Plant DNA Designer is an open-source computational biology platform for designing de novo, crop-optimised plant expression cassettes. It combines validated trait-to-effector mapping, translation-aware multi-objective genetic algorithm optimisation, codon optimisation, CRISPR guide design, plant-specific safety analysis, and automated expression cassette assembly. The platform supports 46 validated traits across 18 crops, runs entirely offline without AI or cloud services, includes a reproducible benchmarking suite against established codon optimisation methods, and generates comprehensive reports for expression, stability, safety, and synthesis readiness. GitHub: https://github.com/Dinesh431786/Plant-DNA-Designer