Characterization of FLOWERING LOCUS C 5 in Brassica rapa L.

Brassica rapa L., which includes Chinese cabbage, turnip, and pak choi, has more complex flowering time regulation than does Arabidopsis thaliana due to the presence of multiple paralogous flowering time genes. FLOWERING LOCUS C (FLC) is one of the key genes regulating the flowering time, and B. rapa has four FLC paralogs. BrFLC5 on the reference genome is deemed a pseudogene because of a mutation (from G to A) in the splice site of the third intron, but there are some accessions with a G nucleotide in the splice site. In this study, we genotyped 310 B. rapa accessions and found that 19 had homozygous and 81 had heterozygous putative functional BrFLC5 alleles. Accessions of turnip showed the highest proportion with a functional BrFLC5 allele. BrFLC5 acts as a floral repressor when overexpressed in A. thaliana. The BrFLC5 expression level varied in pre-vernalized plants, and this transcriptional variation was not associated with the G/A polymorphism in the third intron. Three accessions having a higher BrFLC5 expression in pre-vernalized plants had a 584-bp insertion in the promoter region. Many regions homologous to this 584-bp sequence are present in the B. rapa genome, and this 584-bp inserted region has tandem duplications of an AT-rich sequence in its central region. The possibility that a high expression of a functional BrFLC5 could contribute to producing premature bolting-resistant lines in B. rapa vegetables is discussed. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01405-0.

First report of bacterial panicle blight (BPB) in Rice caused by Burkholderia gladioli in Bangladesh.

Bacterial panicle blight (BPB) has become one of the most destructive diseases of rice worldwide and Burkholderia gladioli and B. glumae are two major pathogens causing BPB (1). This disease causes several types of damage, most importantly grain spotting, rot, and panicle blight, which can result in yield losses of 75% or more (1,3). In recent years, symptoms including sheath rot, grain spotting, grain rot, and panicle blight have been observed in both inbred and hybrid rice varieties. These symptoms resemble those of BPB and cause cultivar-dependent yield losses. (3) also reported the same symptoms for BPB. To confirm the cause of the disease, 21 rice panicles (Haridhan, a local variety) with typical BPB symptoms were collected from a farmer's field in the region of Mymensingh, Bangladesh during the rainy season in mid-October, 2021. Due to the severity of the outbreak, the panicles became dark brown and produced chaffy grains; nearly 100% of the rice panicles in that field were severely infected. To identify the causal pathogen(s), 1g of rice grains from 20 plants with typical BPB symptoms were surface-sterilized by immersing them in 70% ethanol for a few seconds followed by sodium hypochlorite solution (3%) for 1min. The grains were then rinsed with sterilized distilled water three times. Surface-sterilized grains were then ground with a mortar and pestle; 5mL of sterile distilled water was added during grinding. The extracted suspension (20µL) was then either streaked or spread onto the selective medium (S-PG) (2). Bacterial colonies showing purple color on the S-PG medium were selected and purified as candidate pathogens. For molecular characterization, species specific primers targeting gyrB gene were used to perform PCR and resulted in 479bp as reported by (4). To verify further, the PCR products of 16SF & 16SR were amplified and sequenced partially producing around 1400bp (1) and five 16SF partial sequences were deposited into NCBI GenBank (OP108276 to OP108280). 16S rDNA and gyrB revealed almost 99% homology with Burkholderia gladioli (KU851248.1, MZ425424.1) and B. gladioli (AB220893, CP033430) respectively using BLAST analysis. These purified bacterial isolates produced a diffusible light-yellow pigment on King's B medium indicating toxoflavin production (3). The candidate five bacterial isolates were then confirmed by inoculating 10ml suspension 108CFU/mL into the panicles and sheaths of BRRIdhan28 in net house condition as described previously (1). All of the bacterial isolates obtained from the spotted rice grains produced light brown lesions on the inoculated leaf sheath as well as spotting on the grain. To fulfill Koch's postulates, the bacteria were re-isolated from the symptomatic panicles and were confirmed as B. gladioli by analyzing the sequences of gyrB and 16s rDNA genes. Taken together, these results confirmed that B. gladioli is responsible for causing BPB in the rice grain samples that we collected. To our knowledge, this is the first report of BPB caused by B. gladioli in Bangladesh and further research is necessary to develop an effective disease management technique, or else the production of rice will be severely hampered.

Differences in the transcriptional immune response to Albugo candida between white rust resistant and susceptible cultivars in Brassica rapa L.

Albugo candida causing white rust disease decreases the yield of Brassica rapa vegetables greatly. Resistant and susceptible cultivars in B. rapa vegetables have different immune responses against A. candida inoculation, however, the mechanism of how host plants respond to A. candida is still unknown. Using RNA-sequencing, we identified differentially expressed genes (DEGs) between A. candida inoculated [48 and 72 h after inoculation (HAI)] and non-inoculated samples in resistant and susceptible cultivars of komatsuna (B. rapa var. perviridis). Functional DEGs differed between the resistant and susceptible cultivars in A. candida inoculated samples. Salicylic acid (SA) responsive genes tended to be changed in their expression levels by A. candida inoculation in both resistant and susceptible cultivars, but different genes were identified in the two cultivars. SA-dependent systemic acquired resistance (SAR) involving genes were upregulated following A. candida inoculation in the resistant cultivar. Particular genes categorized as SAR that changed expression levels overlapped between A. candida and Fusarium oxysporum f. sp. conglutinans inoculated samples in resistant cultivar, suggesting a role for SAR in defense response to both pathogens particularly in the effector-triggered immunity downstream pathway. These findings will be useful for understanding white rust resistance mechanisms in B. rapa.

Native Trichoderma Induced the Defense-Related Enzymes and Genes in Rice against Xanthomonas oryzae pv. oryzae (Xoo).

The application of Trichoderma is a form of biological control that has been effective in combating Xanthomonas oryzae pv. oryzae, the causative agent of the devastating disease known as bacterial blight of rice. In this present study, four strains of Trichoderma, viz., T. paraviridescens (BDISOF67), T. erinaceum (BDISOF91), T. asperellum (BDISOF08), and T. asperellum (BDISOF09), were collected from the rice rhizosphere and used to test their potentiality in reducing bacterial blight. The expression patterns of several core defense-related enzymes and genes related to SA and JA pathways were studied to explore the mechanism of induced resistance by those Trichoderma strains. The results primarily indicated that all Trichoderma were significantly efficient in reducing the lesion length of the leaf over rice check variety (IR24) through enhancing the expression of core defense-related enzymes, such as PAL, PPO, CAT, and POD activities by 4.27, 1.77, 3.53, and 1.57-fold, respectively, over control. Moreover, the results of qRT-PCR exhibited an upregulation of genes OsPR1, OsPR10, OsWRKY45, OsWRKY62, OsWRKY71, OsHI-LOX, and OsACS2 after 24 h of inoculation with all tested Trichoderma strains. However, in the case of RT-PCR, no major changes in OsPR1 and OsPR10 expression were observed in plants treated with different Trichoderma strains during different courses of time. Collectively, Trichoderma induced resistance in rice against X. oryzae pv. oryzae by triggering these core defense-related enzymes and genes associated with SA and JA pathways.

Tissue Culture in Ornamentals: Cultivation Factors, Propagation Techniques, and Its Application.

Ornamentals come in a variety of shapes, sizes, and colors to suit a wide range of climates, landscapes, and gardening needs. Compared to demand, a shortage of plant materials and diversity force the search for solutions for their constant acquisition and improvement to increase their commercial value, respectively. In vitro cultures are a suitable solution to meet expectations using callus culture, somatic embryogenesis, protoplast culture, and the organogenesis of protocorm-like bodies; many of these techniques are commercially practiced. Factors such as culture media, explants, carbohydrates, plant growth regulators, and light are associated with the success of in vitro propagation. Techniques, especially embryo rescue and somatic hybridization, are widely used to improve ornamentals. The development of synthetic seed allows season-independent seed production and preservation in the long term. Despite the advantages of propagation and the improvement of ornamentals, many barriers still need to be resolved. In contrast to propagation and crop developmental studies, there is also a high scope for molecular studies, especially epigenetic changes caused by plant tissue culture of ornamentals. In this review, we have accumulated and discussed an overall update on cultivation factors, propagation techniques in ornamental plant tissue culture, in vitro plant improvement techniques, and future perspectives.

Whole-Genome DNA Methylation Analysis in Brassica rapa subsp. perviridis in Response to Albugo candida Infection.

DNA methylation is an epigenetic mark associated with several mechanisms in plants including immunity mechanisms. However, little is known about the regulatory role of DNA methylation in the resistance response of Brassica species against fungal diseases. White rust, caused by the fungus Albugo candida, is one of the most widespread and destructive diseases of all the cultivated Brassica species, particularly Brassica rapa L. and Brassica juncea (L.) Czern and Coss. Here, we investigate whole-genome DNA methylation modifications of B. rapa subsp. perviridis in response to white rust. As a result, 233 and 275 differentially methylated regions (DMRs) in the susceptible cultivar "Misugi" and the resistant cultivar "Nanane" were identified, respectively. In both cultivars, more than half of the DMRs were associated with genes (DMR-genes). Gene expression analysis showed that 13 of these genes were also differentially expressed between control and infected samples. Gene ontology enrichment analysis of DMR genes revealed their involvement in various biological processes including defense mechanisms. DMRs were unevenly distributed around genes in susceptible and resistant cultivars. In "Misugi," DMRs tended to be located within genes, while in "Nanane," DMRs tended to be located up and downstream of the genes. However, CG DMRs were predominantly located within genes in both cultivars. Transposable elements also showed association with all three sequence contexts of DMRs but predominantly with CHG and CHH DMRs in both cultivars. Our findings indicate the occurrence of DNA methylation modifications in B. rapa in response to white rust infection and suggest a potential regulatory role of DNA methylation modification in defense mechanisms which could be exploited to improve disease resistance.

Development of a New DNA Marker for Fusarium Yellows Resistance in Brassica rapa Vegetables.

In vegetables of Brassica rapa L., Fusarium oxysporum f. sp. rapae (For) or F. oxysporum f. sp. conglutinans (Foc) cause Fusarium yellows. A resistance gene against Foc (FocBr1) has been identified, and deletion of this gene results in susceptibility (focbr1-1). In contrast, a resistance gene against For has not been identified. Inoculation tests showed that lines resistant to Foc were also resistant to For, and lines susceptible to Foc were susceptible to For. However, prediction of disease resistance by a dominant DNA marker on FocBr1 (Bra012688m) was not associated with disease resistance of For in some komatsuna lines using an inoculation test. QTL-seq using four F2 populations derived from For susceptible and resistant lines showed one causative locus on chromosome A03, which covers FocBr1. Comparison of the amino acid sequence of FocBr1 between susceptible and resistant alleles (FocBr1 and FocBo1) showed that six amino acid differences were specific to susceptible lines. The presence and absence of FocBr1 is consistent with For resistance in F2 populations. These results indicate that FocBr1 is essential for For resistance, and changed amino acid sequences result in susceptibility to For. This susceptible allele is termed focbr1-2, and a new DNA marker (focbr1-2m) for detection of the focbr1-2 allele was developed.

Plant Salinity Tolerance Conferred by Arbuscular Mycorrhizal Fungi and Associated Mechanisms: A Meta-Analysis.

Soil salinity often hinders plant productivity in both natural and agricultural settings. Arbuscular mycorrhizal fungal (AMF) symbionts can mediate plant stress responses by enhancing salinity tolerance, but less attention has been devoted to measuring these effects across plant-AMF studies. We performed a meta-analysis of published studies to determine how AMF symbionts influence plant responses under non-stressed vs. salt-stressed conditions. Compared to non-AMF plants, AMF plants had significantly higher shoot and root biomass (p < 0.0001) both under non-stressed conditions and in the presence of varying levels of NaCl salinity in soil, and the differences became more prominent as the salinity stress increased. Categorical analyses revealed that the accumulation of plant shoot and root biomass was influenced by various factors, such as the host life cycle and lifestyle, the fungal group, and the duration of the AMF and salinity treatments. More specifically, the effect of Funneliformis on plant shoot biomass was more prominent as the salinity level increased. Additionally, under stress, AMF increased shoot biomass more on plants that are dicots, plants that have nodulation capacity and plants that use the C3 plant photosynthetic pathway. When plants experienced short-term stress (<2 weeks), the effect of AMF was not apparent, but under longer-term stress (>4 weeks), AMF had a distinct effect on the plant response. For the first time, we observed significant phylogenetic signals in plants and mycorrhizal species in terms of their shoot biomass response to moderate levels of salinity stress, i.e., closely related plants had more similar responses, and closely related mycorrhizal species had similar effects than distantly related species. In contrast, the root biomass accumulation trait was related to fungal phylogeny only under non-stressed conditions and not under stressed conditions. Additionally, the influence of AMF on plant biomass was found to be unrelated to plant phylogeny. In line with the greater biomass accumulation in AMF plants, AMF improved the water status, photosynthetic efficiency and uptake of Ca and K in plants irrespective of salinity stress. The uptake of N and P was higher in AMF plants, and as the salinity increased, the trend showed a decline but had a clear upturn as the salinity stress increased to a high level. The activities of malondialdehyde (MDA), peroxidase (POD), and superoxide dismutase (SOD) as well as the proline content changed due to AMF treatment under salinity stress. The accumulation of proline and catalase (CAT) was observed only when plants experienced moderate salinity stress, but peroxidase (POD) and superoxide dismutase (SOD) were significantly increased in AMF plants irrespective of salinity stress. Taken together, arbuscular mycorrhizal fungi influenced plant growth and physiology, and their effects were more notable when their host plants experienced salinity stress and were influenced by plant and fungal traits.