Machine learning approaches to predict the Plant-associated phenotype of Xanthomonas strains.

BACKGROUND: The genus Xanthomonas has long been considered to consist predominantly of plant pathogens, but over the last decade there has been an increasing number of reports on non-pathogenic and endophytic members. As Xanthomonas species are prevalent pathogens on a wide variety of important crops around the world, there is a need to distinguish between these plant-associated phenotypes. To date a large number of Xanthomonas genomes have been sequenced, which enables the application of machine learning (ML) approaches on the genome content to predict this phenotype. Until now such approaches to the pathogenomics of Xanthomonas strains have been hampered by the fragmentation of information regarding pathogenicity of individual strains over many studies. Unification of this information into a single resource was therefore considered to be an essential step. RESULTS: Mining of 39 papers considering both plant-associated phenotypes, allowed for a phenotypic classification of 578 Xanthomonas strains. For 65 plant-pathogenic and 53 non-pathogenic strains the corresponding genomes were available and de novo annotated for the presence of Pfam protein domains used as features to train and compare three ML classification algorithms; CART, Lasso and Random Forest. CONCLUSION: The literature resource in combination with recursive feature extraction used in the ML classification algorithms provided further insights into the virulence enabling factors, but also highlighted domains linked to traits not present in pathogenic strains.

Trichoderma-Bioenriched Vermicompost Induces Defense Response and Promotes Plant Growth in Thai Rice Variety "Chor Khing".

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".

Genome-Wide Association Analysis Identifies Candidate Loci for Callus Induction in Rice (Oryza sativa L.).

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.

Accelerating haploid induction rate and haploid validation through marker-assisted selection for qhir1 and qhir8 in maize.

Doubled haploid (DH) technology becomes more routinely applied in maize hybrid breeding. However, some issues in haploid induction and identification persist, requiring resolution to optimize DH production. Our objective was to implement simultaneous marker-assisted selection (MAS) for qhir1 (MTL/ZmPLA1/NLD) and qhir8 (ZmDMP) using TaqMan assay in F2 generation of four BHI306-derived tropical × temperate inducer families. We also aimed to assess their haploid induction rate (HIR) in the F3 generation as a phenotypic response to MAS. We highlighted remarkable increases in HIR of each inducer family. Genotypes carrying qhir1 and qhir8 exhibited 1 - 3-fold higher haploid frequency than those carrying only qhir1. Additionally, the qhir1 marker was employed for verifying putative haploid seedlings at 7 days after planting. Flow cytometric analysis served as the gold standard test to assess the accuracy of the R1-nj and the qhir1 marker. The qhir1 marker showed high accuracy and may be integrated in multiple haploid identifications at early seedling stage succeeding pre-haploid sorting via R1-nj marker.

Classification of the plant-associated lifestyle of Pseudomonas strains using genome properties and machine learning.

The rhizosphere, the region of soil surrounding roots of plants, is colonized by a unique population of Plant Growth Promoting Rhizobacteria (PGPR). Many important PGPR as well as plant pathogens belong to the genus Pseudomonas. There is, however, uncertainty on the divide between beneficial and pathogenic strains as previously thought to be signifying genomic features have limited power to separate these strains. Here we used the Genome properties (GP) common biological pathways annotation system and Machine Learning (ML) to establish the relationship between the genome wide GP composition and the plant-associated lifestyle of 91 Pseudomonas strains isolated from the rhizosphere and the phyllosphere representing both plant-associated phenotypes. GP enrichment analysis, Random Forest model fitting and feature selection revealed 28 discriminating features. A test set of 75 new strains confirmed the importance of the selected features for classification. The results suggest that GP annotations provide a promising computational tool to better classify the plant-associated lifestyle.

NG-Tax 2.0: A Semantic Framework for High-Throughput Amplicon Analysis.

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.