Drought-responsive genes in tomato: meta-analysis of gene expression using machine learning.

Plants have diverse molecular mechanisms to protect themselves from biotic and abiotic stressors and adapt to changing environments. To uncover the genetic potential of plants, it is crucial to understand how they adapt to adverse conditions by analyzing their genomic data. We analyzed RNA-Seq data from different tomato genotypes, tissue types, and drought durations. We used a time series scale to identify early and late drought-responsive gene modules and applied a machine learning method to identify the best responsive genes to drought. We demonstrated six candidate genes of tomato viz. Fasciclin-like arabinogalactan protein 2 (FLA2), Amino acid transporter family protein (ASCT), Arginine decarboxylase 1 (ADC1), Protein NRT1/PTR family 7.3 (NPF7.3), BAG family molecular chaperone regulator 5 (BAG5) and Dicer-like 2b (DCL2b) were responsive to drought. We constructed gene association networks to identify their potential interactors and found them drought-responsive. The identified candidate genes can help to explore the adaptation of tomato plants to drought. Furthermore, these candidate genes can have far-reaching implications for molecular breeding and genome editing in tomatoes, providing insights into the molecular mechanisms that underlie drought adaptation. This research underscores the importance of the genetic basis of plant adaptation, particularly in changing climates and growing populations.

Effects of halotolerant rhizobacteria on rice seedlings under salinity stress.

Avirulent halotolerant plant growth-promoting rhizobacteria (HPGPR) located on the roots' periphery can reduce abiotic stressors (such as salinity and drought), enhance plant productivity. Salinity poses a significant challenge for growing agricultural products, like rice, in the coastal regions. It is crucial to enhance production because of limited arable land and the high growth rate of the population. This study targeted to identify HPGPR from legume root nodules and assessed their effects on rice plants experiencing salt stress in coastal regions of Bangladesh. Based on the culture morphology, biochemical, salt, pH, and temperature tolerance traits, sixteen bacteria were isolated from the root nodules of leguminous plants (Common bean, Yardlong bean, Dhaincha, and Shameplant). All the bacterial strains can tolerate 3 % salt concentration, and capable to survive at the highest 45 °C temperature and pH 11 (without isolate 1). Three preeminent bacteria, Agrobacterium tumefaciens (B1), Bacillus subtilis (B2), and Lysinibacillus fusiformis (B3) were specified through morpho-biochemical and molecular (16S rRNA gene sequence) exploration for inoculation. To assess the plant growth-promoting activities, germination tests are applied where bacterial inoculation increased germination in saline and non-saline conditions. Control group (C) showed 89.47 % and bacterial treated groups (C + B1, C + B2, and C + B3) 95 %, 90 %, and 75 % germination after 2 days of inoculation. In (1 % NaCl) saline condition control group revealed 40 % whereas three groups with bacteria showed 60 %, 40 %, and 70 % germination after 3 days, which increased 70 %, 90 %, 85 %, and 95 % respectively after 4 days of inoculation. The HPGPR significantly improved plant development metrics such as root length, shoot length, fresh and arid biomass yield, chlorophyll content, etc. Our results suggest that the salt-resistant bacteria (Halotolerant) have a great potential role in recuperating plant growth and would be cost-effective as a bio-inoculant in saline conditions to be used as a prospective bio-fertilizer for rice production. These findings indicate that the HPGPR has a substantially promising function in reviving plant development in an eco-friendly manner.

Glucosinolates and Biotic Stress Tolerance in Brassicaceae with Emphasis on Cabbage: A Review.

Glucosinolates (GSLs) and GSL-associated genes are receiving increasing attention from molecular biologists due to their multifunctional properties. GSLs are secondary metabolites considered to be highly active in most Brassica species. Their importance has motivated the discovery and functional analysis of the GSLs and GSL hydrolysis products involved in disease development in brassicas and other plants. Comprehensive knowledge of the GSL content of Brassica species and the molecular details of GSL-related genes will help elucidate the molecular control of this plant defense system. This report provides an overview of the current status of knowledge on GSLs, GSL biosynthesis, as well as hydrolysis related genes, and GSL hydrolysis products that regulate fungal, bacterial, and insect resistance in cabbage and other brassicas.

Development of PCR-Based Molecular Marker for Detection of Xanthomonas campestris pv. campestris Race 6, the Causative Agent of Black Rot of Brassicas.

Xanthomonas campestris pv. campestris (Xcc), the pathogen of black rot which is the most destructive disease of Brassica vegetables throughout the world. Here, we reported two novel sequence-characterized amplified region (SCAR) markers (i.e., XccR6-60 and XccR6-67) for the detection of Xcc race 6 via re-alignment of the complete genome sequences of Xcc races/strains/pathovars. The specificity of SCAR primer sets was verified by mean of PCR amplification using the genomic DNA template of Xcc races/strains/pathovars and two other plant infecting bacterial strains. The PCR result revealed that the XccR6-60 and XccR6-67 primer sets amplified 692-bp and 917-bp DNA fragments, respectively, specifically from race 6, while no visible amplification was detected in other samples. In addition, the SCAR primers were highly sensitive and can detect from a very low concentration of genomic DNA of Xcc race 6. However, the complete genome sequence of Xcc race 6 is not yet publicly available. Therefore, the cloning and sequencing of XccR6-60 and XccR6-67 fragments from race 6 provide more evidence of the specificity of these markers. These results indicated that the newly developed SCAR markers can successfully, effectively and rapidly detect Xcc race 6 from other Xcc races/strains/pathovars as well as other plant pathogenic bacteria. This is the first report for race-specific molecular markers for Xcc race 6.

Glucosinolate Profile and Glucosinolate Biosynthesis and Breakdown Gene Expression Manifested by Black Rot Disease Infection in Cabbage.

Cabbage (Brassica oleracea var. capitata) is an economically important crop in the family Brassicaceae. Black rot disease is a top ranked cabbage disease, which is caused by Xanthomonas campestris pv. campestris (Xcc) and may reduce 50% crop loss. Therefore, we need a clear understanding of black rot disease resistance for sustainable disease management. The secondary metabolites, like Glucosinolate (GSL) presents in Brassica species, which plays a potential role in the defense mechanism against pathogens. However, there is little known about GSL-regulated resistance mechanisms and GSL biosynthesis and the breakdown related gene expression after black rot disease infection in cabbage. In this study, relative expression of 43 biosynthetic and breakdown related GSLs were estimated in the black rot resistant and susceptible cabbage lines after Xcc inoculation. Ten different types of GSL from both aliphatic and indolic groups were identified in the contrasting cabbage lines by HPLC analysis, which included six aliphatic and four indolic compounds. In the resistant line, nine genes (MYB122-Bol026204, MYB34-Bol017062, AOP2-Bo9g006240, ST5c-Bol030757, CYP81F1-Bol017376, CYP81F2-Bol012237, CYP81F4-Bol032712, CYP81F4-Bol032714 and PEN2-Bol030092) showed consistent expression patterns. Pearson's correlation coefficient showed positive and significant association between aliphatic GSL compounds and expression values of ST5c-Bol030757 and AOP2-Bo9g006240 genes as well as between indolic GSL compounds and the expression of MYB34-Bol017062, MYB122-Bol026204, CYP81F2-Bol012237, CYP81F4-Bol032712 and CYP81F4-Bol032714 genes. This study helps in understanding the role of GSL biosynthesis and breakdown related genes for resistance against black rot pathogen in cabbage, which could be further confirmed through functional characterization either by overexpression or knock-out mutation.

Whole-Genome Re-Alignment Facilitates Development of Specific Molecular Markers for Races 1 and 4 of Xanthomonas campestris pv. campestris, the Cause of Black Rot Disease in Brassica oleracea.

Black rot, caused by Xanthomonas campestris pv. campestris (Xcc), is a seed borne disease of Brassicaceae. Eleven pathogenic races have been identified based on the phenotype interaction pattern of differential brassica cultivars inoculated with different strains. Race 1 and 4 are the two most frequent races found in Brassica oleracea crops. In this study, a PCR molecular diagnostic tool was developed for the identification of Xcc races 1 and 4 of this pathogen. Whole genomic sequences of races 1, 3, 4 and 9 and sequences of three other Xanthomonas pathovars/species (X. campestris pv. incanae (Xci), X. campestris pv. raphani (Xcr) and X.euvesicatoria (Xev) were aligned to identify variable regions among races. To develop specific markers for races 1 and 4, primers were developed from a region where sequences were dissimilar in other races. Sequence-characterized amplified regions (SCAR) and insertion or deletion of bases (InDel) were used to develop each specific set of primers. The specificity of the selected primers was confirmed by PCR tests using genomic DNA of seven different Xcc races, two strains of X. campestris pathovars and other species of bacteria. Bacterial samples of the races 1 and 4 isolates were collected from artificially inoculated cabbage leaves to conduct bio-PCR. Bio-PCR successfully detected the two Xcc isolates. By using our race-specific markers, a potential race 1 strain from the existing Korean Xcc collection was identified. The Xcc race 1 and 4-specific markers developed in this study are novel and can potentially be used for rapid detection of Xcc races through PCR.