Showing papers in "Plant Molecular Biology Reporter in 2021"

Allantoin: Emerging Role in Plant Abiotic Stress Tolerance

Abstract: Allantoin is an intermediate product of purine catabolic pathway that helps in nitrogen mobilization in plants. It is ubiquitously present in the plant kingdom and serves as an important N form transported from source to sink. During the recent years, allantoin has emerged as a molecule involved in increasing stress tolerance in plants. Higher allantoin biosynthesis and accumulation in plants is correlated with an increase in different abiotic stress tolerance such as drought, salt, cold, heavy metals and irradiance. Increased allantoin accumulation subsequently activates ABA (abscisic acid) biosynthetic genes which in turn activate its hallmark downstream stress-related genes such as RD26 and 29 (response to desiccation), CAT2 (catalase2), Mn/Fe/Cu/Zn superoxide dismutases and SOS1 (salt overly sensitive 1). External application of allantoin on plants acts as signalling molecule that induces a complex crosstalk between ABA and JA (Jasmonic acid) pathway resulting in increased stress tolerance in plants. Recently, allantoin has been attributed to the role of kin recognition in plants, which highlights its role as a signal molecule that facilitates inter-plant interactions. In this review, we present the up to date understanding of this Nitrogen carrying compound, which has recently emerged as a molecule that plays important roles in abiotic stress tolerance in plants.

Overexpression of AtBBX29 Improves Drought Tolerance by Maintaining Photosynthesis and Enhancing the Antioxidant and Osmolyte Capacity of Sugarcane Plants

Abstract: B-box proteins have emerged as prominent mechanisms for controlling growth and developmental processes and in some instances responses to biotic and abiotic stresses in plants. These proteins mediate transcriptional regulations and protein–protein interactions in cellular signalling processes. B-box proteins thereby play an important role in coordinating physiological and biochemical pathway flux and are therefore ideal targets for controlling stress responses in plants. In this study, the overexpression of an Arabidopsis thaliana B-box gene (BBX29) in sugarcane (Saccharum spp. hybrid) has led to enhanced drought tolerance and delayed senescence under water-deficit conditions when compared to the wild-type plants. Transgenic plants maintained a higher relative water content and better protected its photosynthetic machinery. These plants accumulated more proline and displayed enhanced enzymatic antioxidant activity under drought conditions. Overexpression of AtBBX29 further alleviated the build-up of reactive oxygen species and curtailed oxidative damage, resulting in transgenic plants with improved health and higher survival rates during dehydration. Our results suggested that the AtBBX29 gene influenced an array of physiological and biochemical mechanisms in sugarcane to the advantage of the crop and might be a target to genetically engineer drought tolerance into sugarcane. This is the first report to elucidate B-box protein functionality in a polyploid crop such as sugarcane.

Mitigating Strategies of Gibberellins in Various Environmental Cues and Their Crosstalk with Other Hormonal Pathways in Plants: a Review

Abstract: Phytohormones are chemical substances that in minute concentration instruct a plethora of developmental and physiological responses in plants These signal molecules synthesized within the plant body are referred to as plant growth regulators The available literature revealed that manipulation of phytohormonal content could be a promising approach towards augmentation of environmental stress tolerance in crop plants They play pivotal role in acclimatization against unstable environmental extremes Gibberellins are plant hormones affecting germination, stem elongation, flowering, abolition of dormancy, determination of sex expression, leaf and fruit senescence, and enzymatic stimulation The uncertainty in climatic condition and over expanding population has led to a heap of abiotic stresses in plants Salinity, high temperature, chilling, freezing, heavy metals, drought, flooding, allelochemicals, and radiation are the stresses that hinder development of plants The perception of these stresses by plants occurs in a highly coordinated and interactive manner by triggering the activation of a myriad of elaborate signaling networks in which phytohormones play a significant role The present review describes biosynthesis, signaling, and the potential roles of gibberellins as a tool in mitigating stress, increasing growth, development, and tolerance in plants In future, revelations evolving the comprehensive knowledge to understand the relationship of plant growth regulators and stress conditions are discussed This review also enlightens the latest research progress in GA signaling and its crosstalk with other hormonal pathways, underlying the multitude role of DELLA proteins with components of other hormonal signaling pathways

Genetic Diversity and Population Assessment of Musa L. (Musaceae) Employing CDDP Markers

Abstract: Sixty-six accessions of Musa genus with different genomic groups that consisted of wild relatives and cultivated lines were obtained from the International Transit Center, Belgium, for DNA extraction using Cetyl trimethylammonium bromide method, followed by amplification with Conserved DNA-derived Polymorphism (CDDP) markers for genetic diversity and population assessment. A total of 421 alleles with major allele frequency of 2.051 were detected from the reproducible markers. High genetic diversity (GD, 11.093) and polymorphic information content (0.918) were revealed. The number of polymorphic loci and percentage of polymorphic loci ranged from 59 to 66 and 89.34 to 100, respectively. Using the potential genetic indicators including effective number of alleles, Nei’s genetic diversity, and Shannon’s information index, the AS genomic group was identified to have the highest GD, while the AAA accessions had the lowest GD indices. The GD parameters identified in the accessions were ranked as AS > AAB > AAAA > AA > ABB > wild diploidy > BB > AB > AAA from high to low based on polymorphic loci of the markers. Total intraspecific GD, interspecific GD, and estimate gene flow identified were 0.433, 0.404, and 7.113, respectively. The coefficient of gene differentiation of 0.066 was obtained, indicating 6.57% among the population and 93.43% within the population. Dendrogram analysis produced nine major groups with subgroups at similarity index of 0.814. These CDDP functional gene-based markers were informative and very efficient in resolving GD, and population indices among the banana and plantain accessions of different genomes. The identified CDDP markers might serve as potential tools for selecting suitable training populations for breeding and conservation of Musa species.

Genetic Diversity and Population Structure Analyses of Wild Relatives and Cultivated Cowpea ( Vigna unguiculata (L.) Walp.) from Senegal Using Simple Sequence Repeat Markers

Abstract: Cowpea (Vigna unguiculata (L.)) is an important crop for food security in Senegal; therefore, understanding the genetic diversity of local germplasm is relevant for crop improvement and genetic maintenance in the era of climate change. For this purpose, 15 microsatellite markers were used to estimate the genetic diversity of Senegalese cowpea germplasm, including 671 accessions grown in eight regions and 66 wild relatives and intermediate forms (weedy). For the cultivated, the main expected heterozygosity (mHe) ranged between 0.317 (Fatick) and 0.439 (South). A narrow genetic variation between accessions from the different regions was observed with genetic similarity ranging from 0.861 to 0.965 and genetic differentiation indices (Fst) between 0.018 and 0.100. The accessions from southern Senegal (Kedougou, Sedhiou, and Kolda regions) are more diverse than the others. However, the accessions from the North (Saint-Louis) are genetically different from other regions. The diversity analysis in wild relatives from Senegal, which had never been performed before, revealed that the wild/weedy forms remain more diverse than the cultivated with genetic diversity values (He) of 0.389 and 0.480, respectively. STRUCTURE software divided the Senegalese germplasm into five subpopulations. Three of them (i, ii, and iii) included only cultivated accessions from several regions, one (v) mainly from Saint-Louis, and one (iv) the wild/weedy with some cultivated accessions. Our results support the hypothesis that Vigna unguiculata var. spontanea is the wild progenitor of cowpea. The accessions from the South, the northern recession accessions, and the wild/weedy could serve as sources of new genes for the genetic improvement of cowpea in Senegal.

Transcriptome-Wide Identification and Expression Profiles of Masson Pine WRKY Transcription Factors in Response to Low Phosphorus Stress

Abstract: Masson pine (Pinus massoniana Lamb.) is an economically important conifer tree that can be widely used for timber, pulp, and resin production. However, the phosphate (Pi) deficiency in tropical and subtropical forest soils poses severe challenges for the productivity of masson pine. WRKY transcription factors (TFs) have been proven to play important roles in plant responses to biotic and abiotic stresses, including low Pi stress; however, little is known about their roles in masson pine. To understand the roles of P. massoniana WRKY (PmWRKY) in low Pi stress, 25 putative WRKY TFs with complete WRKY domain from transcriptome sequencing data were identified. Based on their conserved domains and zinc-finger motif, the P. massoniana WRKY were divided into three groups. Structural feature analysis shows that PmWRKY proteins contain WRKYGQK/GKK/GRK domains and a C2H2/C2HC-type zinc-finger structure. To putatively identify the function of PmWRKY members involved in low Pi stress, transcriptional profiles of 17 PmWRKYs in masson pine under different Pi stresses were systematically established using real-time quantitative RT-PCR analysis. Analysis demonstrates that the candidate PmWRKYs were involved in responses to Pi starvation—for example, PmWRKY11, 12, and 13 were upregulated both in P1 (Phosphorus content of 0.01 mM) and P2 (Phosphorus content of 0.06 mM) stresses. The available evidence conclusively sheds light on protein structures, evolutionary relationships, and expression patterns of WRKYs in response to low Pi stress of masson pine, which facilitates further functional identification and molecular breeding for the enhancement of low-phosphorous tolerance in this species.

Genome-Wide Identification and Expression Analysis of Heavy Metal Stress–Responsive Metallothionein Family Genes in Nicotiana tabacum

Abstract: Tobacco (Nicotiana tabacum L.) is the most important non-food cash crop worldwide and has recently been considered a Cd hyperaccumulator. Metallothionein, a small–molecular weight protein with cysteine-rich domains, plays a key role in plant growth, development, and maintenance of metal homeostasis. The understanding of the tobacco metallothionein (MT) gene family remains unclear. Herein, we systematically characterized twelve NtMT genes in the tobacco genome and classified them into three phylogenetic subfamilies. A number of cis-elements related to plant responses to hormones and abiotic stresses were detected in the promoters of NtMT genes. Tissue expression pattern analysis indicated that NtMT4A/4B were expressed only in seeds, and NtMT2C/2F/2G were mainly expressed in roots. Moreover, most of the NtMT genes were highly induced by heavy metal stress and ion deficiency, suggesting their critical role in relieving metal toxicity and maintaining ion homeostasis in tobacco. This was the first study to describe the genome-wide analysis of the NtMT gene family in tobacco, and the results lay a foundation for understanding the functions of NtMT genes for further enhancing plant tolerance to heavy metal toxicity.

Genome-Wide Identification and Characterization of Germin and Germin-Like Proteins (GLPs) and Their Response Under Powdery Mildew Stress in Wheat ( Triticum aestivum L.)

Abstract: Germin and germin-like proteins (GLPs) play multifaceted roles in plants and participate in signaling processes associated with host–pathogen interactions and response to abiotic stress signaling. Despite the important roles in plant survival and response to the environment, few reports exist about the activity and function of the GLP family in common wheat (Triticum aestivum L.). In this study, we performed a genome-wide identification of the GLP family in wheat and identified 258 GLP genes. Through phylogenetic analysis, the GLPs of Arabidopsis, rice, and wheat were divided into six groups, and each group had a similar genetic structure and a conserved motif. Chromosome 4B has the largest cluster region of TaGLPs among all chromosomes. The cis-regulatory elements in the promoter of TaGLPs, which are critical for the function of wheat GLPs and related to stress and development, are detected. The expression profiles of wheat GLPs under Blumeria graminis f. sp. tritici (Bgt) invasion were investigated using the RNA sequencing analysis and validated using quantitative real-time polymerase chain reaction (qRT-PCR) method. Most of the Bgt resistance-related TaGLP genes are located on the fourth homologous group chromosomes, indicating that pathogens resistance-related TaGLP genes repeat in large tandem in specific chromosomal regions during evolution. These results will help us understand the function of the GLP family in wheat and explore the mechanism of wheat GLPs genes in biotic resistance.

Cotton Chitinase Gene GhChi6 Improves the Arabidopsis Defense Response to Aphid Attack

Abstract: Despite the involvement of many members of the chitinase family in the plant immune system, the exact functions of most chitinases remain poorly understood, especially in plant defense responses to phytophagous insects. Here, the gene GhChi6, which encodes a chitinase protein in Gossypium hirsutum, was shown to be induced by cotton aphid feeding and mechanical wounding. Overexpression of GhChi6 in Arabidopsis plants improved their defense response to aphids. The activities of chitinase and PPO in GhChi6 transgenic Arabidopsis plants were higher than those in wild-type plants. Callose deposition in leaves from GhChi6 transgenic Arabidopsis plants was clearly increased compared with wild-type plants. The levels of AtEDS1, AtPAD4, and AtEDS5 in the SA signaling pathway were higher in GhChi6 transgenic Arabidopsis Line4 than those in wild-type plants, while the expression levels of AtLOX2 in the JA signaling pathway and AtEIN2 in the ethylene signaling pathway were lower in GhChi6 transgenic Arabidopsis Line4 than those in wild-type plants. These results collectively showed that the cotton chitinase gene GhChi6 modulated the plant defense response to aphid attack, which may help guide strategies for improving cotton aphid prevention.

Genetic Dissection of Component Traits for Salinity Tolerance at Reproductive Stage in Rice

Abstract: Rice is highly sensitive to salt stress at flowering stage. With the objective of detection of quantitative trait loci (QTLs) in multi-environment for this stage, 180 backcross-derived lines (BC3F5) from salt tolerant donor Pokkali (AC41585) and recurrent parent IR 64 were subjected to evaluation in saline (EC = 8 dSm−1) and non-saline environments in wet season of 2014 and 2015 employing a novel phenotyping protocol. Nine multi-environmental consistent QTLs for spikelet degeneration, K+ concentration in flag leaf, stress susceptibility index for grain (SSI-Grain) and spikelet sterility (SSI-STE) on chromosomes1, 2, 3, 4 and 11 with 17–42% phenotypic variances were detected. Among several digenic epistatic interactions, one was associated with the main effect QTL (qSSI-STE-11-1) over the years. Similarly genotype × environment interaction associated with two additive QTLs, qDEG-S-2-2 and qSSI-STE-2-1 had positive effect on the resultant phenotype. Functional genes encoding calmodulin-binding protein and potassium transporter were predicted inside the consistent QTLs. Detected stable QTLs, associated markers, predicted genes and derived introgression lines with these QTLs could be utilized in future breeding programme.

Genome-wide Analysis of WRKY Transcription Factor Family in Melon (Cucumis Melo L.) and Their Response to Powdery Mildew

Abstract: The WRKY family is a large group of transcription factors found in higher plants; it plays an important role in many aspects of biological processes. However, there is very little information about this family in melon (Cucumis melo L.). In our research, 57 candidate WRKY genes in the melon genome were identified. According to their structural and phylogenetic features, the 57 CmWRKY genes were classified into three groups, I, II, and III, and the group II was further divided into five subgroups. Group I included 11 members that all have two conservative WRKY domains and a C2H2-type zinc finger motif; Group II contains 41 WRKY gene family members, that all have a WRKY domain and a C2H2-type zinc finger motif. Five members that all have a conservative WRKY domain and a C2HC-type zinc finger motif are classified as Group III. The expression of 16 selected melon WRKY genes was detected by quantitative real-time PCR after sprayed with salicylic acid (SA) or powdery mildew infection. qRT-PCR analysis showed that 16 CmWRKY genes exhibited distinct expression patterns upon powdery mildew infection, and the expression levels of nine genes were inhibited, and seven genes were induced. After being sprayed with SA, the expression levels of 11 genes were inhibited, and five genes were induced. The data here provide an important basis for further functional studies of the WRKY gene in melon resistance.

Methylation Status of Arabidopsis DNA Repair Gene Promoters During Agrobacterium Infection Reveals Epigenetic Changes in Three Generations

Abstract: Agrobacterium tumefaciens is a unique pathogen with the ability to transfer a portion of its DNA, the T-DNA, to other organisms The role of DNA repair genes in Agrobacterium transformation remains controversial In order to understand if the host DNA repair response and dynamics was specific to bacterial factors such as Vir proteins, T-DNA, and oncogenes, we profiled the expression and promoter methylation of various DNA repair genes These genes belonged to nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), homologous recombination (HR), and non-homologous end joining (NHEJ) pathways We infected Arabidopsis plants with different Agrobacterium strains that lacked one or more of the above components so that the influence of the respective factors could be analysed Our results revealed that the expression and promoter methylation of most DNA repair genes was affected by Agrobacterium, and it was specific to Vir proteins, T-DNA, oncogenes, or the mere presence of bacteria In order to determine if Agrobacterium induced any transgenerational epigenetic effect on the DNA repair gene promoters, we studied the promoter methylation in two subsequent generations of the infected plants Promoters of at least three genes, CEN2, RAD51, and LIG4 exhibited transgenerational memory in response to different bacterial factors We believe that this is the first report of Agrobacterium-induced transgenerational epigenetic memory of DNA repair genes in plants In addition, we show that Agrobacterium induces short-lived DNA strand breaks in Arabidopsis cells, irrespective of the presence or absence of virulence genes and T-DNA

Genome-Wide Identification and Expression Analysis of the Carotenoid Cleavage Oxygenase Gene Family in Five Rosaceae Species

Abstract: The carotenoid cleavage oxygenases (CCOs), which include carotenoid cleavage dioxygenases (CCDs) and 9-cis-epoxycarotenoid dioxygenases (NCEDs), are enzymes that are critical to the mediation of the degradation of carotenoids to apocarotenoids. In this study, we identified a total of 12, 20, 11, 8, and 10 CCO genes from Pyrus bretschneideri, Malus domestica, Fragaria vesca, Prunus mume, and Prunus persica, respectively. Phylogenetic analysis showed that these CCO genes clustered into six groups (NCED, CCD1, CCD4, CCD7, CCD8, and CCD-like). Gene structure analysis revealed that CCO genes within the same groups showed similar exon numbers and contained similar motifs. Duplication analysis revealed that tandem duplication played a significant role in the expansion of CCO members in Malus domestica. Purifying selection was involved in the evolution of CCO genes in Pyrus bretschneideri. The transcriptomic data-based expression analysis revealed that the CCO genes exhibited distinct patterns of expression in the roots, leaves, buds, and fruit. The expression patterns based on qRT-PCR showed that there were greater differences on the relative expression levels of PbCCD1 and PbCCD5 between cultivars “Enli” (inflorescence sparsely branched) and “Jinxiangshui” (inflorescence copiously branched) in the three different stages of flower bud morphological differentiation, revealing the possibility of involvement of these genes in the branching of the pear inflorescence. This study provides a valuable resource for further investigations of CCO gene functions in Rosaceae species.

Genome Editing: Revolutionizing the Crop Improvement

Abstract: Modern biotechnology is progressed to sequence-specific, site-directed, precise, and safe strategies for genetic manipulation. The genome-editing strategy is being proposed as one of the most promising tools for genomic study and crop improvement. The basic mechanism involved in genetic manipulations through programmable nucleases is recognition of target genomic loci and binding of effector DNA-binding domain (DBD), double-strand breaks (DSBs) in target DNA by the restriction endonucleases (FokI and Cas) and the repair of DSBs through homology-directed recombination (HDR) or non-homologous end joining (NHEJ). The less efficient and more precise HDR results in the replacement of nucleotides, whereas the more efficient and error-prone NHEJ results in the insertion or deletion of nucleotides. The genome-editing strategies like ZFN, TALEN, and CRISPR/Cas involved in genome editing are being employed to add the desirable trait(s) and remove the undesirable. The impact of gene editing application in crop improvement has proven it the next-generation tool to enhance agricultural productivity. The modifications in crop plants include biotic and abiotic stresses, nutritional improvements, alteration in phenotype, and other characters such as crafting male sterility, haploid production, and increase in yield. The repurposing of CRISPR applications by catalytically inactive Cas9 marks CRISPR as an indispensable tool for genome editing and beyond in biological research. However, the genome-edited plants may have unintended alteration(s) that create biosafety risks. The tools are eventually progressing for more accuracy and efficiency to ensure the safety of consumers and the environment. This article is an attempt to review these genome-editing strategies, the biochemistry attributed to application in crop improvement, and the associated challenges.

Unraveling Physiological and Metabolomic Responses Involved in Phlox subulata L. Tolerance to Drought Stress

Abstract: Metabolic responses are important for plant adaptation to abiotic stress. To investigate the responses of Phlox subulata L. to drought stress, we analyzed its physiological and metabolic changes using gas chromatography-mass spectrometer. Based on the physiological indices, P. subulata L. has tolerance to drought to some degree. Our results showed that there were a total of 30 key metabolites induced by drought stress, including amino acids, organic acids, sugars and sugar alcohols, nucleic acid and its derivatives, and other organic compounds. The glutamic acid-mediated proline biosynthesis pathway is continuously upregulated under drought stress, which could regulate osmotic pressure and maintain intracellular environmental stability. More secondary metabolites are used to increase glycolysis and tricarboxylic acid cycle, to accelerate energy production and to enhance the glutamic acid-mediated proline biosynthesis pathway, which are necessary to increase osmotic regulation. Prolonged drought stress induced progressive accumulation of compatible osmolytes, such as proline and inositol, sugars, and amino acids. Therefore, drought caused systemic alterations in metabolic networks involving transamination, TCA cycle, gluconeogenesis/glycolysis, glutamate-mediated proline biosynthesis, shikimate-mediated secondary metabolisms, and the metabolism of pyrimidine. These data suggest that plants may utilize these physiological and metabolomic adjustments as adaptive responses in the early stages of drought stress. These results deepen our understanding of the mechanisms involved in P. subulata L. drought tolerance, which will help improve the understanding of drought’s effects on plant systems.

ISSR Analysis Reveals High Genetic Variation in Strawberry Three-Way Hybrids Developed for Tropical Regions

Abstract: The cultivated strawberry (Fragaria × ananassa Duch.) is a species of temperate origin, and the extension of this crop into tropical regions is dependent on genetic breeding. Breeders in the UNICENTRO’s Strawberry Breeding Program (USBP) selected, from among 2,000 hybrids, 40 hybrids that were adapted to photoperiod and temperature conditions of tropical regions. In this study, we used inter-simple sequence repeat to characterize 40 three-way hybrids developed by USBP and evaluated the genetic relationship of these hybrids with commercial cultivars, heirloom cultivars, and single hybrids. We used nine inter-simple sequence repeat primers to genotype 14 commercial cultivars, five heirloom cultivars, five single hybrids (SH), 20 three-way hybrids with short-day behavior (SDH), and 20 three-way hybrids with photoperiod-insensitive behavior (PIH). The percentage of polymorphism (100%) and both, the Nei genetic diversity (h = 0.34) and the Shannon index (I = 0.51), showed high variability and diversity, respectively, in the evaluated strawberry genotypes. Commercial cultivars showed the highest diversity indices (h = 0.30, I = 0.46), followed by PIH hybrids (h = 0.27, I = 0.41). In the dendrogram, the genotypes were distributed into three groups (commercial cultivars, heirloom cultivars, and single hybrids; SDH and PIH). This clustering was confirmed by principal coordinate analysis and Bayesian inference analysis. The overall analysis of the data revealed the efficacy of USBP in three-way hybrid development with different genetic characteristics compared with those of available commercially cultivars. These hybrids have substantial potential in becoming new strawberry cultivars.

Identification of Genes Involved in Root Growth Inhibition Under Lead Stress by Transcriptome Profiling in Arabidopsis

Abstract: Lead (Pb) is a heavy metal with high toxicity to plants. Root is the major organ to respond to Pb stress. However, little is known about how plant roots perceive Pb stress signaling. Here, we describe the transcriptome of Arabidopsis root tips under Pb stress using the RNA-seq assay. A total of 703 differentially expressed genes (DEGs) were identified and expressed at every time points. Some early-responsive DEGs (1 h) were predicted to be negatively involved in cell elongation and cell expansion, while some late-responsive DEGs (24 h) positively participated in defense of oxidative stress. Hydrogen peroxide (H2O2) and superoxide (O2−) were increased significantly in root tips under Pb stress. Cell wall extension related gene XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 18 (XTH18) was induced in root tips, and xth18 showed reduced root growth inhibition by Pb stress. Our results revealed the potential mechanism of root growth inhibition by Pb stress and shed light for the further study.

Overexpression of CpSIZ1, a SIZ/PIAS-Type SUMO E3 Ligase from Wintersweet (Chimonanthus praecox), Delays Flowering, Accelerates Leaf Senescence and Enhances Cold Tolerance in Arabidopsis

Abstract: Wintersweet (Chimonanthus praecox L.) is a traditional winter-flowering plant in China and a popular cut flower in winter. Its unique flowering characteristics under cold stress may involve the regulation of a large number of proteins. Protein post-translational modification is an important regulating type for the gene function. However, little is known about the post-translational modification in wintersweet. SUMOylation is an important post-translational modification in eukaryotes. Small ubiquitin-like modifier (SUMO) E3 ligases perform multiple functional regulatory activities in plants via SUMOylation. Here, we cloned and identified a SIZ/PIAS-type SUMO E3 ligase, CpSIZ1, from wintersweet. CpSIZ1 shared high similarity with other SIZ1 proteins. Quantitative real-time PCR (qRT-PCR) indicated that CpSIZ1 was expressed in all tissues tested, with the highest expression in flower wither period of stage 6, and followed by mature leaves except for different flower development stages. The ectopic expression of CpSIZ1 in Arabidopsis, including the CpSIZ1 overexpression in siz1-2 mutant (HB line) and CpSIZ1 overexpression in WT (OE line), not only promoted vegetative growth, delayed flowering and accelerated leaf senescence, but also improve the cold tolerance in Arabidopsis. Therefore, our studies have enrich the understanding of function of SIZ1 gene in woody plant, and provide a good foundation for further research on the post-translational modification regulation mechanism in this winter-flowering plant.

Proteomic Study to Understand Promotive Effects of Plant-Derived Smoke on Soybean (Glycine max L.) Root Growth Under Flooding Stress

Abstract: Plant-derived smoke plays a key role in plant growth Proteomic technique was used for underlying mechanisms of plant-derived smoke on the growth of soybean (Glycine max L) under flooding stress The length and weight of soybean root increased with 2000 parts per million plant-derived smoke under flooding stress within 4 days Altered proteins by plant-derived smoke treatment under flooding stress were mainly related to protein metabolism, stress, and redox Furthermore, proteins related to mitochondrial electron transport chain decreased by flooding stress; however, they increased by addition of plant-derived smoke under flooding stress Based on the results of proteomic analysis, confirmation experiments were performed ATPase abundance and ATP content increased with the treatment of plant-derived smoke under flooding stress Furthermore, the ascorbate/glutathione cycle was activated with the treatment of plant-derived smoke under flooding stress These results suggest that plant-derived smoke improves the root growth of soybean with energy production and reactive oxygen scavenging even if it is under flooding stress, which might positively regulate soybean tolerance towards flooding stress

Chromatin-Level Differences Elucidate Potential Determinants of Contrasting Levels of Cold Sensitivity in Maize Lines

Abstract: Maize is a subtropical, cold-sensitive species. However, some varieties of this species have the potential to withstand long-term low temperatures, even at the seedling stage. The molecular basis of this phenomenon has not been determined. In a chromatin-level study, we compared the cold-stress reaction of seedlings of two maize inbred lines showing contrasting levels of cold sensitivity. The cold-tolerant line was selected based on field data and previous physiological and transcriptomic level studies. The first condition of gene expression—chromatin accessibility—was assessed by formaldehyde-aided isolation of regulatory elements method and DNA sequencing. Potentially expressed genes and cis-regulatory sequences open for interaction with transcription factors have been defined. The results of this study suggest that during cold stress, the tolerant maize line shifted resources from growth to defense. This shift was shown by potential hormone-level events—degradation of growth-promoting gibberellins and synthesis of jasmonic and abscisic acids. This finding is congruent with the xeromorphic morphology of seedlings of the cold-tolerant line and their ability to regrow when stress ceases. It is a common reaction of cold-tolerant maize lines. Moreover, in the cold-tolerant line, several genes from the low-temperature signaling pathways were potentially expressed. Additionally, numerous stress-response AP2/EREBP-binding cis-motifs were accessible in the cold-tolerant line. Differently in the cold-sensitive B73 line, MADS-binding cis-motifs were the most abundant. Development of the photosynthetic apparatus is crucial for the survival of maize seedlings at low temperature. Our results suggest efficient photosynthesis in seedlings of the cold-tolerant line, as was described earlier in physiological-level analyses.

Humic Acid as a Biostimulant in Improving Drought Tolerance in Wheat: the Expression Patterns of Drought-Related Genes

Abstract: Plants develop a series of physiological, biochemical, and molecular responses to survive in drought stress. Many drought-related genes with various functions which regulated by ABA-dependent and independent pathways have been identified in wheat. However, studies on the effect of biostimulants on drought-related genes are limited and unclear. As a biostimulant, humic acid (HA) has enormous roles on plant growth, yield, and protection of resistance in various abiotic stresses, but its relation to drought-related genes is unknown. Here, we aimed to determine the relationships between drought stress generated by − 6 bar and − 8 bar PEG6000 and ABA and HA treatments on total oxidant status (TOS) and total antioxidant status (TAS) and expression of miRNA target genes (AP2, GRF, LAC, CSD1/CSD2, and Plastocyanin) on tolerant (Aksel 2000 and Kirkpinar 79) and susceptible (Atli 2002 and Kirmizi Kilcik) bread wheat (Triticum aestivum L.) genotypes. According to the results, the expression of the genes varied depending on genotype and tissue and it was determined whether the genes used ABA-dependent or ABA-independent mechanisms to provide tolerance to stress in our promoter analysis. Also, the irregularities of the biochemical changes and expression of genes that were caused by PEG6000 could be improved by HA considering the positive effects on genes.

Genetic Diversity and Population Structure of a Medicinal Herb Houttuynia cordata Thunb. of North-East India.

Abstract: Intra-species genetic variability assessment is an effective tool in formulating genetic improvement and germplasm conservation strategies. Houttuynia cordata Thunb. is a semidomesticated medicinal herb consumed widely in traditional diet in North-Eastern India. In the present study, an effort has been made to assess the genetic diversity of H. cordata Thunb. from Brahmaputra valley of North-East India. A total of 545 genotypes from 18 populations of H. cordata Thunb. from four different regions, i.e. North-East, North-West, South-East and South-West, with respect to river Brahmaputra were collected and population genetic diversity and structure were analysed using ISSR molecular markers. Population genetic structure analysis using unweighted pair group method with averages (UPGMA)-based hierarchical cluster analysis, principal coordinate analysis (PCoA) and model-based clustering in STRUCTURE program revealed that the population of H. cordata Thunb. grouped according to regional distribution and forms four genetically distinct clusters. The analysis of molecular variance showed that differentiation among regions was significant with 60% genetic variation among region, 3% genetic variation among population within region and 37% genetic variation within population. We found wide variation in Nei’s gene diversity (Hj) ranging from 0.07782 in Margherita population to 0.13634 in Barapani population. Furthermore, Nei’s gene diversity within population (Nei’s Hs) and total gene diversity (Ht) were found to be 0.1081 and 0.1769 respectively. The genetic differentiation among 18 population was high (Fst = 0.3894; p < 0.001) with relatively restricted gene flow (Nm = 0.6564). Based on the result of this study, we suggest ex situ conservation could be an appropriate measure to adequately capture the total genetic diversity of H. cordata Thunb. populations of North-East India by selecting few individuals from different populations.

Comparative Metabolic Profiling of Two Contrasting Date Palm Genotypes Under Salinity

Abstract: Since specific metabolites may be associated with salinity tolerance, this study aimed to decipher the salinity tolerance mechanism in date palm based on the information encoded by the metabolomic profiles of the salt-tolerant “Umsila” and salt-susceptible “Zabad” cultivars when grown under salinity conditions. Changes in the metabolomic profiles of the leaf and root tissues were determined using hydrophilic interaction liquid chromatography (HILIC) and reverse-phase liquid chromatography (RPLC) mass spectrometry. The global untargeted metabolomic analysis showed the presence of 4878 metabolites accumulated in leaf and root tissues of the date palm seedlings. Principal component analysis (PCA) revealed the presence of unique groups of metabolites for each treatment and tissue type. Pathway analysis showed the involvement of some of these metabolites in the biosynthesis of several types of membranous lipids and glycolipids molecules such as 18:0-lyso-phosphatidylethanolamine (lysoPE), and also the synthesis of cell-wall components such as 16-hydroxy hexadecanoic acid, which is an intermediate metabolite in cutin, suberin, and wax biosynthesis. Moreover, antioxidant flavonoids such as (+)-catechin and epicatechin, vitamins such as B9, phytohormone-associated compounds such as dihydrozeatin-9-N-glucoside-O-glucoside, and osmolytes such as the sulfonic amino acid taurine were all significantly (p ≤ 0.05, FWER ≤ 0.05) altered in response to salinity in both cultivars. These results indicate that salinity tolerance in date palm involved a multi-dimensional mechanism, which includes the modification of the cell-wall and cellular membranes, the production of oxygen species scavengers, the adjustment of cellular osmotic pressure, and probably the alteration of the hormonal balance. The intracultivar metabolomic profile comparison strategy performed in this study represents an approach that may pave the road toward the identification of salinity tolerance mechanisms in date palm based on the final protein products.

Differential Changes in D1 Protein Content and Quantum Yield of Wild and Cultivated Barley Genotypes Caused by Moderate and Severe Drought Stress in Relation to Oxidative Stress

Abstract: The aim of this study was to investigate the effects of drought stress on oxidative damage and efficiency of PSII photochemistry in barley and compare the varietal response of different genotypes including Yusof (tolerant), Moroc9-75 (sensitive), and wild barley (HS) to drought. Plants were subjected to different levels of soil water availability including control, moderate, and severe drought stress. Exposure to drought stress led to decrease in leaf water potential, biomass production, and stomatal conductance (gs) in all genotypes. Drought induced an increase in H2O2 content followed by increase in malondialdehyde (MDA) as a final result of lipid peroxidation. Drought stress also resulted in reduction of D1 protein content in all genotypes and decreased the maximal quantum yield of PSII photochemistry (FV/FM). These parameters were more affected in Moroc9-75 cultivar by drought stress compare to Yusof and HS genotype. Based on our results, drought-induced reactive oxygen species may decrease PSII photochemistry either through peroxidation of thylakoid membranes or interfering with D1 protein synthesis, necessary for proper function of PSII.

Investigation on the Conserved MicroRNA Genes in Higher Plants

Abstract: Analysis of evolving microRNA repertoires within the plant domain can further corroborate our understanding of genome evolution and plasticity. An extensive collection of relatively unbiased miRBase-registered plant miRNAs and predicted unlisted MIRs from 23 plant ESTs were examined. As a result, 4324 pre-miRNAs were predicted and classified in 656 miRNA gene families with mostly being transposons (57.81%). From 216 newly identified pre-miRNAs, 103 distinct types belonged to reduced complexity/repeated regions. Collinearity between the numbers of miRNAs in each species with the relevant sizes of genomes was absent. Duplications of MIRs were evident, with higher MIR paralogs in Liliopsida compared with dicots. Due to the lack of an apparent pattern of phylogeny, Dollo maximum parsimony was used that established the acceleration of gains and potential losses of miRNA gene families within Mesangiospermae during the last 200 million years ago. Phylogenetic analysis of Liliopsida in contrast to Eudicotyledons agreed with the reconstructed tree based on the possible expansion of distinguished MIR families. In marked contrast to dicots, the degrees of resemblance in Liliopsida were higher than their direct predecessors. Analyses of recent monophyletic lineages were illustrative of miRNA horizontal genes transfer.

SCAR Marker Development for the Identification of Elite Germplasm of Moringa Oleifera Lam.-A Never Die Plant

Abstract: Moringa oleifera Lam. (drumstick) belongs to the family Moringaceae that is originated from sub-Himalayan tracts of Northern India distributed worldwide in the tropics and sub-tropics. Immature pods and fresh leaves are widely used as vegetable and are rich source of minerals and vitamins. In the present work, we made an attempt to develop and use a set of RAPD-SCAR marker for the identification of superior germplasm of M. oleifera from the accessions collected from South India. Initially, 120 trees were surveyed based on total fruit yield, and single fruit weight from Karnataka, Kerala, and Tamil Nadu states of India; 23 plants had 50% higher fruit yield and single fruit weight than average and were selected as Candidate Plus Trees (CPTs). On the basis of morphological and biochemical analysis, CPT17 was selected as elite germplasm. Random amplified polymorphic DNA (RAPD) analysis of CPTs indicated 89.61% polymorphism among 23 CPTs. These markers could be used in marker-assisted selection and breeding programs in M. oleifera. Further, an attempt to develop a set of RAPD-SCAR marker for the identification of superior germplasm of M. oleifera was made. RAPD primer OPA-19 (CAAACGTCGG) revealed a unique band (1500-bp) in CPT17. The specific RAPD band was recovered from the gel, cloned, and sequenced. BLAST analysis of the CPT17 specific sequences revealed that no considerable similarity with known protein. Based on these unique characterized sequences, specific primers for CPT17 were designed. Specific amplification profile of this primer proved it as a SCAR marker (F2R2) for CPT17 genotype.

Inhibition of Maize Caffeate 3-O-Methyltransferase by Nitecapone as a Possible Approach to Reduce Lignocellulosic Biomass Recalcitrance

Abstract: Maize (Zea mays) caffeate 3-O-methyltransferase (ZmaysCOMT, EC 2.1.1.68), a key enzyme of the phenylpropanoid pathway, catalyzes the O-methylation of caffeic acid to ferulic acid, a precursor of lignin polymer and a crucial component of the cell wall structure. Plant cell wall recalcitrance is due to lignin, and the discovery of specific inhibitors of ZmaysCOMT could be useful to increase the digestibility of the lignocellulose biomass and improve the production of cellulosic biofuels. In this work, we have modeled the three-dimensional structure of ZmaysCOMT and prospected promising inhibitors by using virtual screening techniques. A set of 1668 putative candidates was screened from a virtual library and docked in the active site of the enzyme, and nitecapone was selected as one of the most promising enzyme inhibitors. Details of the mode of inhibition were assessed by in silico simulation and in vitro assays of nitecapone on the enzyme. In comparison with the nitecapone-free control, kinetics parameters showed different values of Vmax and KM, suggesting a kinetic profile such as mixed inhibition of the ZmaysCOMT. In brief, we suggest that the nitecapone-induced inhibition of ZmaysCOMT may serve as a non-transgenic strategy to explore the biosynthesis of ferulic acid and lignin, their relationships with the recalcitrance of lignocellulosic biomass, and, possibly, to improve bioethanol production.

Global Analysis of Gene Expression Profiles in Glutinous Rice 89-1 ( Oryza sativa L.) Seedlings Exposed to Chilling Stress

Abstract: Rice (Oryza sativa) is a tropical cereal crop that is severely affected by chilling stress at the seedling stage, although glutinous rice 89-1 (Gr89-1) in Chongqing, China, shows tolerance to low temperatures and overwintering ability. However, little research has been conducted on the mechanisms regulating chilling stress in Gr89-1. In this study, a comprehensive of transcriptional profiles of Gr89-1 seedlings at the three-leaf stage was conducted after a 4 °C treatment for 2, 6, 12, 24, or 48 h. Overall, 2993 differentially expressed genes were detected in Gr89-1 seedlings upon cold exposure. Gene Ontology testing and pathway analysis revealed differentially expressed genes involved in transcriptional regulation, carbohydrate metabolism, plant hormone signal, and cell wall composition. A total of 243 transcription factors were differentially expressed during the cold treatment; in particular, the AP2/EREBP, bHLH, NAC, WRKY, C2H2, and TIFY families were generally upregulated after cold treatment, whereas the mTERF and GNAT families were downregulated. Chilling stress changed the starch and sucrose metabolism, coupled with the accumulation of sucrose and trehalose level, and increases in jasmonic acid level in Gr89-1 seedlings. Furthermore, a number of the cell wall-related genes identified in the present study were also differentially expressed during the cold treatment. The genes and pathways identified in the current study increase our understanding of the mechanisms underlying cold resistance in rice seedlings.

Identification of QTLs for Seed Dormancy in Cultivated Peanut Using a Recombinant Inbred Line Mapping Population

Abstract: Seed dormancy is an important breeding trait for the development of certain types of peanut cultivars. Peanut cultivars with seed dormancy can inhibit preharvest sprouting in which the sprouting may increase susceptibility to preharvest aflatoxin contamination. The recombinant inbred line (RIL) mapping population derived from a cross of Tifrunner, a dormant Runner type, and GT-C20, a non-dormant Spanish type, were planted in the field for 2 years, and the freshly harvested seeds were used for seed dormancy tests at 7, 14, 21, and 28 days during germination. There were three RILs from 2-year tests with no dormancy (T48, T83, T160) and two lines with strong dormancy (T11, T163). This RIL population was genotyped using peanut SNP array ‘Axiom_Arachis’ 58 K, and two major seed dormancy QTLs were anchored on chromosome A04 and A05 with 43.16% and 51.61% of the phenotype variation explained (PVE), respectively. The QTL mapped on chromosome A05 had been anchored on a physical map interval of 98 kb (157.538–157.636 Mb) from which a possible candidate gene (Arahy.KB746A, ethylene-responsive transcription factor) was identified. Reference to the peanut physical map and flanking sequences, DNA markers can be developed for these two QTLs and used in marker-assisted breeding selection for seed dormancy in peanut.

Third-Generation Sequencing Indicated that LncRNA Could Regulate eIF2D to Enhance Protein Translation Under Heat Stress in Populus simonii

Abstract: As global temperatures rise, plants are being increasingly exposed to high-temperature stress. Although long non-coding RNAs (lncRNAs) are regulatory elements of gene expression under heat stress in trees, the limitation of sequencing technology and methods in identifying lncRNAs has hindered the exploration of their roles. To explore the role of lncRNAs in response to heat stress, we treated Populus simonii seedlings at 40 °C for 1 h and performed third-generation sequencing (Iso-Seq) and high-throughput RNA sequencing (RNA-seq). A total of 239,142,803 short reads were used to correct 101,791 long reads (average length 2400 bp) resulting in 101,791 full-length transcripts and representing 45,217 genes. Then, 829 lncRNAs were identified, including 757 sense lncRNAs (91.31%), 25 long intergenic non-coding RNAs (3.02%), seven antisense lncRNAs (0.84%), and 40 sense intronic lncRNAs (4.83%). Using the criteria |log2Fold Change| ≥ 1 and q-value < 0.05, 2787 genes and 21 lncRNAs were observed to be differentially expressed under heat stress. Functional annotation showed that these genes were associated with “response to stress”, “response to stimulus”, and “unfolded protein binding”. Furthermore, 149 genes were predicted as targets of 17 significantly differentially expressed lncRNAs. A total of 11 genes in significantly enriched gene ontology (GO) terms were annotated, including four genes encoding disease resistance proteins targeted by lncPs2 and seven eukaryotic translation initiation factor 2D (eIF2D) genes targeted by lncPs3. Expression and functional analysis revealed that lncPs3 and five eIF2Ds were synergistically upregulated, indicating that lncPs3 may enhance protein translation by regulating eIF2D in response to heat stress.