Functional classification of rice flanking sequence tagged genes using MapMan terms and global understanding on metabolic and regulatory pathways affected by dxr mutant having defects in light response

Cytological, genetic and transcriptomic characterization of a cucumber albino mutant

Photosynthesis, a fundamental process for plant growth and development, is dependent on chloroplast formation and chlorophyll synthesis. Severe disruption of chloroplast structure results in albinism of higher plants. In the present study, we report a cucumber albino alc mutant that presented white cotyledons under normal light conditions and was unable to produce first true leaf. Meanwhile, alc mutant could grow creamy green cotyledons under dim light conditions but died after exposure to normal light irradiation. No chlorophyll and carotenoid were detected in the alc mutant grown under normal light conditions. Using transmission electron microscopy, impaired chloroplasts were observed in this mutant. The genetic analysis indicated that the albino phenotype was recessively controlled by a single locus. Comparative transcriptomic analysis between the alc mutant and wild type revealed that genes involved in chlorophyll metabolism and the methylerythritol 4-phosphate pathway were affected in the alc mutant. In addition, three genes involved in chloroplast development, including two FtsH genes and one PPR gene, were found to have negligible expression in this mutant. The quality of RNA sequencing results was further confirmed by real-time quantitative PCR analysis. We also examined 12 homologous genes from alc mutant in other plant species, but no genetic variation in the coding sequences of these genes was found between alc mutant and wild type. Taken together, we characterized a cucumber albino mutant with albinism phenotype caused by chloroplast development deficiency and this mutant can pave way for future studies on plastid development.

Adaptation insights from comparative transcriptome analysis of two Opisthopappus species in the Taihang mountains

Opisthopappus is a major wild source of Asteraceae with resistance to cold and drought. Two species of this genus (Opisthopappus taihangensis and O. longilobus) have been employed as model systems to address the evolutionary history of perennial herb biomes in the Taihang Mountains of China. However, further studies on the adaptive divergence processes of these two species are currently impeded by the lack of genomic resources. To elucidate the molecular mechanisms involved, a comparative analysis of these two species was conducted. Among the identified transcription factors, the bHLH members were most prevalent, which exhibited significantly different expression levels in the terpenoid metabolic pathway. O. longilobus showed higher level of expression than did O. taihangensis in terms of terpenes biosynthesis and metabolism, particularly monoterpenoids and diterpenoids. Analyses of the positive selection genes (PSGs) identified from O. taihangensis and O. longilobus revealed that 1203 genes were related to adaptative divergence, which were under rapid evolution and/or have signs of positive selection. Differential expressions of PSG occurred primarily in the mitochondrial electron transport, starch degradation, secondary metabolism, as well as nucleotide synthesis and S-metabolism pathway processes. Several PSGs were obviously differentially expressed in terpenes biosynthesis that might result in the fragrances divergence between O. longilobus and O. taihangensis, which would provide insights into adaptation of the two species to different environments that characterized by sub-humid warm temperate and temperate continental monsoon climates. The comparative analysis for these two species in Opisthopappus not only revealed how the divergence occurred from molecular perspective, but also provided novel insights into how differential adaptations occurred in Taihang Mountains.

Transcriptome profiling of developing leaf and shoot apices to reveal the molecular mechanism and co-expression genes responsible for the wheat heading date

Background

Wheat is one of the most widely planted crops worldwide. The heading date is important for wheat environmental adaptability, as it not only controls flowering time but also determines the yield component in terms of grain number per spike.

Results

In this research, homozygous genotypes with early and late heading dates derived from backcrossed progeny were selected to conduct RNA-Seq analysis at the double ridge stage (W2.0) and androgynous primordium differentiation stage (W3.5) of the leaf and apical meristem, respectively. In total, 18,352 differentially expressed genes (DEGs) were identified, many of which are strongly associated with wheat heading date genes. Gene Ontology (GO) enrichment analysis revealed that carbohydrate metabolism, trehalose metabolic process, photosynthesis, and light reaction are closely related to the flowering time regulation pathway. Based on MapMan metabolic analysis, the DEGs are mainly involved in the light reaction, hormone signaling, lipid metabolism, secondary metabolism, and nucleotide synthesis. In addition, 1,225 DEGs were annotated to 45 transcription factor gene families, including LFY, SBP, and MADS-box transcription factors closely related to flowering time. Weighted gene co-expression network analysis (WGCNA) showed that 16, 336, 446, and 124 DEGs have biological connections with Vrn1-5 A, Vrn3-7B, Ppd-1D, and WSOC1, respectively. Furthermore, TraesCS2D02G181400 encodes a MADS-MIKC transcription factor and is co-expressed with Vrn1-5 A, which indicates that this gene may be related to flowering time.

Conclusions

RNA-Seq analysis provided transcriptome data for the wheat heading date at key flower development stages of double ridge (W2.0) and androgynous primordium differentiation (W3.5). Based on the DEGs identified, co-expression networks of key flowering time genes in Vrn1-5 A, Vrn3-7B, WSOC1, and Ppd-1D were established. Moreover, we discovered a potential candidate flowering time gene, TraesCS2D02G181400. Taken together, these results serve as a foundation for further study on the regulatory mechanism of the wheat heading date.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07797-7.

A web-based tool for the prediction of rice transcription factor function

Transcription factors (TFs) are an important class of regulatory molecules. Despite their importance, only a small number of genes encoding TFs have been characterized in Oryza sativa (rice), often because gene duplication and functional redundancy complicate their analysis. To address this challenge, we developed a web-based tool called the Rice Transcription Factor Phylogenomics Database (RTFDB) and demonstrate its application for predicting TF function. The RTFDB hosts transcriptome and co-expression analyses. Sources include high-throughput data from oligonucleotide microarray (Affymetrix and Agilent) as well as RNA-Seq-based expression profiles. We used the RTFDB to identify tissue-specific and stress-related gene expression. Subsequently, 273 genes preferentially expressed in specific tissues or organs, 455 genes showing a differential expression pattern in response to 4 abiotic stresses, 179 genes responsive to infection of various pathogens and 512 genes showing differential accumulation in response to various hormone treatments were identified through the meta-expression analysis. Pairwise Pearson correlation coefficient analysis between paralogous genes in a phylogenetic tree was used to assess their expression collinearity and thereby provides a hint on their genetic redundancy. Integrating transcriptome with the gene evolutionary information reveals the possible functional redundancy or dominance played by paralog genes in a highly duplicated genome such as rice. With this method, we estimated a predominant role for 83.3% (65/78) of the TF or transcriptional regulator genes that had been characterized via loss-of-function studies. In this regard, the proposed method is applicable for functional studies of other plant species with annotated genome.

Physiological and transcriptome analysis reveal molecular mechanism in Salvia miltiorrhiza leaves of near-isogenic male fertile lines and male sterile lines

Background

Our previous study finds that male sterility in Salvia miltiorrhiza could result in stunted growth and reduced biomass, but their molecular mechanisms have not yet been revealed. In this article, we investigate the underlying mechanism of male sterility and its impact on plant growth and metabolic yield by using physiological analysis and mRNA sequencing (RNA-Seq).

Results

In this study, transcriptomic and physiological analysis were performed to identify the mechanism of male sterility in mutants and its impact on plant growth and metabolic yield. Through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, it is found that the pathways are mainly enriched in processes including organ development, primary metabolic process and secondary metabolic process. Physiological analysis show that the chloroplast structure of male sterile mutants of S. miltiorrhiza is abnormally developed, which could result in decrease in leaf gas exchange (A, E and g_s), chlorophyll fluorescence (F_v, F_m and F_v/F_m), and the chlorophyll content. Expression level of 7 differentially expressed genes involved in photosynthesis-related pathways is downregulated in male sterile lines of S. miltiorrhiza, which could explain the corresponding phenotypic changes in chlorophyll fluorescence, chlorophyll content and leaf gas exchange. Transcriptomic analysis establishes the role of disproportionating enzyme 1 (DPE1) as catalyzing the degradation of starch, and the role of sucrose synthase 3 (SUS3) and cytosolic invertase 2 (CINV2) as catalyzing the degradation of sucrose in the S. miltiorrhiza mutants. The results also confirm that phenylalanine ammonialyase (PAL) is involved in the biosynthesis of rosmarinic acid and salvianolic acid B, and flavone synthase (FLS) is an important enzyme catalyzing steps of flavonoid biosynthesis.

Conclusions

Our results from the physiological and transcriptome analysis reveal underlying mechanism of plant growth and metabolic yield in male sterile mutants, and provide insight into the crop yield of S. miltiorrhiza.

Laser-induced breakdown spectroscopy assisted chemometric methods for rice geographic origin classification

The problems of adulteration and mislabeling are very common in the food industry. Laser-induced breakdown spectroscopy (LIBS) coupled with chemometric methods has many intrinsic advantages on adulteration analysis of various materials. In this work, several chemometric algorithms, i.e., principal component analysis (PCA), decision tree (DT), random forest (RF), partial least squares discriminant analysis (PLS-DA), linear discriminant analysis (LDA), and support vector machine (SVM), were carried out assisted by LIBS technology to study the classification performances on rice geographic origins. A series of samples, including 20 kinds of rice samples from different geographic origins, was detected using LIBS with no pretreatment processes. For data analysis, PCA was employed to reduce the input variables, and to reduce the collinearity of LIBS spectral results as well. The results showed the classification accuracies of the mentioned chemometric algorithms of DT, RF, PLS-DA, LDA, and SVM with 89 input variables of 86.80%, 96.30%, 96.80%, 98.60%, and 99.20%, respectively. At the same time, the operation times of these algorithms were 3.81 s, 54.64 s, 3.63 s, 2.09 s, and 531.01 s, respectively. On the other hand, 30 principal components of input variables were also tested under the same conditions. The classification accuracies for the above algorithms were 81.60%, 98.00%, 95.70%, 98.40%, and 99.20%, respectively. The operation times were 2.01 s, 4.88 s, 3.67 s, 0.36 s, and 308.55 s, respectively. In addition, the five-fold cross-validation classification accuracies with 30 input variables for DT, RF, PLS-DA, LDA, and SVM were 83.75%, 97.95%, 94.75%, 98.35%, and 99.25%, respectively. As a result, LDA was demonstrated to be the best and most efficient tool for rice geographic origin classification assisted by LIBS with high accuracy and analytical speed, which has great potential for rapid identification of adulterated products in agriculture without use of any chemical reagent.

Comparative Expression Analysis of Rice and Arabidopsis Peroxiredoxin Genes Suggests Conserved or Diversified Roles Between the Two Species and Leads to the Identification of Tandemly Duplicated Rice Peroxiredoxin Genes Differentially Expressed in Seeds

BACKGROUND

Peroxiredoxins (PRXs) have recently been identified as plant antioxidants. Completion of various genome sequencing projects has provided genome-wide information about PRX genes in major plant species. Two of these -- Oryza sativa (rice) and Arabidopsis -- each have 10 PRX members. Although significant progress has been made in understanding their biological roles in Arabidopsis, those functions in rice, a model crop plant, have not been well studied.

RESULTS

We performed a comparative expression analysis of rice and Arabidopsis PRXs. Our phylogenetic analysis revealed that one subgroup contains three rice and three Arabidopsis Type-II PRXs that are expressed ubiquitously. This suggests that they are involved in housekeeping functions to process reactive oxygen species (ROS). Within the second subgroup, expression of Os1-CysPrxA (LOC_Os7g44430) and AtOs1-CysPrx is conserved in seeds while Os1-CysPrxB (LOC_Os7g44440) shows a root-preferential pattern of expression. We used transgenic plants expressing the GUS reporter gene under the control of the promoters of these two tandem duplicates to confirm their meta-expression patterns. Our GUS expression data from developing seeds and those that were germinating indicated that Os1-CysPrxB is involved in root development, as initiated from the embryo, while Os1-CysPrxA has roles in regulating endosperm development near the aleurone layer. For the third and fourth subgroups, the rice PRXs are more likely to show leaf/shoot-preferential expression, while those from Arabidopsis are significantly expressed in the flowers and seeds in addition to the leaf/shoot. To determine the biological meaning of those expression patterns that were dominantly identified in rice PRXs, we analyzed three rice genes showing leaf/shoot-preferential expression in a mutant of the light-responsive 1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr) gene and found that two of them were significantly down-regulated in the mutant.

CONCLUSION

A global expression analysis of the PRX family in rice identified tandem duplicates, Os1-CysPrxA and Os1-CysPrxB, in the 1-CysPrx subgroup that are differentially expressed in developing seeds and germinating seeds. Analysis of the cis-acting regulatory elements (CREs) revealed unique CREs responsible for embryo and root or endosperm-preferential expression. In addition, the presence of leaf/shoot-preferential PRXs in rice suggests that they are required in that crop because those plants must tolerate a higher light intensity in their normal growth environment when compared with that of Arabidopsis. Downregulation of two PRXs in the dxr mutant causing an albino phenotype, implying that those genes have roles in processing ROS produced during photosynthesis. Network analysis of four PRXs allowed us to model regulatory pathways that explain the underlying protein interaction network. This will be a useful hypothetical model for further study.

Crosstalk between diurnal rhythm and water stress reveals an altered primary carbon flux into soluble sugars in drought-treated rice leaves

Plants retain rhythmic physiological responses when adapting to environmental challenges. However, possible integrations between drought conditions and those responses have not received much focus, especially regarding crop plants, and the relationship between abiotic stress and the diurnal cycle is generally not considered. Therefore, we conducted a genome-wide analysis to identify genes showing both diurnal regulation and water-deficiency response in rice (Oryza sativa). Among the 712 drought-responsive genes primary identified, 56.6% are diurnally expressed while 47.6% of the 761 that are down-regulated by drought are also diurnal. Using the β-glucuronidase reporter system and qRT-PCR analyses, we validated expression patterns of two candidate genes, thereby supporting the reliability of our transcriptome data. MapMan analysis indicated that diurnal genes up-regulated by drought are closely associated with the starch-sucrose pathway while those that are down-regulated are involved in photosynthesis. We then confirmed that starch-sucrose contents and chlorophyll fluorescence are altered in a diurnal manner under drought stress, suggesting these metabolic diurnal alterations as a novel indicator to evaluate the drought response in rice leaves. We constructed a functional gene network associated with the starch-sucrose KEGG metabolic pathway for further functional studies, and also developed a regulatory pathway model that includes OsbZIP23 transcription factor.

OsPhyB-Mediating Novel Regulatory Pathway for Drought Tolerance in Rice Root Identified by a Global RNA-Seq Transcriptome Analysis of Rice Genes in Response to Water Deficiencies

Water deficiencies are one of the most serious challenges to crop productivity. To improve our understanding of soil moisture stress, we performed RNA-Seq analysis using roots from 4-week-old rice seedlings grown in soil that had been subjected to drought conditions for 2-3 d. In all, 1,098 genes were up-regulated in response to soil moisture stress for 3 d, which causes severe damage in root development after recovery, unlikely that of 2 d. Comparison with previous transcriptome data produced in drought condition indicated that more than 68% of our candidate genes were not previously identified, emphasizing the novelty of our transcriptome analysis for drought response in soil condition. We then validated the expression patterns of two candidate genes using a promoter-GUS reporter system in planta and monitored the stress response with novel molecular markers. An integrating omics tool, MapMan analysis, indicated that RING box E3 ligases in the ubiquitin-proteasome pathways are significantly stimulated by induced drought. We also analyzed the functions of 66 candidate genes that have been functionally investigated previously, suggesting the primary roles of our candidate genes in resistance or tolerance relating traits including drought tolerance (29 genes) through literature searches besides diverse regulatory roles of our candidate genes for morphological traits (15 genes) or physiological traits (22 genes). Of these, we used a T-DNA insertional mutant of rice phytochrome B (OsPhyB) that negatively regulates a plant's degree of tolerance to water deficiencies through the control of total leaf area and stomatal density based on previous finding. Unlike previous result, we found that OsPhyB represses the activity of ascorbate peroxidase and catalase mediating reactive oxygen species (ROS) processing machinery required for drought tolerance of roots in soil condition, suggesting the potential significance of remaining uncharacterized candidate genes for manipulating drought tolerance in rice.

Comparative Transcriptome Reveals Benzenoid Biosynthesis Regulation as Inducer of Floral Scent in the Woody Plant Prunus mume

Mei (Prunus mume) is a peculiar woody ornamental plant famous for its inviting fragrance in winter. However, in this valuable plant, the mechanism behind floral volatile development remains poorly defined. Therefore, to explore the floral scent formation, a comparative transcriptome was conducted in order to identify the global transcripts specifying flower buds and blooming flowers of P. mume. Differentially expressed genes were identified between the two different stages showing great discrepancy in floral volatile production. Moreover, according to the expression specificity among the organs (stem, root, fruit, leaf), we summarized one gene cluster regulating the benzenoid floral scent. Significant gene changes were observed in accordance with the formation of benzenoid, thus pointing the pivotal roles of genes as well as cytochrome-P450s and short chain dehydrogenases in the benzenoid biosynthetic process. Further, transcription factors like EMISSION OF BENZENOID I and ODORANT I performed the same expression pattern suggesting key roles in the management of the downstream genes. Taken together, these data provide potential novel anchors for the benzenoid pathway, and the insight for the floral scent induction and regulation mechanism in woody plants.

A Systematic View of the MLO Family in Rice Suggests Their Novel Roles in Morphological Development, Diurnal Responses, the Light-Signaling Pathway, and Various Stress Responses

The Mildew resistance Locus O (MLO) family is unique to plants, containing genes that were initially identified as a susceptibility factor to powdery mildew pathogens. However, little is known about the roles and functional diversity of this family in rice, a model crop plant. The rice genome has 12 potential MLO family members. To achieve systematic functional assignments, we performed a phylogenomic analysis by integrating meta-expression data obtained from public sources of microarray data and real-time expression data into a phylogenic tree. Subsequently, we identified 12 MLO genes with various tissue-preferred patterns, including leaf, root, pollen, and ubiquitous expression. This suggested their functional diversity for morphological agronomic traits. We also used these integrated transcriptome data within a phylogenetic context to estimate the functional redundancy or specificity among OsMLO family members. Here, OsMLO12 showed preferential expression in mature pollen; OsMLO4, in the root tips; OsMLO10, throughout the roots except at the tips; and OsMLO8, expression preferential to the leaves and trinucleate pollen. Of particular interest to us was the diurnal expression of OsMLO1, OsMLO3, and OsMLO8, which indicated that they are potentially significant in responses to environmental changes. In osdxr mutants that show defects in the light response, OsMLO1, OsMLO3, OsMLO8, and four calmodulin genes were down-regulated. This finding provides insight into the novel functions of MLO proteins associated with the light-responsive methylerythritol 4-phosphate pathway. In addition, abiotic stress meta-expression data and real-time expression analysis implied that four and five MLO genes in rice are associated with responses to heat and cold stress, respectively. Upregulation of OsMLO3 by Magnaporthe oryzae infection further suggested that this gene participates in the response to pathogens. Our analysis has produced fundamental information that will enhance future studies of the diverse developmental or physiological phenomena mediated by the MLO family in this model plant system.