87%, respectively, with large spatial variations in effects. Changes in climate are projected to reduce average corn and soybean yields by 39-68% and 86-92%, respectively, by 2050 relative to 2013-2017 depending on the warming scenario. After incorporating estimated effects of climate-neutral technological advances, the net change in yield ranges from (-)13 to 62% for corn and (-)57 to (-)26% for soybeans in 2050 relative to 2013-2017. Our analysis uncovers the inherent trade-offs and limitations of existing approaches to crop adaptation.

Drought responsiveness in black pepper (Piper nigrum L.): Genes associated and development of a web-genomic resource

Black pepper (Piper nigrum L.; 2n = 52; Piperaceae), the king of spices, is a perennial, trailing woody flowering vine and has global importance with widespread dietary, medicinal, and preservative uses. It is an economically important germplasm cultivated for its fruit and the major cash crop in >30 tropical countries. Crop production is mainly affected by drought stress. The present study deals with the candidate gene identification from drought-affected black pepper leaf transcriptome generated by Illumina Hiseq2000. It also aims to mine putative molecular markers (namely SSRs, SNPs, and InDels) and generate primers for them. The identification of transcription factors and pathways involved in drought tolerance is also reported here. De novo transcriptome assembly was performed with trinity assembler. In total, 4914 differential expressed genes, 2110 transcriptional factors, 786 domains and 1137 families, 20,124 putative SSR markers, and 259,236 variants were identified. At2g30105 (unidentified gene containing leucine-rich repeats and ubiquitin-like domain), serine threonine protein kinase, Mitogen-activated protein kinase, Nucleotide Binding Site-Leucine Rich Repeat, Myeloblastosis-related proteins, basic helix-loop-helix are all found upregulated and are reported to be associated with plant tolerance against drought condition. All these information are catalogued in the Black Pepper Drought Transcriptome Database (BPDRTDb), freely accessible for academic use at http://webtom.cabgrid.res.in/bpdrtdb/. This database is a good foundation for the genetic improvement of pepper plants, breeding programmes, and mapping population of this crop. Putative markers can also be a reliable genomic resource to develop drought-tolerant variety for better black pepper productivity.

Autophagy in Plant Abiotic Stress Management

Plants can be considered an open system. Throughout their life cycle, plants need to exchange material, energy and information with the outside world. To improve their survival and complete their life cycle, plants have developed sophisticated mechanisms to maintain cellular homeostasis during development and in response to environmental changes. Autophagy is an evolutionarily conserved self-degradative process that occurs ubiquitously in all eukaryotic cells and plays many physiological roles in maintaining cellular homeostasis. In recent years, an increasing number of studies have shown that autophagy can be induced not only by starvation but also as a cellular response to various abiotic stresses, including oxidative, salt, drought, cold and heat stresses. This review focuses mainly on the role of autophagy in plant abiotic stress management.

Chitosan-Selenium Nanoparticle (Cs-Se NP) Foliar Spray Alleviates Salt Stress in Bitter Melon

Salt stress severely reduces growth and yield of plants. Considering the positive effects of selenium (Se) and chitosan (Cs) separately against abiotic stress, in these experiments, we synthesized chitosan-selenium nanoparticles (Cs-Se NPs) and investigated their ability to reduce the negative effects of salt stress on growth and some biochemical parameters of bitter melon (Momordica charantia). Bitter melon plants were grown at three NaCl salinity levels (0, 50, and 100 mM) and a foliar spray of Cs-Se NPs (0, 10, and 20 mg L-1) was applied. Some key morphological, biochemical, and physiological parameters in leaf samples and essential oil from fruit were measured at harvest. Salinity decreased growth and yield while foliar application of Cs-Se NPs increased these critical parameters. Furthermore, Cs-Se NPs enhanced bitter melon tolerance to salinity by increasing antioxidant enzyme activity, proline concentration, relative water content, and K+, and decreasing MDA and H2O2 oxidants and Na aggregation in plant tissues. Yield was also improved, as the highest amount of essential oils was produced by plants treated with Cs-Se NPs. Generally, the greatest improvement in measured parameters under saline conditions was obtained by treating plants with 20 mg L-1 Cs-Se NPs, which significantly increased salinity tolerance in bitter melon plants.

Genome-wide identification and characterization of Lectin receptor-like kinase (LecRLK) genes in mungbean (Vigna radiata L. Wilczek)

Lectins are a diverse group of proteins found throughout plant species. Numerous lectins are involved in many important processes such as organogenesis, defense mechanism, signaling, and stress response. Although the mungbean whole genome sequence has been published, distribution, diversification, and gene structure of lectin genes in mungbean are still unknown. A total of 73 putative lectin genes with kinase domain have been identified through BLAST and HMM profiling. Furthermore, these sequences could be classified into three families, such as G-type, L-type, and C-type VrLecRLKs. 59 out of 73 VrLecRLKs were distributed on to 11 chromosomes, whereas rest could not be anchored onto any specific chromosome. Gene structure analysis revealed a varying number of exons in 73 VrLecRLK genes. Gene ontology annotations were grouped into three categories like biological processes, cellular components and molecular functions, which were associated with signaling pathways, defense responses, transferase activity, binding activity, and kinase activity. The comprehensive and systematic studies of LecRLK genes family provides a reference and foundation for further functional analysis of VrLecRLK genes in mungbean.

Medicago sativa and Medicago truncatula Show Contrasting Root Metabolic Responses to Drought

Drought is an environmental stressor that affects crop yield worldwide. Understanding plant physiological responses to stress conditions is needed to secure food in future climate conditions. In this study, we applied a combination of plant physiology and metabolomic techniques to understand plant responses to progressive water deficit focusing on the root system. We chose two legume plants with contrasting tolerance to drought, the widely cultivated alfalfa Medicago sativa (Ms) and the model legume Medicago truncatula (Mt) for comparative analysis. Ms taproot (tapR) and Mt fibrous root (fibR) biomass increased during drought, while a progressive decline in water content was observed in both species. Metabolomic analysis allowed the identification of key metabolites in the different tissues tested. Under drought, carbohydrates, abscisic acid, and proline predominantly accumulated in leaves and tapRs, whereas flavonoids increased in fibRs in both species. Raffinose-family related metabolites accumulated during drought. Along with an accumulation of root sucrose in plants subjected to drought, both species showed a decrease in sucrose synthase (SUS) activity related to a reduction in the transcript level of SUS1, the main SUS gene. This study highlights the relevance of root carbon metabolism during drought conditions and provides evidence on the specific accumulation of metabolites throughout the root system.

Biotechnological Perspectives of Omics and Genetic Engineering Methods in Alfalfa

For several decades, researchers are working to develop improved major crops with better adaptability and tolerance to environmental stresses. Forage legumes have been widely spread in the world due to their great ecological and economic values. Abiotic and biotic stresses are main factors limiting legume production, however, alfalfa (Medicago sativa L.) shows relatively high level of tolerance to drought and salt stress. Efforts focused on alfalfa improvements have led to the release of cultivars with new traits of agronomic importance such as high yield, better stress tolerance or forage quality. Alfalfa has very high nutritional value due to its efficient symbiotic association with nitrogen-fixing bacteria, while deep root system can help to prevent soil water loss in dry lands. The use of modern biotechnology tools is challenging in alfalfa since full genome, unlike to its close relative barrel medic (Medicago truncatula Gaertn.), was not released yet. Identification, isolation, and improvement of genes involved in abiotic or biotic stress response significantly contributed to the progress of our understanding how crop plants cope with these environmental challenges. In this review, we provide an overview of the progress that has been made in high-throughput sequencing, characterization of genes for abiotic or biotic stress tolerance, gene editing, as well as proteomic and metabolomics techniques bearing biotechnological potential for alfalfa improvement.

Stress responsive gene regulation in relation to hydrogen sulfide in plants under abiotic stress

Plants often face a variety of abiotic stresses, which affects them negatively and lead to yield loss. The antioxidant system efficiently removes excessive reactive oxygen species and maintains redox homeostasis in plants. With better understanding of these protective mechanisms, recently the concept of hydrogen sulfide (H₂ S) and its role in cell signaling has become the center of attention. H₂ S has been recognized as a third gasotransmitter and a potent regulator of growth and development processes such as germination, maturation, senescence and defense mechanism in plants. Because of its gaseous nature, H₂ S can diffuse to different part of the cells and balance the antioxidant pools by supplying sulfur to cells. H₂ S showed tolerance against a plethora of adverse environmental conditions like drought, salt, high temperature, cold, heavy metals and flood via changing in level of osmolytes, malonaldialdehyde, Na⁺ /K⁺ uptake, activities of H₂ S biosynthesis and antioxidative enzymes. It also promotes cross adaptation through persulfidation. H₂ S along with calcium, methylglyoxal and nitric oxide, and their cross talk induces the expression of mitogen activated protein kinases as well as other genes in response to stress. Therefore, it is sensible to evaluate and explore the stress responsive genes involved in H₂ S regulated homeostasis and stress tolerance. The current article is aimed to summarize the recent updates on H₂ S-mediated gene regulation in special reference to abiotic stress tolerance mechanism, and cross adaptation in plants. Moreover, new insights into the H₂ S-associated signal transduction pathway have also been explored.

Comparing and Contrasting the Multiple Roles of Butenolide Plant Growth Regulators: Strigolactones and Karrikins in Plant Development and Adaptation to Abiotic Stresses

Strigolactones (SLs) and karrikins (KARs) are both butenolide molecules that play essential roles in plant growth and development. SLs are phytohormones, with SLs having known functions within the plant they are produced in, while KARs are found in smoke emitted from burning plant matter and affect seeds and seedlings in areas of wildfire. It has been suggested that SL and KAR signaling may share similar mechanisms. The α/β hydrolases DWARF14 (D14) and KARRIKIN INSENSITIVE 2 (KAI2), which act as receptors of SL and KAR, respectively, both interact with the F-box protein MORE AXILLARY GROWTH 2 (MAX2) in order to target SUPPRESSOR OF MAX2 1 (SMAX1)-LIKE/D53 family members for degradation via the 26S proteasome. Recent reports suggest that SLs and/or KARs are also involved in regulating plant responses and adaptation to various abiotic stresses, particularly nutrient deficiency, drought, salinity, and chilling. There is also crosstalk with other hormone signaling pathways, including auxin, gibberellic acid (GA), abscisic acid (ABA), cytokinin (CK), and ethylene (ET), under normal and abiotic stress conditions. This review briefly covers the biosynthetic and signaling pathways of SLs and KARs, compares their functions in plant growth and development, and reviews the effects of any crosstalk between SLs or KARs and other plant hormones at various stages of plant development. We also focus on the distinct responses, adaptations, and regulatory mechanisms related to SLs and/or KARs in response to various abiotic stresses. The review closes with discussion on ways to gain additional insights into the SL and KAR pathways and the crosstalk between these related phytohormones.

The dynamic responses of plant physiology and metabolism during environmental stress progression

At adverse environmental conditions, plants produce various kinds of primary and secondary metabolites to protect themselves. Both primary and secondary metabolites play a significant role during the heat, drought, salinity, genotoxic and cold conditions. A multigene response is activated during the progression of these stresses in the plants which stimulate changes in various signaling molecules, amino acids, proteins, primary and secondary metabolites. Plant metabolism is perturbed because of either the inhibition of metabolic enzymes, shortage of substrates, excess demand for specific compounds or a combination of these factors. In this review, we aim to present how plants synthesize different kinds of natural products during the perception of various abiotic stresses. We also discuss how time-scale variable stresses influence secondary metabolite profiles, could be used as a stress marker in plants. This article has the potential to get the attention of researchers working in the area of quantitative trait locus mapping using metabolites as well as metabolomics genome-wide association.

Polyamines and Legumes: Joint Stories of Stress, Nitrogen Fixation and Environment

Polyamines (PAs) are natural aliphatic amines involved in many physiological processes in almost all living organisms, including responses to abiotic stresses and microbial interactions. On other hand, the family Leguminosae constitutes an economically and ecologically key botanical group for humans, being also regarded as the most important protein source for livestock. This review presents the profuse evidence that relates changes in PAs levels during responses to biotic and abiotic stresses in model and cultivable species within Leguminosae and examines the unreviewed information regarding their potential roles in the functioning of symbiotic interactions with nitrogen-fixing bacteria and arbuscular mycorrhizae in this family. As linking plant physiological behavior with "big data" available in "omics" is an essential step to improve our understanding of legumes responses to global change, we also examined integrative MultiOmics approaches available to decrypt the interface legumes-PAs-abiotic and biotic stress interactions. These approaches are expected to accelerate the identification of stress tolerant phenotypes and the design of new biotechnological strategies to increase their yield and adaptation to marginal environments, making better use of available plant genetic resources.

Metabolic reprogramming in nodules, roots, and leaves of symbiotic soybean in response to iron deficiency

To elucidate the mechanism of adaptation of leguminous plants to iron (Fe)-deficient environment, comprehensive analyses of soybean (Glycine max) plants (sampled at anthesis) were conducted under Fe-sufficient control and Fe-deficient treatment using metabolomic and physiological approach. Our results show that soybeans grown under Fe-deficient conditions showed lower nitrogen (N) fixation efficiency; however, ureides increased in different tissues, indicating potential N-feedback inhibition. N assimilation was inhibited as observed in the repressed amino acids biosynthesis and reduced proteins in roots and nodules. In Fe-deficient leaves, many amino acids increased, accompanied by the reduction of malate, fumarate, succinate, and α-ketoglutarate, which implies the N reprogramming was stimulated by the anaplerotic pathway. Accordingly, many organic acids increased in roots and nodules; however, enzymes involved in the related metabolic pathway (e.g., Krebs cycle) showed opposite activity between roots and nodules, indicative of different mechanisms. Sugars increased or maintained at constant level in different tissues under Fe deficiency, which probably relates to oxidative stress, cell wall damage, and feedback regulation. Increased ascorbate, nicotinate, raffinose, galactinol, and proline in different tissues possibly helped resist the oxidative stress induced by Fe deficiency. Overall, Fe deficiency induced the coordinated metabolic reprogramming in different tissues of symbiotic soybean plants.

Modern Trends in Plant Genome Editing: An Inclusive Review of the CRISPR/Cas9 Toolbox

Increasing agricultural productivity via modern breeding strategies is of prime interest to attain global food security. An array of biotic and abiotic stressors affect productivity as well as the quality of crop plants, and it is a primary need to develop crops with improved adaptability, high productivity, and resilience against these biotic/abiotic stressors. Conventional approaches to genetic engineering involve tedious procedures. State-of-the-art OMICS approaches reinforced with next-generation sequencing and the latest developments in genome editing tools have paved the way for targeted mutagenesis, opening new horizons for precise genome engineering. Various genome editing tools such as transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs), and meganucleases (MNs) have enabled plant scientists to manipulate desired genes in crop plants. However, these approaches are expensive and laborious involving complex procedures for successful editing. Conversely, CRISPR/Cas9 is an entrancing, easy-to-design, cost-effective, and versatile tool for precise and efficient plant genome editing. In recent years, the CRISPR/Cas9 system has emerged as a powerful tool for targeted mutagenesis, including single base substitution, multiplex gene editing, gene knockouts, and regulation of gene transcription in plants. Thus, CRISPR/Cas9-based genome editing has demonstrated great potential for crop improvement but regulation of genome-edited crops is still in its infancy. Here, we extensively reviewed the availability of CRISPR/Cas9 genome editing tools for plant biotechnologists to target desired genes and its vast applications in crop breeding research.

Differential responses of molecular mechanisms and physiochemical characters in wild and cultivated soybeans against invasion by the pathogenic Fusarium oxysporum Schltdl

Cultivated soybean (Glycine max) was derived from the wild soybean (Glycine soja), which has genetic resources that can be critically important for improving plant stress resistance. However, little information is available pertaining to the molecular and physiochemical comparison between the cultivated and wild soybeans in response to the pathogenic Fusarium oxysporum Schltdl. In this study, we first used comparative phenotypic and paraffin section analyses to indicate that wild soybean is indeed more resistant to F. oxysporum than cultivated soybean. Genome-wide RNA-sequencing approach was then used to elucidate the genetic mechanisms underlying the differential physiological and biochemical responses of the cultivated soybean, and its relative, to F. oxysporum. A greater number of genes related to cell wall synthesis and hormone metabolism were significantly altered in wild soybean than in cultivated soybean under F. oxysporum infection. Accordingly, a higher accumulation of lignins was observed in wild soybean than cultivated soybean under F. oxysporum infection. Collectively, these results indicated that secondary metabolites and plant hormones may play a vital role in differentiating the response between cultivated and wild soybeans against the pathogen. These important findings may provide future direction to breeding programs to improve resistance to F. oxysporum in the elite soybean cultivars by taking advantage of the genetic resources within wild soybean germplasm.

Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses

Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.

VvmiR160s/VvARFs interaction and their spatio-temporal expression/cleavage products during GA-induced grape parthenocarpy

BACKGROUND

Grape (Vitis vinifera) is highly sensitive to gibberellin (GA), which effectively induce grape parthenocarpy. Studies showed that miR160s and their target AUXIN RESPONSIVE FACTOR (ARF) responding hormones are indispensable for various aspects of plant growth and development, but their functions in GA-induced grape parthenocarpy remain elusive.

RESULTS

In this study, the morphological changes during flower development in response to GA treatments were examined in the 'Rosario Bianco' cultivar. The precise sequences of VvmiR160a/b/c/d/e and their VvARF10/16/17 target genes were cloned, sequenced and characterized. The phylogenetic relationship and intron-exon structure of VvARFs and other ARF family members derived from different species were investigated. All VvmiR160s (except VvmiR160b) and VvARF10/16/17 had the common cis-elements responsive to GA, which support their function in GA-mediated grape parthenocarpy. The cleavage role of VvmiR160s-mediated VvARF10/16/17 was verified in grape flowers. Moreover, spatio-temporal expression analysis demonstrated that among VvmiR160 family, VvmiR160a/b/c highly expressed at late stage of flower/berry development, while VvARF10/16/17showed a reverse expression trend. Interestingly, GA exhibited a long-term effect through inducing the expression of VvmiR160a/b/c/e to increase their cleavage product accumulations from 5 to 9 days after treatment, but GA enhanced the expressions of VvARF10/16/17 only at short term. Pearson correlation analysis based on expression data revealed a negative correlation between VvmiR160a/b/c and VvARF10/16/17 in flowers not berries during GA-induced grape parthenocarpy.

CONCLUSIONS

This work demonstrated that the negative regulation of VvARF10/16/17 expression by VvmiR160a/b/c as key regulatory factors is critical for GA-mediated grape parthenocarpy, and provide significant implications for molecular breeding of high-quality seedless berry.

Impact of Climate Change on Crops Adaptation and Strategies to Tackle Its Outcome: A Review

Agriculture and climate change are internally correlated with each other in various aspects, as climate change is the main cause of biotic and abiotic stresses, which have adverse effects on the agriculture of a region. The land and its agriculture are being affected by climate changes in different ways, e.g., variations in annual rainfall, average temperature, heat waves, modifications in weeds, pests or microbes, global change of atmospheric CO₂ or ozone level, and fluctuations in sea level. The threat of varying global climate has greatly driven the attention of scientists, as these variations are imparting negative impact on global crop production and compromising food security worldwide. According to some predicted reports, agriculture is considered the most endangered activity adversely affected by climate changes. To date, food security and ecosystem resilience are the most concerning subjects worldwide. Climate-smart agriculture is the only way to lower the negative impact of climate variations on crop adaptation, before it might affect global crop production drastically. In this review paper, we summarize the causes of climate change, stresses produced due to climate change, impacts on crops, modern breeding technologies, and biotechnological strategies to cope with climate change, in order to develop climate resilient crops. Revolutions in genetic engineering techniques can also aid in overcoming food security issues against extreme environmental conditions, by producing transgenic plants.

Molecular Characterization and Expression Profile Analysis of Heat Shock Transcription Factors in Mungbean

Heat shock transcription factors (Hsfs) are essential elements in plant signal transduction pathways that mediate gene expression in response to various abiotic stresses. Mungbean (Vigna radiata) is an important crop worldwide. The emergence of a genome database now allows for functional analysis of mungbean genes. In this study, we dissect the mungbean Hsfs using genome-wide identification and expression profiles. We characterized a total of 24 VrHsf genes and classified them into three groups (A, B, and C) based on their phylogeny and conserved domain structures. All VrHsf genes exhibit highly conserved exon-intron organization, with two exons and one intron. In addition, all VrHsf proteins contain 16 distinct motifs. Chromosome location analysis revealed that VrHsf genes are located on 8 of the 11 mungbean chromosomes, and that seven duplicated gene pairs had formed among them. Moreover, transcription patterns of VrHsf genes varied in different tissues, indicating their different roles in plant growth and development. We identified multiple stress related cis-elements in VrHsf promoter regions 2 kb upstream of the translation initiation codons, and the expression of most VrHsf genes was altered under different stress conditions, suggesting their potential functions in stress resistance pathways. These molecular characterization and expression profile analyses of VrHsf genes provide essential information for further function investigation.

Genome editing using CRISPR/Cas9-targeted mutagenesis: An opportunity for yield improvements of crop plants grown under environmental stresses

Developing more crops able to sustainably produce high yields when grown under biotic/abiotic stresses is an important goal, if crop production and food security are to be guaranteed in the face of ever-increasing human population and unpredictable global climatic conditions. However, conventional crop improvement, through random mutagenesis or genetic recombination, is time-consuming and cannot keep pace with increasing food demands. Targeted genome editing (GE) technologies, especially clustered regularly interspaced short palindromic repeats (CRISPR)/(CRISPR)-associated protein 9 (Cas9), have great potential to aid in the breeding of crops that are able to produce high yields under conditions of biotic/abiotic stress. This is due to their high efficiency, accuracy and low risk of off-target effects, compared with conventional random mutagenesis methods. The use of CRISPR/Cas9 system has grown very rapidly in recent years with numerous examples of targeted mutagenesis in crop plants, including gene knockouts, modifications, and the activation and repression of target genes. The potential of the GE approach for crop improvement has been clearly demonstrated. However, the regulation and social acceptance of GE crops still remain a challenge. In this review, we evaluate the recent applications of the CRISPR/Cas9-mediated GE, as a means to produce crop plants with greater resilience to the stressors they encounter when grown under increasing stressful environmental conditions.

Strigolactones in plant adaptation to abiotic stresses: An emerging avenue of plant research

Phytohormones play central roles in boosting plant tolerance to environmental stresses, which negatively affect plant productivity and threaten future food security. Strigolactones (SLs), a class of carotenoid-derived phytohormones, were initially discovered as an "ecological signal" for parasitic seed germination and establishment of symbiotic relationship between plants and beneficial microbes. Subsequent characterizations have described their functional roles in various developmental processes, including root development, shoot branching, reproductive development, and leaf senescence. SLs have recently drawn much attention due to their essential roles in the regulation of various physiological and molecular processes during the adaptation of plants to abiotic stresses. Reports suggest that the production of SLs in plants is strictly regulated and dependent on the type of stresses that plants confront at various stages of development. Recently, evidence for crosstalk between SLs and other phytohormones, such as abscisic acid, in responses to abiotic stresses suggests that SLs actively participate within regulatory networks of plant stress adaptation that are governed by phytohormones. Moreover, the prospective roles of SLs in the management of plant growth and development under adverse environmental conditions have been suggested. In this review, we provide a comprehensive discussion pertaining to SL-mediated plant responses and adaptation to abiotic stresses.

Metabolomics and Transcriptomics in Legumes Under Phosphate Deficiency in Relation to Nitrogen Fixation by Root Nodules

Phosphate (Pi) deficiency is a critical environmental constraint that affects the growth and development of several legume crops that are usually cultivated in semi-arid regions and marginal areas. Pi deficiency is known to be a significant limitation for symbiotic nitrogen (N2) fixation (SNF), and variability in SNF is strongly interlinked with the concentrations of Pi in the nodules. To deal with Pi deficiency, plants trigger various adaptive responses, including the induction and secretion of acid phosphatases, maintenance of Pi homeostasis in nodules and other organs, and improvement of oxygen (O2) consumption per unit of nodule mass. These molecular and physiological responses can be observed in terms of changes in growth, photosynthesis, and respiration. In this mini review, we provide a brief introduction to the problem of Pi deficiency in legume crops. We then summarize the current understanding of how Pi deficiency is regulated in legumes by changes in the transcriptomes and metabolomes found in different plant organs. Finally, we will provide perspectives on future directions for research in this field.

Spatio-temporal expression of miRNA159 family members and their GAMYB target gene during the modulation of gibberellin-induced grapevine parthenocarpy

Grapevine, Vitis vinifera, is an important economic fruit crop that is highly sensitive to gibberellin (GA), and the exogenous application of GA can efficiently induce grapevine parthenocarpy. However, the molecular mechanisms underlying this process remain elusive. In this study, morphological changes during flower development in response to GA treatments were examined in the 'Zuijinxiang' cultivar. To obtain insights into the roles of miRNA159s in GA-induced grapevine parthenocarpy, VvmiR159a, VvmiR159b, VvmiR159c, and their target gene VvGAMYB were isolated, sequenced and characterized. Spatial-temporal expression analyses showed that VvmiR159c exhibited the highest expression levels at 4 d before flowering, followed by a gradual decrease, while VvGAMYB displayed an opposite pattern of expression with the lowest expression at the corresponding stage in response to GA treatment. A cleavage interaction between VvmiR159s and VvGAMYB and variations of their cleavage roles were confirmed in grapevine floral development. In addition, the potential roles of VvmiR159s in GA signaling were investigated through DELLA-protein repressors, indicating that GA-DELLA (SLR1)-VvmiR159c-VvGAMYB is the key signaling regulatory module in grapevine. Our findings provide novel insights into the GA-responsive roles of VvmiR159s in modulating grapevine floral development, which have important implications for the molecular breeding of high-quality seedless grapevine berry.

The number of measurements needed to obtain high reliability for traits related to enzymatic activities and photosynthetic compounds in soybean plants infected with Phakopsora pachyrhizi

Asian rust affects the physiology of soybean plants and causes losses in yield. Repeatability coefficients may help breeders to know how many measurements are needed to obtain a suitable reliability for a target trait. Therefore, the objectives of this study were to determine the repeatability coefficients of 14 traits in soybean plants inoculated with Phakopsora pachyrhizi and to establish the minimum number of measurements needed to predict the breeding value with high accuracy. Experiments were performed in a 3x2 factorial arrangement with three treatments and two inoculations in a random block design. Repeatability coefficients, coefficients of determination and number of measurements needed to obtain a certain reliability were estimated using ANOVA, principal component analysis based on the covariance matrix and the correlation matrix, structural analysis and mixed model. It was observed that the principal component analysis based on the covariance matrix out-performed other methods for almost all traits. Significant differences were observed for all traits except internal CO2 concentration for the treatment effects. For the measurement effects, all traits were significantly different. In addition, significant differences were found for all Treatment x Measurement interaction traits except coumestrol, chitinase and chlorophyll content. Six measurements were suitable to obtain a coefficient of determination higher than 0.7 for all traits based on principal component analysis. The information obtained from this research will help breeders and physiologists determine exactly how many measurements are needed to evaluate each trait in soybean plants infected by P. pachyrhizi with a desirable reliability.