Plant Gene最新文献

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 Here, we identified a total of 102 MADS-box unigenes in Coffea sp., being 81 unpublished.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.

Field and molecular experiments were conducted between May and August 2021 at the research farm of the Department of Botany, University of Ibadan and International Institute of Tropical Agriculture, Ibadan respectively. Morphological and molecular variability in 40 tomato accessions were investigated in this study. Five accessions from local markets in Ibadan, two varieties from seed companies, three varieties from Benue State and Oyo State, and thirty accessions from the National Center for Genetic Resources and Biotechnology (NACGRAB) were evaluated. The experiment was arranged in a randomised complete block design (RCBD) with three replicates. Significant (p < 0.05) variation was observed for days to germination, hypocotyl colour, primary leaf length, primary leaf width, number of leaves, plant height, number of leaves under first inflorescence, number of inflorescence, days to first fruiting, foliage density and internode length (cm). The cumulative values for the first three components (74.80%) accounted for variation among the 40 accessions in the principal component analysis. All yield related characters correlated positively with both the number of leaves and plant height. The study revealed that NGB/05081, NGB/00714, NGB/05075, NGB/00696, NGB/00735b and Hausa (Dugbe) accessions performed the best in growth and yield characters, while NGB/00735b and NGB/00759 were early maturing accessions. The Tp 124 and Tp 121 primers were highly polymorphic and had high gene diversities. Sixteen tomato accessions were amplified for marker genes nodZ-A and nodZ-B. Five of these accessions showed high growth, while seven produced high yield, implying positive influence on the improvement of these accessions. However, the nifh marker gave no amplification.

In this study, we investigated the leaf treatment effects of a novel trace elements calcium-based fluid mixture with a supposed biostimulant action on Solanum lycopersicum L. cv. Micro-Tom. Seedlings were grown on standard peat substrate and treated with two different products: a calcium-based fluid mixture and a common calcium fertilizer, CaCl₂. Both treatments were compared to an untreated control. We first investigated the effects of treatments on fruit yield and dry matter production in greenhouse-grown tomato. These effects were then assessed in leaves by gene expression profiling of 60 genes involved in different biological pathways and functional categories, and by ionomic analysis. Leaf treatment on tomato with the calcium-based fluid mixture allowed the highest fruit yield per plant (6.17 fruits plant⁻¹) and above-ground dry matter (13.99 g plant⁻¹) to be obtained. Also, 4 genes related to the nutrient transporter category, NCX, NRAMP3, SI BOR2, and CHLM, were upregulated in plants treated with the novel product. CRK, a gene related to the calcium-dependent protein kinases (CDPK), was upregulated in plants treated with the novel product whereas SODCC.1, a gene related to the superoxide dismutase family, was downregulated in the same plants. A substantial reduction of elemental contents was observed for CaCl₂-treated plants, while the novel Ca-based mixture increased the leaf mineral content of Zn (+61%) and Mn (+65%). These results highlighted the biostimulant activity of the novel product resulting in changes in fruit yield and dry matter production, gene expression, and ionome profiles of tomato leaves.

Hydroxycitric acid (HCA) is one of the proven natural antiobesity agents enriched in the fruits of Garcinia gummi-gutta (L.) Roxb. (Family: Clusiaceae). The present research work was carried out to evaluate the genetic variability among 35 candidate plus trees (CPTs) using HCA estimated through HPLC and start codon targeted (SCoT) molecular markers. The association analysis between phenotypic and genotypic traits was also conducted. The selected CPTs showed an average HCA content of 29.11 mg/g and Gar 17 had the highest (48.32 mg/g) followed by Gar 6 (45.48 mg/g). SCoT marker analysis revealed that 19 primers, out of 30 yielded a total of 151 bands with 66.89% polymorphic bands. Principal coordinate analysis (PCoA) organized the CPTs into the four quadrants of a scatterplot irrespective of HCA content. Dendrogram based on neighbour joining method proved its reproducibility by its bootstrapping values, and it has three clusters. STRUCTURE analysis opened the probability of two assumed subpopulations within the selected individuals. Association analysis based on a general linear model (GLM) agreed with the strong association of SCoT 5d allele with HCA content, which also supports the promising nature of Gar 6 as per previous findings. Analysis based on HCA and SCoT markers was effective in tracing out the genetic variabilities among the CPTs and the marker-trait association. The findings are the first in G. gummi-gutta, best of our knowledge.

Aquaporins (AQPs), which are an essential type of membrane proteins, play roles in plant growth and stress tolerance by acting as channels for water homeostasis and nutrient uptake. These membrane proteins are important for the survival of different plant species under changing climates. However, the functional involvement of AQPs in jute is still unexplored. We conducted a genome-wide investigation into two cultivated jute species and identified 33 CoAQP and 31 CcAQP genes in the Corchorus olitorius and C. capsularis genomes, respectively. In both species, AQPs were classified into five phylogenetic subfamilies (PIPs, NIPS, SIPs, TIPs, and XIPs). Functional prediction of conserved NPA motif, ar/R selectivity filters, and Froger's position identified diversity in substrate specificity within the subfamilies of Jute AQPs. Investigation on putative cis-regulatory motifs revealed an enrichment of light, defense and stress responsiveness cis-element in the promoter regions. RNA-seq analysis showed the expression pattern of Co and CcAQPs under abiotic stresses and in organ development. Among the AQP genes, three (NIP6–1, SIP1–1, TIP4–1) were highly expressed in fiber cells, three (PIP1–1, PIP1–2, PIP2–1) in stem and leaf, and one (NIP7–1) in flower of both species. There were differential levels of expression patterns in response to salinity, drought, and waterlogging. In both species, two genes (XIP-1-1 and PIP1–3) showed a decreased level of expression with the increased level of waterlogging. Six AQPs (PIP1–1, PIP1–3, PIP2–1, NIP1–2 along with CcSIP1–2 and CoSIP2–1) showed upregulation under salt stress. On the other hand, two genes, PIP1–3 and PIP2–1, were overexpressed under drought stress. Results from this study provided detailed insights into the complexities of jute AQPs and their biological functions in adaptation, which can be useful for future varietal development programs.

As a popular berry fruit rich in vitamin C, kiwifruit (family Actinidiaceae) is economically important. RNA interference (RNAi) is one of the main mechanisms of plant resistance to viruses, and small RNAs also mediate growth, development, and resistance to stress and disease. The RNAi pathway involves three main types of proteins: Dicer-like (DCL), RNA-dependent RNA polymerase (RDR), and Argonaute (AGO). To gain a deeper understanding of small RNA formation and stress resistance mechanisms in kiwifruit, a comparative analysis of RNAi core gene regulatory families in Actinidiaceae was conducted. A total of 49, 20, and 111 RDR, DCL, and AGO genes were obtained from Actinidiaceae and initially corrected seven of them due to potential misannotation. These genes could be distinguished into four RDR, four DCL, and seven AGO protein classes and showed abundant subcellular localization and structural variation characteristics. Furthermore, the potential evolution of these RNAi-related genes was preliminarily characterized and clarified their unique expression profiles in tissues (expression patterns in different tissues and potential differences in gene expression between species) and in response to stresses (pathogen induction and storage). In conclusion, in this study, a systematic identification and comparative analysis of the RNAi core protein regulator family of Actinidiaceae was performed, and expression analysis was conducted on Actidia chinensis. These results are expected to reveal the evolutionary trends of the RNAi core protein family of Actinidiaceae and provide a reference for the evolutionary process of natural differences in sRNA formation and stress resistance in kiwifruit.

Early responsive to dehydration 6 (ERD6)-like is one of the least studied subfamily in plants. Initial evidences based on couple of genes suggest that members of this family are tonoplastic and export glucose to cytosol from tonoplast. However, no information is available on ERD6-like genes in agricultural crops except limited information on Brassica species. In this study, we identified 8, 12, 6 and 7 ERD6-like genes, respectively in Cicer arietinum, Arachis hypogea, Oryza sativa and Glycine max. These and A. thaliana genes were divided into five subgroups based on phylogenetic analysis of proteins. C. arietinum genes were characterized in detail and new nomenclature to these genes was proposed to overcome ambiguities in names of genes. Intron/exon numbers did not vary much among the genes, however, gene/mRNA/coding region/ untranslated regions and proteins showed considerable length variations. Though isoforms were reported for two genes, isoforms of only CaERD6-like 6.3 could be confirmed experimentally. While motifs and transmembrane domains varied among the ERD6-like proteins, all belonged to glucose transport subfamily suggesting those to be glucose transporters. Transcription of genes varied among four chickpea organs with higher expression in some organs and lower in others. Under cold-stress, three genes over-expressed in leaves and roots whereas four genes down-regulated in leaves and two in roots. This is the first report on genome wide identification of ERD6-like genes in four crops of agricultural importance and detailed characterization and expression analysis in chickpea organs under normal growth conditions and cold-stress.

Excess metals in the soil are a known type of abiotic stress and many plant species have evolved specific metal resistance mechanisms to cope and avoid or reduce toxicity symptoms. Studies on P. tremuloides genetic response to nickel are limited. This present study aims to 1) Assess gene expression dynamics in P. tremuloides seedlings treated with varying concentrations of nickel salts and, 2) Compare gene expression profiles among the different treatment groups. Trembling aspen (Populus tremuloides) seedlings were treated with varying concentrations of nickel nitrates (150 mg Ni / 1 kg of dry soil, 800 mg / kg, and 1, 600 mg / kg). The whole genome expression was analyzed using Illumina sequencing. Overall, 52,987 genes were identified from which 36,770 genes were selected as differently expressed. In general, there was an increase in number of differentially expressed genes as the nickel concentration increased when compared to water. The number of downregulated (439–600) and upregulated (123–560) genes increases with the nickel concentration increase. A detailed analysis suggested that the 800 mg / kg nickel concentration is the threshold at which an early abiotic stress response may be triggered as seen by the highly upregulated LEA protein and two calcium binding proteins when compared to water. For the highest nickel concentration, 7-deoxyloganetin glucosyltransferase was highly upregulated while an auxin response factor, Flavonol 3-sulfotransferase, and a predicted ABC transporter family protein were downregulated. The heatmap showed that the genes were grouped into six clusters based on the changes in expression as nickel concentration increased. The cluster of genes that had increased gene expression with increasing nickel concentration also had multiple enriched Gene ontology (GO) terms related to heavy metal and abiotic stress including metal ion transport, antioxidant activity, photosynthesis, and ribosomal activity. GO terms that decreased in expression with increasing nickel concentrations include ATP and ADP binding, protein kinase activity, integral component of membrane, protein phosphorylation and transmembrane transport.

The endoplasmic reticulum (ER) is an organelle responsible for regulating protein synthesis in plants. High salinity can lead to the accumulation of misfolded proteins, resulting in an ER stress response mechanism known as the unfolded protein response (UPR). Failure of the UPR to reverse the effect of protein misfolding will activate programmed cell death (PCD). Metacaspase genes are known regulate PCD in plants. This study aims to provide a comprehensive analysis of the expression patterns of type II rice metacaspase (OsMC) genes in response to ER and salinity stress in rice leaf. Among five type II metacaspases in the rice genome, OsMC4, OsMC5, and OsMC8 expressions were found to be upregulated during treatment with tunicamycin (ER stress) and sodium chloride, NaCl (salinity stress). A construct of taqRFP::OsMC4, controlled by the CaMV35S promoter, was generated and transformed into rice calli. The transgenic rice calli overexpressing taqRFP::OsMC4 demonstrated significant changes in the expression of the ER stress-marker genes, protein disulfide isomerase (OsPDI), and binding immunoglobulin protein (OsBiP). The results from this analysis provide preliminary evidence that at least one of the type II metacaspases, OsMC4, is be able to reduce ER and salinity stresses in rice. Further functional analysis of OsMC genes in ER and salinity stress tolerance could be carried out in transgenic rice overexpressing OsMCs in the future to improve stress tolerance.

Simple summary

Oryza sativa, commonly known as rice, is one of the most consumed crops in the world. In response to multiple biotic and abiotic factors, a series of endoplasmic reticulum (ER) stress response regulators are activated. There is evidence that high salinity triggers ER stress in plants. This study aims to determine the level of gene expression among type II metacaspases in rice in response to ER and salinity stress and to assess how they may be linked to PCD in rice calli. Three metacaspase genes, OsMC4, OsMC5, and OsMC8, have been observed to have significant expression post-treatment with tunicamycin in rice leaf. Overexpression of taqRFP::OsMC4 in rice calli significantly reduces the expression level of the stress markers, OsBiP and OsPDI, indicating that the stress level is relatively lower in the transgenic calli compared to the wild-type calli. Therefore, overexpression of taqRFP::OsMC4 in rice may increase rice tolerance towards ER and salinity stress. These expression analyses of the OsMCs family provide valuable information for further functional studies on the biological roles of OsMCs in ER and salinity stress responses.

Most plant metabolites are biosynthesized via organelles, including peroxisome. From the mutant analyses, Arabidopsis ATP-binding cassette (ABC) transporter ABCD1 is reported to be implicated in the peroxisomal import of β-oxidation substrates, which are biosynthetic intermediates for central and specialized metabolites. However, little was explored about ABCD1 in plants except for AtABCD1 and two barley homologs, HvABCD1 and 2. The present study investigated the expression profiles of ABCD1 genes of petunia and tobacco that produce various metabolites, including volatile benzenoid/phenylpropanoids (VBPs) and ubiquinone. PhABCD1 expression was ubiquitous and at particularly high levels (2.2- to 2.8-fold compared to roots) in leaves, limbs, and tubes. NsABCD1 was expressed in roots, stems, leaves, sepals, and flowers; specifically, a relatively high expression level (3.2-fold compared to roots) was observed in sepals. Yeast extract and methyl jasmonate induced the expression of the NtABCD1 gene significantly (1.3- and 2.5-fold, respectively) in N. tabacum BY-2 cells. These results suggest that the expression of ABCD1 would be related to the biosynthesis of metabolites beneficial for plant environmental adaptation in petunia and tobacco. The current study provides new insights into the mechanism of metabolite biosynthesis and ABC transporter function in Solanaceae plants.