Bacterial quantitative trait-locus mapping

A method for identifying quantitative trait-loci in bacteria comprising:

• providing two starting bacterial strains, wherein the two starting strains comprise selectable markers compatible with each other in that either at least one of the two starting bacterial strains is a wild type prototroph strain without an antibiotic resistance gene and the other starting bacterial strain is double auxotroph and comprises two different antibiotic resistance genes, or the two starting bacterial strains are each a single auxotroph strain comprising an antibiotic resistance gene and differ from each other in auxotrophy and antibiotic resistance;
• inducing at least two rounds of genomic recombination, wherein the at least two rounds of genomic recombination comprises
• (i) inducing a first round of genomic recombination between a population of a first starting strain and a population of a second starting strain to obtain first generation progeny bacteria,
• (ii) selecting among the first generation progeny bacteria to obtain two populations of bacteria that have undergone genomic recombination using two different selective media, wherein each selective medium kills both starting bacterial strains and allows only one of the two populations of the first generation progeny bacteria to live,
• (iii) inducing a second round of genomic recombination between one of the two selected populations of the first generation progeny bacteria and a population of bacteria that comprises a selectable marker compatible with the first selected population of the first generation progeny bacteria and that is selected from the group consisting of:
• (a) the other of the two selected populations of the first generation progeny bacteria,
• (b) a population of a strain that is otherwise genetically identical to one of the two starting strains,
• (c) a population of a strain that is different from both starting strains, and
• (d) a population of bacteria selected from progeny bacteria from induced genomic recombination between two different starting strains, thereby obtaining second generation progeny bacteria;
• (iv) selecting among the second generation progeny bacteria for two populations of bacteria that have undergone genomic recombination using two selective media, wherein each selective medium kills both populations of bacteria used in the second round of genomic recombination, and allows only one of the two populations of the second generation progeny bacteria to live, and
• (v) obtaining the selected two populations of the second generation progeny bacteria as two populations of a final generation progeny bacteria, or inducing at least one more round of genomic recombination and selecting between a first selected population of the second generation progeny bacteria and a population of bacteria that comprises a selectable marker compatible with the first selected population of the second generation progeny bacteria to obtain two populations of a final generation progeny bacteria;
• determining the sequences of the genomes of the two populations of the final generation progeny bacteria, thereby determining genetic variations within the genomes of the two populations the final generation progeny bacteria;
• determining at least one phenotype of the two populations of the final generation progeny bacteria;
• and
• performing a population-wide analysis to identify genetic variations that associate with the at least one phenotype, thereby identifying quantitative-trait loci that are associated with the at least one phenotype.