Plant Gene最新文献

The transcriptomes of two distinct physiological moments of root dehydration condition were scrutinized in cowpea. The RD25 (first 25 min after root dehydration imposition) physiological data did not indicate significant alterations. For the other treatment, 150 min under root dehydration (RD150), all physiological data indicated that the studied cultivar was under stress. The physiological differences between RD25 and RD150 reverberated in the respective transcriptomes. The sets of in silico differentially expressed isoforms showed specificity for each treatment time. The comparison of T25 | UR [up-regulated transcripts in T25 (RD25 vs. Cont25)] vs. T150 | UR [up-regulated transcripts in T150 (RD150 vs. Cont150)] enriched GO terms (associated with abiotic stresses), despite certain similarities, showed us that they were associated with the respective physiological moments. Concerning gene families, a large portion of those present in the T25 | UR were associated with signaling processes; for T150 | UR, a miscellany of families (from transcription factors to nonenzymatic proteins) was observed. The plotting of transcriptomics data in the KEGG Pathway database indicated a change in the topology of activated metabolic modules in T25 | UR vs. T150 | UR. For the latter, it was observed that most activated modules were associated with specialized metabolism. C2H2 and BPC1 transcription factors (TFs) sites were enriched at T25 | UR and T150 | UR gene promoters, suggesting the importance of these TFs for cowpea response to root dehydration. Our work provides insights into specific molecular actors and pathways, enhancing our global understanding of cowpea stress response.

The traditional Basmati rices grown in north-western foothills of Himalayas in India are known world-wide for their exquisite aroma and exceptional eating and cooking qualities. These varieties are tall and suffer heavy losses due to their susceptibility to lodging as well as blast disease. In present study, we improved a popular traditional Basmati rice variety ‘Ranbir Basmati’ for semi-dwarfism and resistance to blast by incorporating the semi-dwarfing gene, sd1 and two blast resistance genes, Pi9 and Pi54 through marker-assisted backcross breeding. Combining marker-assisted background selection with stringent phenotypic selection for aroma and seed quality traits during backcrossing enabled faster recovery of recurrent parent genome and reconstitution of the genomic regions associated with Basmati quality traits in the gene pyramided lines. All pyramided lines were significantly short statured with a reduction of 23.46 to 40.26 cm in height, as compared to recurrent parent, with many of them exhibiting higher grain yield and superior quality attributes than Ranbir Basmati. The yield superiority of the pyramided lines primarily resulted from the improvement in panicle number and semi-dwarf stature conferred by sd1 gene. The gene pyramided lines showed complete resistance to five highly virulent blast races that collectively showed compatibility with 16 different resistance genes, suggesting the broad-spectrum resistance in these lines. The semi-dwarf, high yielding and blast resistant lines generated herein are potential candidates for release as cultivars for overcoming losses in Ranbir Basmati due to lodging and blast disease.

Rice is a major food crop and provides nutrition for half of the world's population. Rice production is majorly affected by drought at different developmental stages and accounted for annual yield loss depending on the intensity of drought. Hence, the need to study the molecular mechanism in a holistic manner behind drought tolerance is a prerequisite to mitigating this problem. Therefore, in the current study, the drought tolerance mechanism of rice plants was elucidated through a meta-analysis on the publically available transcriptomic datasets by integrating these datasets using a R package to remove the batch effects and applying machine learning approaches for prediction robustness and accuracy. Thus, the classifier model identified 128 essential genes through feature selection algorithms and classification methods on training datasets. The comprehensive study revealed that Naïve Bayes classification and correlation-based feature selection was robust in the prediction of essential genes. The accuracy and performance of the classification model was validated with the independent test dataset and the prediction accuracy of the classifier was 93% with ROC (0.972) and F-measures (0.927). Further, the biological significance of the identified genes in drought tolerance was assessed. The current analysis highlighted the regulatory roles of novel genes such as Os01g0844300, Os06g0246500, Os05g03733900, Os05g0550600 Os08g0442900, Os08g0104400, Os01g0256500, Os02g0259900 and Os05g0572700 in the enhancement of drought tolerance mechanisms. Thus the identified genes might be the potential targets for molecular breeding of drought-tolerant rice cultivars.

Herbicide and antibiotic tolerance genes serve as useful selectable markers for the development of transgenic plants expressing other transgenes. It may be desirable for regulatory or safety reasons to silence the herbicide tolerance trait after transformants have been selected. However, because the genes of interest and the marker gene are usually tightly linked, traditional segregation-based strategies for elimination of undesirable transgenes are usually unsuccessful. Here, we created Nicotiana tabacum plants that carry a single copy of a Cas9 gene, a nuclease in the clustered regularly interspaced short palindromic repeats (CRISPR) system, physically linked to the selectable marker gene bar for tolerance to the herbicide glufosinate (Basta, Liberty). Here, bar was targeted within the genome by introducing bar-specific single guide RNAs (sgRNAs) to the N. tabacum line in vitro, resulting in abolishment of the glufosinate-tolerance trait in mature plants. Sequence analysis of the bar gene revealed a frame-shift mutation at a sgRNA target site, confirming efficacy of the strategy.

In the era of frequently changing global climatic conditions (like temperature extremes, drought or flooding, soil and air quality or light levels) along with rapidly increasing global population, reducing agriculturally viable land area and soil microflora and soil quality degradation pose a serious threat on crop performance thus on global food security. The climatic variables significantly affect the species reproduction and performance in terms of crop produce. Plant biotechnology has progressed a lot starting from conventional breeding approaches to genetic engineering, genome editing and speed breeding, but so far little has been achieved to develop climate resilient/abiotic stress tolerant and high yielding crop varieties. The reasons may be the complex nature of stress factors, as well as the complexity of genetic regulatory networks. Therefore, the ‘plant gene regulatory network’ is crucial to understand the plant development and survival under various environmental insults.

Long-lived trees experience high risk of damage due to the various types of stresses over their lifespans. Epigenetic regulation is involved in gene regulation, genome integrity, and inhibition of exogenous genetic elements, which are functions important for long-term survival. To narrow down the candidate genes related to tree longevity among diverse epigenetic regulatory genes, it is necessary to identify epigenetic regulatory genes with increased copy number in long-lived tree species as compared to in short-lived annual and perennial herb species. In the present study, to find out the epigenetic regulatory genes with increased copy number in tree species as compared to in annual and perennial herb species, we conducted the systematic comparison of copy number variation in 121 gene families involved in various epigenetic regulatory pathways across 85 plant species with different lifespans using a genome database. Among these 121 gene families, the gene family encoding BRUSHY1/TONSOKU/MGOUN3 (BRU1/TSK/MGO3) and that encoding SILENCING DEFECTIVE 3 (SDE3) were found to exhibit significantly higher copy number of genes in tree species than in both perennial and annual herb species. BRU1/TSK/MGO3 is involved in chromatin modifications and plays an important role in the maintenance of meristems, genome integrity, and the inheritance of chromatin states. SDE3 is involved in RNA silencing and has an important role in antiviral defense through posttranscriptional gene silencing. The systematic comparison of copy number variation in diverse epigenetic regulatory gene families among plant species can find out epigenetic regulatory genes with increased copy number in long-lived tree species and enhance subsequent studies for understanding the relationship between epigenetic regulation and tree longevity.

MicroRNAs (miRNAs) are endogenous small non-coding RNAs, known as chief regulators for cellular growth and development in plants. Nicotiana rustica (N. rustica), also known as Aztec tobacco is the second most widely used lucrative crop for tobacco production across the globe. Since the miRNAs of Nicotiana rustica have never been reported, we employed a genome-wide computational approach which resulted in 101 potential candidates of miRNAs, belonging to 73 families, followed by stringent filtration criteria. Statistical analysis confirmed the occurrence of uracil as the dominant initial biased nucleotide base at 5 prime ends of mature miRNAs that may lead to a significant role in miRNA biogenesis and or miRNA mediated gene regulation. Due to unavailability of target sequences, the RNAseq data of N. rustica leaf, flower, stem, and root were retrieved, assembled de novo and concatenated into a clustered customized transcript dataset. The study validates miR160, miR393, miR397, miR403 & miR529 miRNAs and confirmed their targets through experimentally proven literature evidence. These miRNAs can modulate the biological role in transcription regulation, defense response, transporter activity, hormonal signaling and different protein kinase activities. Collectively, this study reports putative miRNAs and their role in Aztec tobacco development and stress response.

Under acidic soil and Aluminum (Al) stress conditions, the crop plants are facing several growth defects. Particularly significant decrease in root growth, nutrient uptake and low yield are the very common problems. Besides, several organic acid transporters are involved in Al sensing, transport and detoxification mechanisms. In this study, Al stress tolerance of mungbean plants was studied under different Al stress conditions. The results showed that the mungbean plants are severely affected by Al stress and released significant amount of malate in hydroponics media when compared with control plants. Based on this study and expression analysis of Al stress responsive genes, further, we developed ALMT1 overexpressors and ALMT1-RNAi transgenic plants of mungbean to analyse the acid soil tolerance. Later, these transgenic mungbean plants were challenged with different Al concentrations to check their stress responses. The ALMT1-RNAi lines showed almost no root growth variations in hydroponics media when compared to wild-type (WT) plants under normal growth conditions but displayed significant decrease in root length on exposure to Al. Further, when AtALMT1 was overexpressed, even in absence of Al ions, there was approximately 12% increase in length of primary roots when compared with WT. Malate efflux was almost doubled in the AtALMT1 overexpressed plant lines whereas KD lines showed around 36% drop in malate efflux under Al stress conditions. Therefore, based on these observations, we concluded that VrALMT1 has a significant role on Al stress tolerance responses in mungbean plants.

Banana is one of the most abundant crops produced annually in the Philippines. The presence of banana bunchy top virus (BBTV) leading to banana bunchy top disease is one of the factors hindering the continuous production of the fruit crop. The use of an appropriate and stable internal control gene as reference in validation of differentially-expressed genes in an organism is important. This study aims to identify appropriate internal control genes for differential gene expression analysis in Musa balbisiana and Musa acuminata specific for BBTV infection. RNA extraction, complementary DNA (cDNA) synthesis and RT-qPCR (quantitative real time polymerase chain reaction) of BBTV-resistant and BBTV-susceptible Musa genotypes were performed. The RT-qPCR quantification data were then subjected to analysis on RefFinder software and geomean ranking values were calculated along with the four statistical algorithms (delta C_q, Genorm, BestKeeper and NormFinder). Based on the comprehensive ranking values in the software, L2 gene was the most suitable internal control gene for the differential expression analysis of both BBTV-resistant and BBTV-susceptible banana accessions. The internal control gene is recommended for the validation of selected candidate resistance and host factor genes in response to BBTV infection.

Understanding the mechanisms responsible for plant tolerance under various abiotic stresses is linked to understanding heat shock proteins (Hsps). The Hsp20 subfamily is the main family of heat shock proteins, but little is known about this family in common bean (Phaseolus vulgaris L.), an important agricultural crop sensitive to temperature and salt stress. We identified 41 candidate common bean Hsp20 genes (PvHsp20). We mapped the PvHsp20 genes according to their chromosomal locations and found 49 duplications, 35 segmental and 14 tandem. Subsequent gene structure analysis identified regions of exons, introns, and conserved motifs. In the phylogenetic analysis, all PvHsp20 genes were grouped into 11 subfamilies, except for two genes that could not be classified. Synteny analysis revealed that Hsp20 genes from the common bean are highly related to soybean. Promoter analysis of PvHsp20 genes showed the presence of hormone-related, light-responsive and stress-responsive cis-regulatory elements. 8 PvHsp20 genes were under the regulation of 8 PvmiRNA genes. The in silico expression profile showed that PvHsp20 was differentially expressed. The gene expression of the PvHsp20-31, PvHsp20-27, PvHsp-2, and PvHsp20-39 genes in the roots of the Ispir genotype suggested that these genes might play a vital role in the salt tolerance mechanism. Our results provide new information, contribute to understanding PvHsp20 genes, and validate their role in mitigating the adverse effects triggered by abiotic stresses.