NG-Tax 2.0 is a semantic framework for FAIR high-throughput analysis and classification of marker gene amplicon sequences including bacterial and archaeal 16S ribosomal RNA (rRNA), eukaryotic 18S rRNA and ribosomal intergenic transcribed spacer sequences. It can directly use single or merged reads, paired-end reads and unmerged paired-end reads from long range fragments as input to generate de novo amplicon sequence variants (ASV). Using the RDF data model, ASV’s can be automatically stored in a graph database as objects that link ASV sequences with the full data-wise and element-wise provenance, thereby achieving the level of interoperability required to utilize such data to its full potential. The graph database can be directly queried, allowing for comparative analyses of over thousands of samples and is connected with an interactive Rshiny toolbox for analysis and visualization of (meta) data. Additionally, NG-Tax 2.0 exports an extended BIOM 1.0 (JSON) file as starting point for further analyses by other means. The extended BIOM file contains new attribute types to include information about the command arguments used, the sequences of the ASVs formed, classification confidence scores and is backwards compatible. The performance of NG-Tax 2.0 was compared with DADA2, using the plugin in the QIIME 2 analysis pipeline. Fourteen 16S rRNA gene amplicon mock community samples were obtained from the literature and evaluated. Precision of NG-Tax 2.0 was significantly higher with an average of 0.95 vs 0.58 for QIIME2-DADA2 while recall was comparable with an average of 0.85 and 0.77, respectively. NG-Tax 2.0 is written in Java. The code, the ontology, a Galaxy platform implementation, the analysis toolbox, tutorials and example SPARQL queries are freely available at http://wurssb.gitlab.io/ngtax under the MIT License.

Vermicompost (VC) produced by African nightcrawler earthworms (Eudrilus eugeniae) is a natural fertilizer with a rich microbial community. Trichoderma asperelloides PSU-P1 is an effective antagonistic microorganism with multifaceted activity mechanisms. This research aimed to develop Trichoderma-bioenriched vermicompost (TBVC) to promote plant growth and induce the defense response in the Thai rice variety “Chor Khing”. T. asperelloides PSU-P1 was tested against Rhizoctonia solani, the pathogen of sheath blight disease, using a dual-culture assay. The results showed that T. asperelloides PSU-P1 effectively inhibited R. solani in vitro growth by 70.48%. The TBVC was prepared by adding a conidial suspension (10⁸ conidia/mL) to vermicompost. The viability of Trichoderma persisted in the vermicompost for 6 months and ranged from 1.2 to 2.8 × 10⁷ CFU/mL. Vermicompost water extracts significantly enhanced seed germination, root length, and shoot length compared to a control group (p < 0.05). Plants that received the TBVC displayed significantly longer shoot and root lengths and higher total chlorophyll content than control plants (p < 0.05). The TBVC induced defense response by increasing the enzyme activity of peroxidase (POD) and polyphenol oxidase (PPO) in comparison with control plants. Rice grown in the TBVC had a significantly reduced incidence of sheath blight caused by R. solani in comparison with control rice (p < 0.05). Furthermore, the fungal community of rice plants was analyzed via the high-throughput next-generation sequencing of the internal transcribed spacer (ITS). The fungal community in the TBVC had greater alpha diversity than the community in the VC. Phylum Ascomycota was dominant in both samples, and a heat map showed that Trichoderma was more prevalent in the TBVC than in the VC. Our results indicate that the enrichment of VC with Trichoderma increases growth, enhances the defense response, and reduces the incidence of sheath blight disease in the Thai rice variety “Chor Khing”.

Nitrogen use efficiency (NUE) is important for the growth and development of rice and is significant in reducing the costs of rice production. OsNRT1.1b is involved in nitrate assimilation, and the alleles at position 21,759,092 on chromosome 10 clearly separate indica (Pathum Thani 1 (PTT1) and Homcholasit (HCS)) and japonica (Azucena and Leum Pua (LP)) rice varieties. Rice morphological and physiological traits were collected at three nitrogen levels (N0 = 0 kg ha⁻¹, N7 = 43.75 kg ha⁻¹, and N14 = 87.5 kg ha⁻¹). Leaf and tiller numbers in PTT1 and HCS at N7 and N14 were two to three times higher than those at N0. At harvest, the biomass yield in PTT1 was the highest, while the total grain number in HCS was the maximum. The leaf widths and total chlorophyll contents (SPAD units) of Azucena and LP increased with nitrogen application as well as photosynthetic pigment parameters; for example, plant senescence reflectance indices (PSRIs), structure-insensitive pigment indices (SIPIs), and modified chlorophyll absorption ratio indices (MCARIs) were highly related in the japonica varieties. PTT1 and HCS, both carrying the A allele at OsNRT1.1b, had better NUE than Azucena and LP with the G allele. HCS, overall, had better NUE than PTT1. The translation to grain yield of assimilates was remarkable in PTT1 and HCS compared with Azucena and LP. In addition, HCS converted biomass for a 75% higher yield than PTT1. The ability of HCS to produce high yields was achieved even at N7 nitrogen fertilization, manifesting efficient use of nitrogen.

Callus induction (CI) is a critical trait for transforming desirable genes in plants. A genome-wide association study (GWAS) analysis was conducted on the rice germplasms of 110 Indica rice accessions, in which three tissue culture media, B5, MS, and N6, were used for the CI of those rice panels’ mature seeds. Seven quantitative trait loci (QTLs) on rice chromosomes 2, 6, 7, and 11 affected the CI percentage in the three media. For the B5 medium, one QTL (qCI–B5–Chr6) was identified on rice chromosome 6; for the MS medium, two QTLs were identified on rice chromosomes 2 and 6 (qCI–MS–Chr2 and qCI–MS–Chr6, respectively); for the N6 medium, four QTLs were identified on rice chromosomes 6, 7, and 11 (qCI–N6–Chr6.1 and qCI–N6–Chr6.2, qCI–N6–Chr7, and qCI–N6–Chr11, respectively). Fifty-five genes were identified within the haplotype blocks corresponding to these QTLs, thirty-one of which showed haplotypes associated with different CI percentages in those media. qCI–B5–Chr6 was located in the same region as qCI–N6–Chr6.2, and the Caleosin-related family protein was also identified in this region. Analysis of the gene-based haplotype revealed the association of this gene with different CI percentages in both B5 and N6 media, suggesting that the gene may play a critical role in the CI mechanism. Moreover, several genes, including those that encode the beta-tubulin protein, zinc finger protein, RNP–1 domain-containing protein, and lysophosphatidic acid acyltransferase, were associated with different CI percentages in the N6 medium. The results of this study provide insights into the potential QTLs and candidate genes for callus induction in rice that contribute to our understanding of the physiological and biochemical processes involved in callus formation, which is an essential tool in the molecular breeding of rice.

Bacterial wilt, caused by Ralstonia solanacearum, is a major constraint to tomato production globally. To uncover resistance loci and develop efficient molecular tools for breeding, we conducted disease phenotyping over two growing seasons, which revealed consistent variation in resistance and moderate broad-sense heritability (H² = 0.22–0.28), suggesting a genetic basis. A genome-wide association study (GWAS) was performed on a diverse panel of 267 tomato accessions, evaluated against two R. solanacearum strains. A major resistance locus was identified on chromosome 12, with the strongest association observed at SNP S12_2992992, located within a gene encoding a leucine-rich repeat (LRR) receptor-like protein. Haplotype analysis indicated that the resistance-associated allele is relatively rare (~13.5%) in the population, underscoring its potential value in breeding programs. Functional validation in an F₂ population derived from a cross between the susceptible ‘Seedathip6’ and the resistant ‘Hawaii 7996’ confirmed that the TT genotype at S12_2992992 was significantly associated with enhanced resistance. A Kompetitive Allele Specific PCR (KASP) marker was developed for this SNP, facilitating cost-effective and high-throughput selection. Collectively, these findings establish S12_2992992 as a robust and functionally informative marker, offering a valuable tool for accelerating bacterial wilt resistance breeding in tomato through marker-assisted selection.

Tomatoes (Solanum lycopersicum L.) represent a valuable crop species cultivated on a global scale, with Thailand playing a notable role in Southeast Asia’s agricultural landscape. However, a comprehensive understanding of the genetic underpinnings, population dynamics, and genetic correlations among tomato cultivars within Thailand remains relatively nascent. This study conducted an extensive analysis of 283 tomato accessions sourced from Thailand’s largest germplasm repository, employing approximately 2.4 million single-nucleotide polymorphisms (SNPs) obtained through whole-genome sequencing (WGS). The results of the genetic diversity assessment demonstrate a consistent delineation of groups, as indicated by UPGMA clustering, revealing five distinct clusters, while population structure analysis unveils twelve subpopulations. These findings underscore the limited genetic reservoir within Thai tomato germplasm, providing valuable insights for germplasm management strategies and offering a promising avenue for the refinement of breeding programs aimed at enhancing tomato genetics.