PhytoGenix
Genomic Resistance & Breeding Intelligence Platform

PhytoGenix
Genomic Disease Resistance Engine

Empower plant breeders and agronomists to identify disease-resistant crop varieties faster, simulate virtual crosses before planting, and eliminate agricultural yield losses using genomic intelligence.

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R-Gene & Disease Knowledge

Explore characterized NLR receptors, RLKs, and loss-of-susceptibility alleles across all major crop-pathogen systems.

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Virtual Cross Simulator

Simulate Mendelian recombination for $F_1, F_2, F_3$, and Backcross populations ($N=200$) to predict progeny resistance distribution.

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Multi-Trait & Genome Maps

Balance disease resistance vs. harvest yield to avoid yield drag, with interactive chromosome ideograms and outbreak simulations.

Supported Agricultural Crops & Pathogens (Curated from resistance_genes.csv)
🥔 Potato (Solanum tuberosum) 🌾 Rice (Oryza sativa) 🌾 Wheat (Triticum aestivum) 🌾 Barley (Hordeum vulgare) 🍅 Tomato (Solanum lycopersicum) 🫑 Pepper (Capsicum annuum) 🌱 Soybean (Glycine max) 🌱 Arabidopsis (Arabidopsis thaliana)

PhytoGenix User Guide & Benefits

A complete guide on how to use PhytoGenix and how it accelerates plant breeding while preventing crop losses.

How to Use This App (Step-by-Step)

Step 1 Select Target Crop

Click on any crop from the top bar (e.g. Potato, Rice, Wheat, Tomato) to instantly load its genome map, target pathogens, and pre-characterized R-genes.

Step 2 Explore R-Gene Catalog

Browse the R-Gene & Disease Catalog (Column #1) to understand characterized resistance genes, efficacy rates, and effector mechanisms.

Step 3 Screen & Triage Varieties

Navigate to Screening & GEBV Table. View predicted resistance scores, filter for Elite Resistant (≥80%) lines, and inspect alleles.

Step 4 Simulate Virtual Crosses

Open Virtual Cross Simulator, pick Parent A × Parent B, pick generation ($F_1, F_2, F_3, BC_1$), and simulate offspring resistance segregation.

Step 5 Multi-Trait Optimization

Check the Multi-Trait Pareto Optimizer radar and scatter charts to ensure selected varieties maintain high harvest yields and drought tolerance.

Step 6 Ingest & Export Trial Sheets

Upload laboratory CSV/VCF files via Ingest Genotypes and click Export Screening Sheet for field trials.

How Users Benefit from PhytoGenix

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Accelerate Breeding Cycles by 3 to 5 Years

Traditional plant breeding requires seasons of manual inoculation and field phenotyping. PhytoGenix predicts genomic resistance values in seconds directly from genotype marker matrices.

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Reduce Crop & Economic Losses by up to 80%

Identify and discard vulnerable accessions before large-scale commercial planting, protecting farmers from catastrophic outbreaks like Late Blight (P. infestans), Rice Blast (M. oryzae), and Ug99 Stem Rust (P. graminis).

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Eliminate Yield Drag (No Trade-off Penalty)

Breeders often sacrifice yield when introducing wild resistance genes. The built-in Pareto Optimizer helps you choose lines on the optimal frontier balancing disease immunity with harvest yield.

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Zero-Waste Digital Crossing Simulator

Test hundreds of parent mating combinations digitally. Only invest greenhouse resources in crossing blocks that show a high probability of double-homozygous ($R/R$) stacked progeny.

Potato (Solanum tuberosum)

Tetraploid/diploid staple tuber crop vulnerable to oomycete blights, viruses, and cyst nematodes.

Characterized Pathogen & Resistance Gene Registry

Curated directly from verified plant genomics databases and resistance_genes.csv.

6
Evaluated Varieties
3
Elite Resistant Lines (≥80%)
78%
Average Panel GEBV Index
Climate & Disease Outbreak Stress Simulator
Simulate how humidity and spore inoculum load impact field resistance in real time.
85%
Variety / Line ID Overall GEBV Score Disease Resistance Breakdown Yield (t/ha) Drought Tol. Breeding Triage Actions

Accession × Pathogen Resistance Heatmap Matrix

≥80% Immune 60-79% Moderate <40% Defenseless
Virtual Cross & Mendelian Simulator
Simulate genetic recombination and predict progeny resistance before physical crossing.
82%
Expected Progeny Mean
64%
Elite Resistant Progeny
38%
Stacked Homozygotes (R/R)

Progeny Resistance Segregation

Top 10 Simulated Progeny

Rank / ID Predicted Score Yield Status
Multi-Trait Pareto Frontier Optimizer
Balance disease resistance vs. harvest yield to prevent yield drag.

Performance Radar

Resistance vs. Harvest Yield Scatter

Interactive Chromosome Map
Click on any R-gene or QTL pin to inspect molecular details.
Major R-Gene Polygenic QTL
AI Agronomist Breeding Intelligence