Systems and methods for genetic engineering of a polyploid organism

A system for genetically modifying at least one nucleic acid sequence of interest in a polyploid organism, the system comprising:

• a. a first nucleic acid construct comprising:
• i. a site-specific recombination system selected from a Cre-Lox, VCre-V-LoxP, SCre-SLoxP, Vicavox, Flp-FRT, Dre-Rox, λ-Int-attP, R-RRT, Kw-KwRT, Kd-KdRT, B2-B2RT, and B3-B3RT;
• ii. a first antibiotic resistance reporter gene;
• and
• iii. regions of homology to a first locus in an essential nucleic acid sequence in the organism flanking the site-specific recombination system and the first reporter gene for integration of the first nucleic acid construct into the first locus, wherein the organism is a cyanobacterium;
• b. at least a second nucleic acid construct comprising:
• i. a nucleic acid sequence selected from a native sequence, a heterologous sequence, an insertion sequence, and a substitution sequence;
• ii. a second antibiotic resistance reporter gene;
• and
• iii. recombination recognition sequences of the site-specific recombination system of a(i) flanking the second reporter gene or flanking the second reporter gene and the nucleic acid sequence of b(i);
• iv. regions of homology to a second locus in a neutral integration site (NIS), the second locus flanking the nucleic acid sequence of b(i) and the second reporter gene for integration of the second nucleic acid construct into the second locus.