Biology subjects

Amorim, L.

Publications and source records attributed to Amorim, L..

4 recordsLinked to original sources

bioRxiv2025

Integrative Multi-Omics Analysis Reveals Stress-Specific Molecular Architectures in Soybean under Drought and Rust Infection

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, represents a major constraint to soybean cultivation, with yield losses approaching 90% in the absence of effective control strategies. When coupled with the increasing incidence of drought driven by climate change, the co-occurrence of these biotic and abiotic pressures imposes a complex challenge for crop resilience. In this study, we explored the molecular responses of soybean (Glycine max) to concurrent water limitation and ASR infection through an integrative analysis of transcriptomic and metabolomic datasets. To capture both linear and conditional relationships among molecular features, we employed Weighted Gene Co-expression Network Analysis (WGCNA) alongside Copula Graphical Models (CGMs). WGCNA identified 17 gene co-expression modules exhibiting significant correlations with 27 annotated metabolites. Among these, abscisic acid showed consistent associations with drought-responsive modules enriched in central metabolic pathways and transcription factors such as Dof and bHLH. In contrast, modules linked to fungal infection were correlated with dipeptides and D-galacturonic acid, implicating early defense signaling and cell wall remodeling. The CGM framework further revealed sparse, condition-specific networks of differentially expressed genes and metabolites directly associated with each stressor, including genes encoding a dirigent-like protein, pentatricopeptide repeat proteins, and a nucleoredoxin, as well as metabolites such as inosine, Epi-dihydrophaseic acid and 2-oxoadipic acid. Notably, no gene or metabolite was found to be directly responsive to both stresses, underscoring the modular and stress-specific architecture of soybean defense. Together, these results highlight a hierarchical regulatory structure and demonstrate the value of combining correlation-based and dependency-driven models to identify candidate targets for multi-stress resilience breeding.

plant biology↗

bioRxiv2025

Transcriptome Profiling of Resistance Genes Analogs in Soybean's Cross-Tolerance to Water Limitation and Rust Stress

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, is the most destructive foliar disease of soybean, with yield losses up to 90%. With climate change intensifying drought and expanding disease incidence, it is critical to understand how combined abiotic and biotic stresses influence plant defense. We investigated the transcriptomic response of a susceptible soybean cultivar to ASR infection under normal and water-limited conditions at four infection stages (12, 24, 72, and 192 hours after-inoculation). We observed a biphasic expression of defense-related genes, particularly resistance gene analogs (RGAs), with an early peak at 12 hours and a late resurgence at 192 hours. Combined stress induced a greater number of differentially expressed genes (DEGs) than rust alone, especially at early infection. Among the differentially expressed RGAs (RGADEs), over 64% belonged to the TM-LRR class, and NBS-LRR genes were the most enriched at known ASR resistance loci, particularly Rpp2. Water limitation strongly modulated gene expression at late stages, revealing stress-specific transcriptional reprogramming. These findings reveal cross-tolerance mechanisms in soybean, highlight the temporal dynamics of RGADEs under dual stress, and provide targets for developing cultivars with improved resilience to both rust and water scarcity.

plant biology↗

bioRxiv2024

Mating-compatibility genes employed as diagnostic markers to identify novel incursions of the myrtle rust pathogen Austropuccinia psidii

Austropuccinia psidii is the causal agent of myrtle rust in over 480 species within the family Myrtaceae. Lineages of A. psidii are structured by host in its native range, and some have success on new-encounter hosts. For example, the pandemic biotype has spread beyond South America, and proliferation of other lineages is an additional risk to biodiversity and industries. Efforts to manage A. psidii incursions, including lineage differentiation, relies on variable microsatellite markers. Testing these markers is time-consuming and complex, particularly on a large scale. We designed a novel diagnostic approach targeting the fungal mating-type HD (homeodomain) transcription factor locus to address these limitations. The HD locus (bW1/2-HD1 and bE1/2-HD2) is highly polymorphic, facilitating clear biological predictions about its inheritance from founding populations. To be considered the same lineage, all four HD alleles must be identical. Our lineage diagnostics relies on PCR amplification of the HD locus in different genotypes of A. psidii followed by amplicon sequencing using Oxford Nanopore Technologies (ONT) and comparative analysis. The lineage-specific assay was validated on four isolates with existing genomes, uncharacterized isolates, and directly from infected leaf material. We reconstructed HD alleles from amplicons and confirmed their sequence identity relative to their reference. Genealogies using HD alleles confirmed the variations at the HD loci among lineages/isolates. Our study establishes a robust diagnostic tool, for differentiating known lineages of A. psidii based biological predictions. This tool holds promise for detecting new pathogen incursions and can be refined for broader applications, including air-sample detection and mixed-isolate infections.

plant biology↗

bioRxiv2024

Complementary approaches to dissect late leaf rust resistance in an interspecific raspberry population

Over the last ten years, global raspberry production has increased by 47.89%, based on the red species (Rubus idaeus). However, the black raspberry species (Rubus occidentalis), although less consumed, is resistant to one of the most important diseases for the crop, the late leaf rust caused by Acculeastrum americanum fungus, to which the red ones are susceptible. In this context, genetic resistance is the most sustainable way to control the disease, mainly because there are no registered fungicides for late leaf rust in the crop in Brazil. Therefore, the aim was to understand the genetic architecture that controls resistance to late rust in raspberries. For that, we used an interspecific diversity panel between the cited above species, two different statistical approaches to associate the phenotypes to the markers (GWAS and copula graphical models), and two phenotyping methodologies from the first to the seventeenth day after inoculation (high-throughput phenotyping with a multispectral camera and traditional phenotyping by disease severity scores). Our findings indicate that a locus of higher effect possibly controls the resistance to late leaf rust, as both GWAS and the network suggested the same marker. Furthermore, a candidate defense-related gene cluster is close to this marker. Finally, the best stage to evaluate for disease severity is thirteen days after inoculation, confirmed by both traditional and high-throughput phenotyping. Although the network and GWAS indicated the same higher effect genomic region, the network identified other different regions complementing the genetic control comprehension.

genetics↗