Plant Gene最新文献

Salinity is a stress factor that decreases global agricultural yield. Crops such as rice, tomato, potato, and legumes are susceptible to salt, thus this problem requires urgent attention. Disruption of carbohydrate metabolism can have negative effects on stress tolerance. Sucrose phosphate synthase (SPS) enzymes operate in a key regulatory step in sucrose synthesis. Therefore, they have a significant role in the regulation of sugar metabolism. This study focused on the function of the SPS homolog -pvSPS4- in the roots of legume crop common bean under salinity stress. We previously showed that pvSPS4 expression is root-specific and is upregulated under salt stress in a salt-tolerant common bean genotype. This upregulation was accompanied by an accumulation of sugars in the roots. In the current study, using the same genotype, we generated composite common bean plants with wild-type shoot and pvSPS4 knock-down roots. Composite plants exhibited a more sensitive phenotype under salt stress compared to control and mock plants. pvSPS4 knock-down disturbed the root glucose/sucrose ratio and balance of Ca⁺², Mg⁺², and K⁺ in both root and leaves which resulted in a reduction in photosynthetic pigments together with osmoregulation and antioxidant capability. Our results imply that pvSPS4 is an important gene for carbohydrate balance regulation under salt-stress in the common bean root tissues and sets an example for the significance of mainly disregarded roles of SPS genes in sink tissues.

Eucalyptus is one of the mainstays of the forest industry, contributing high-quality raw materials for pulp, paper, wood, and energy production. The typical approaches to reveal the genetic basis of important traits include classical Quantitative Trait Locus (QTL) mapping and Genome-Wide Association Studies (GWAS) approaches, but these are typically expensive and time-consuming. Here we evaluate the potential of Extreme-Phenotype GWAS (XP-GWAS) to identify candidate genes underlying a quantitative trait in Eucalyptus, using the timing of leaf heteroblasty as a case study. XP-GWAS involves genotyping pools of individuals grouped by extreme and opposed phenotypes from a population or a diversity panel and studying their allele frequency. Using a previous phenotyped trial of E. globulus, we sequenced pools of 50 individuals that notably differ in the onset of adult foliage. Since the genetic basis of heteroblasty is well understood, we first searched for previously identified genes. Secondly, we searched for new candidate genes and also evaluated the copy number variation (CNVs) that may be involved in this process. We found marginally significant SNPs associated with previously described microRNAs, and interesting new non-coding RNAs. Disease resistance genes were also uncovered, probably as a consequence of indirectly selecting resistant trees, although a possible interaction between resistance and heteroblasty cannot be disregarded either. Our work shows the utility and limitations of XP-GWAS analysis to explore the genetic basis of Eucalyptus.

Molecular markers play an effective role in estimating the genetic similarity, variation, diversity, and population structure of different plants. Various factors associated with in vitro culture conditions may cause genetic variation in tissue cultured regenerants. The main goal of the present study was to determine the genetic uniformity of plantlets regenerated through in vitro culture of protocorms, shoot tips, and sodium alginate coated artificial seeds of Cymbidium aloifolium (L.) Sw. and its non-tissue cultured source mother plant using molecular markers such as Random Amplified Polymorphic Deoxyribonucleic acid (RAPD) and Inter Simple Sequence Repeats (ISSR). Ten RAPD and five ISSR primers were used to amplify the genomic DNA isolated from the in vivo plant and randomly selected micropropagated plants. Nine out of ten RAPD primers amplified a total of 256 loci while five ISSR primers amplified a total of 99 loci. The combined data of RAPD and ISSR markers showed low polymorphism. Among the tested plants, dendrograms constructed through UPGMA analysis of RAPD and ISSR markers revealed high genetic similarity between the mother plant and in vitro cultured regenerants. Among the different in vitro regenerants, protocorm-derived plants showed 91% genetic homogeneity to that of the mother plant. Thus, both molecular markers proved to be equally efficient for genetic fidelity studies in C. aloifolium. Hence, this research successfully assessed the genetic fidelity of in vitro cultured plants which could be useful in reintroducing true-to-type plants through plant tissue culture techniques.

Oilseed Brassicas are economically important crops, with Brassica napus, B. juncea, and B. rapa constituting prominent oilseed resources in the Indian subcontinent and across the world. Improving of oil yield, quality, and resistance to abiotic and biotic stresses in oilseed Brassicas warrants concerted efforts. Owing to quantitative nature, the genetic basis of these traits is complex, and can be significantly improved by incorporating the knowledge of precise genetic regulation of these traits. MicroRNAs (miRNAs) can act as attractive targets for crop improvement as they fine-tune gene expression by targeting genes negatively. Here we highlight the emerging evidences of miRNA-mediated regulation of genes controlling several development traits and stress-related traits in oilseed Brassicas. At least 13 miRNAs have so far been well elucidated in oilseed Brassicas using miRNA overexpression, mutation and target mimic approaches, in regulation of different agronomic traits. Further, at least 29 high-throughput small RNA profiling studies have proffered crucial miRNA-target pair candidates for further investigation. This knowledge so far remains unutilized in designing crop improvement programs in oilseed Brassicas. However, there are sufficient evidences to suggest that miRNAs as well as their target genes can be successfully employed in breeding as well as genome editing-mediated engineering of oilseed crops for improving their agricultural traits.

Within the subfamily Panicoideae, the Cenchrus genus which is distributed in both tropical and subtropical regions worldwide—is economically important in terms of their production levels. For milkshed areas, one of the most important pastures is kikuyu (Cenchrus clandestinus), which represents the basic forage used for feeding in a number of countries. In this study, the kikuyu grass (Cenchrus clandestinus) plastome was sequenced, assembled, and annotated to broaden the information and the set of available genomic data. One whole-genome shotgun (WGS) library was constructed using Nextera preparation kits and was sequenced in an Illumina MiSeq platform. In addition, the genomic organization and arrangement of genes as well as their phylogenetic relationship with other species of the family Poaceae were compared using 81 protein-coding genes. The present study characterized and annotated the complete plastome of kikuyu grass, Cenchrus clandestinus, as an informative contribution for future studies potentially investigating the evolution of plant genomes and, specifically, aiming to elucidate the phylogenetic relationships within the family Poaceae,Overall, the results indicate that the structure and organization are conserved compared with other references within the family Poaceae. Phylogenetic relationships confirmed the position of kikuyu within the Cenchrus genus, and they are consistent with previous results obtained for other species of the subfamily Panicoideae.

Glycolate Oxidase (GOX) is a key enzyme in photorespiration, a complex metabolic pathway in plants that affects photosynthesis efficiency and one of its most prominent products is hydrogen peroxide (H₂O₂). Photosynthetic pathways and H₂O₂ production can drastically differ between C3 and C4 plants which have distinctions in the photorespiration machinery. Such contrasts critically impact physiological processes in plants, such as development and stress responses. However, few studies bring light to evolutionary and structural aspects of the photorespiration components, and comparative analyses of gene families related to photorespiration in C3 and C4 plants are lacking. In the present study, we present the first genome-wide comparative analysis of the GOX gene family in plants, comparing relevant evolutionary and structural aspects of distinct GOX orthologs in plant families. The evolutionary relationships, gene structure, conserved motifs, promoter cis-element prediction, chromosome location, and interspecific collinearity were analyzed in order to gain a better understanding of the GOX gene family in plants. Family-dependent evolutionary and structural divergence were observed among distinct GOX genes, with higher gene conservation among Fabaceae family members. High sequence divergence found among Fabaceae and Poaceae GOX orthologs may impact functional divergence among these gene families. This comparative study provides a comprehensive picture of evolutionary and structural aspects of the GOX gene family in plants, as well as emphasizes the involvement of GOX orthologs in plant stress responses.

Alkaloids sourced from medicinally important plants have wide impact on human health and well-being. Ajmaline, a monoterpenoid indole alkaloid have divergent pharmacological applications and require large scale production. Rauvolfia serpentina (Apocynaceae) is an important source of ajmaline. Our present work encompasses computational phylogenetic approach towards understanding the ancestry and divergence of six of the most important enzymes of ajmaline biosynthetic pathway- Strictosidine synthase (STR1, EC 4.3.3.2), Strictosidine glucosidase (SGR1, EC 3.2.1.105), Polyneuridine aldehyde esterase (PNAE, EC 3.1.1.78), Vinorine synthase (ACT/VS, EC 2.3.1.160), Vinorine hydroxylase (CYP5437/VH, EC 1.14.13.75) and Acetylajmalan esterase (AAE, EC 3.1.1.80). The highly restricted distribution of the genes represents their conservative nature and other than the members of Apocynaceae the genes of Ajmaline biosynthesis were found to be distributed in Rubiaceae, Malvaceae, Solanaceae, Oleaceae, Gelsemiaceae, Fabaceae, Fragaceae etc. Identification of conserved domains of the enzymes were analysed based on the sequence homology of related plants. Amino acid sequences of STR1 showed highly variable N-terminal region in contrast to SGR1 and VH where the N-terminal sequence showed more conservation than C-terminal half. PNAE and VS showed high conservation throughout the sequence. Homology modeling and in silico structural analysis of the enzymes provide valuable insight for further structural and functional experimentation. The results reflected conservation of the core catalytic domain in all the six enzymes studied which is useful for structure-based evolution studies or for rational design and modulation of the enzyme's substrate specificity. Extensive literature survey resulted in identification of homologous genes of the aforementioned enzymes in Arabidopsis thaliana whose expressions at different stress conditions and developmental stages were investigated in publicly available microarray-based platform. The genes were found to be upregulated under different biotic and abiotic stresses. Also differential expression was detected at developmental stages.The data presented here will positively contribute towards deciphering the intricacies of reaction mechanism and steer bioengineering of alkaloid production to benefit mankind.

Maize is grown worldwide and much of the world depends on its production, which is lessened by insect and fungal pests. Many maize genes with the potential to improve pest resistance exist in non-functional forms in several inbreds but are functional in those that show resistance. One such gene, encoding a metallothionein protein, was located from a resistance locus of maize inbred GE440, which shows resistance to some Fusarium spp. pathogens. The identified gene, encoding ZmMT10, is disrupted in many maize inbreds, including the commonly used inbred B73. When introduced into maize callus, transformants often significantly increased resistance to F. proliferatum, but were often less effective against F. graminearum. Some transformed callus with the ZmMT10 gene also retarded growth of two classes of insect pests, fall armyworms and corn earworms. Recombinant ZmMT10 was purified from Escherichia coli. The purified protein was found to bind zinc, copper, and nickel and scavenged reactive oxygen species in vitro, which are possible mechanisms for its antiinsect and antifungal activities. In bioassays, the purified protein retarded growth of fall armyworms and corn earworms, but did not show activity against fungi, suggesting that the antifungal activity observed in callus tissue is dependent on the interaction with other plant factors. The inclusion of the identified gene in new plant varieties should increase resistance to both insects and fungi.

MADS-box is a family of transcription factors widely found in different kingdoms and essential for plant development. Understanding the evolution and functioning of such genes in developmental processes is essential to develop more adapted crops and guarantee food production. However, genome-wide analyses of MADS-box genes are poorly explored in tropical perennial species with complex phenological cycles and floral synapomorphic characters, such as Coffea sp. Moreover, Coffea arabica L. is unique in its genre being the only autogamous and tetraploid species, formed from the hybridization of the parental diploid genomes C. canephora and C. eugenioides, offering an opportunity to study recent ploidization and functionalization events. Here, we identified a total of 102 MADS-box unigenes in Coffea sp., being 81 unpublished. They were classified into Type I and II proteins (MIKC* and MIKC^C), 42 and 60 respectively, and categorized in the currently described subgroups. A chromosomal map revealed an irregular distribution and low positional variation of genes between homologous parental chromosomes. Gene structure analysis showed higher similarity for genes closely related, but a variable number of introns and its lengths between distant ones. Next, in order to provide functional insights, we determined the expression profiles of these genes in RNA-Seq libraries of different coffee tissues. Transcripts relative to Type II proteins presented a broader expression pattern than Type I, with low expression values and restricted to specific libraries. Thus, our work contributed to elucidating the evolutionary history of MADS-box genes in Rubiaceae, providing perspectives to functional studies and useful to direct breeding programs.