Biology subjects

Camargo, L. E. A.

Publications and source records attributed to Camargo, L. E. A..

3 recordsLinked to original sources

bioRxiv2025

Soil Determines Microbial Functionality and Genotype Guides Endophytic Recruitment to Adaptability in Sugarcane Systems

Soil properties critically shape sugarcane growth and its microbiome, yet their influence on gene expression remains unclear. We investigated the combined effects of soil type (clayey and sandy loam) and sugarcane genotype (IACSP-5503 and IACSP-6007) on microbiome composition and plant transcriptional profiles. Bacterial communities from soils and stalk tissues, as well as transcriptomes of 48-hour sprouted buds grown for 10 months, were analyzed. Results showed that IACSP-5503 (adapted to low-fertility soils) and IACSP-6007 (less adapted) recruited endophytic microbiota in a soil-genotype-dependent manner. In sandy loam, IACSP-5503 promoted diverse plant growth-promoting bacteria (PGPB) (including Burkholderia, Leifsonia, and Mycobacterium), associated with nitrogen fixation, hormone production, and stress tolerance, while IACSP-6007 displayed reduced PGPB diversity and transcriptomic signatures of nutrient deficiencies. Conversely, in clayey soil, IACSP-6007 recruited more PGPBs (such as Pseudomonas, Bacillus and Klebsiella) linked to nutrient acquisition and defense responses. Both genotypes exhibited enhanced expression of defense- and antioxidant-related genes in clayey soil, suggesting priming effects. Overall, our findings reveal soil-dependent, genotype-specific microbial recruitment strategies, including a potential "cry for help" mechanism in IACSP-5503, reflecting adaptation under nutrient-poor conditions. The combined 16S metataxonomic and transcriptome data offered insights into how soil and genotype shape microbial recruitment and transcriptional plasticity in sugarcane.

genetics↗

bioRxiv2025

Developing a model to implement marker-assisted selection for root-knot nematode resistance in common bean

Common bean (Phaseolus vulgaris L.) is a vital crop for direct human consumption, with essential nutrients and valuable protein that provides food security in developing countries. However, its cultivation faces significant threats from Meloidogyne incognita, a root-knot nematode (RKN), resulting in considerable yield loss. Developing crop resistance remains a key strategy for mitigating nematode infections. To investigate the genetic architecture of common bean responses to RKN (specifically, race 3 of M. incognita), we performed controlled crosses between the genotypes IAC-Tybata and Branquinho with contrasting resistance. The resulting segregating population (F2) of 333 individuals was genotyped using GBS (genotyping-by-sequencing). We used a phenotyping approach, already optimized in the lab, to collect trait data for a subset of 200 F2:3 families. Evaluations of egg mass (EM), root-galling index (GI), and root dry mass (RM) were conducted 30 days after RKN inoculation under greenhouse conditions, in a completely randomized design with ten replicates. Linkage and quantitative trait loci (QTL) mapping were performed, while functional mapping of associated regions facilitated identification of candidate genes. A linkage map encompassing 954 SNPs assigned to 11 linkage groups totaling 1,687 cM formed the basis for Interval Mapping (IM), Composite Interval Mapping (CIM), and Multiple Interval Mapping (MIM), revealing four major QTLs (on Pv03, Pv05, Pv08, and Pv10) and epistasis between QTL on Pv08 and on Pv10 associated with the GI trait. No significant QTL were identified for EM and RM. The model enabled calculation of genotypic values through marker-assisted selection (MAS). The high correlation between observed and predicted values (0.72) underscores the models significance. Candidate genes previously associated with nematode resistance were also identified within the QTL interval on chromosome Pv10. Our results will be valuable for future selection of varieties resistant to this important crop disease.

genetics↗

bioRxiv2023

Single-cell mutation rate of turnip crinkle virus (-)-strand replication intermediates

Viruses with single-stranded, positive-sense (+) RNA genomes incur high numbers of errors during replication, thereby creating diversified genome populations from which new, better adapted viral variants can emerge. However, a definitive error rate is known for a relatively few (+) RNA plant viruses, due to challenges to account for perturbations caused by natural selection and/or experimental set-ups. To address these challenges, we developed a new approach that exclusively profiled errors in the (-)-strand replication intermediates of turnip crinkle virus (TCV), in singly infected cells. A series of controls and safeguards were devised to ensure errors inherent to the experimental process were accounted for. This approach permitted the estimation of a TCV error rate of 8.47 X 10-5 substitution per nucleotide site per cell infection. Importantly, the characteristic error distribution pattern among the 50 copies of 2,363-base-pair cDNA fragments predicted that nearly all TCV (-) strands were products of one replication cycle per cell. Furthermore, some of the errors probably elevated error frequencies by lowering the fidelity of TCV RNA-dependent RNA polymerase, and/or permitting occasional re-replication of progeny genomes. In summary, by profiling errors in TCV (-)-strand intermediates incurred during replication in single cells, this study provided strong support for a stamping machine mode of replication employed by a (+) RNA virus. Author SummaryMost (+) RNA viruses introduce replication errors at relatively high frequencies. As a result, it is of vital importance for these viruses to purge lethal errors in a timely manner. TCV, a plant-infecting small (+) RNA virus, was proposed to encode a Bottleneck, Isolate, Amplify, Select (BIAS) mechanism that compel swift clearance of lethal errors by bottlenecking the number of replicating genome copies to one per cell. A crucial prediction of this BIAS model is that such bottlenecking also acts on progeny genome copies, preventing them from repeating replication in the cells of their own genesis. The current study tested this prediction by developing a carefully controlled, readily reproducible approach to profile errors and error distributions in (-)-stranded replication intermediates of TCV. We found that most of replication-generated (-) strands descended from the primary (+) strands through a single replication cycle. This finding adds fresh support to the BIAS model.

evolutionary biology↗