High efficiency large scale chromosomal genome manipulation

A method of increasing recombination between one or more chromosomal segments in the genome of a crop plant cell, the method comprising:

• (i) providing the plant cell with a DNA break inducing agent designed to bind and cleave the genomic target site, wherein the plant cell is incubated at a temperature that is greater than 28° C. such that the higher temperature effect increases chromosomal modification efficiency at the genomic target site by facilitating DNA end-joining, compared to a control plant cell not comprising such oligonucleotides;
• or providing the plant cell with a DNA break inducing agent that is engineered to bind and recurrently cleave the genomic target site such that the cleaved chromosomal ends at the genomic target site remain accessible for a substantially longer time to enable chromosomal modification at the genomic target site by facilitating DNA end-joining, compared to a control plant cell not comprising the recurrent cutting DNA break inducing agent;
• and
• (ii) regenerating a crop plant from the plant cell, wherein the crop plant comprises recombined chromosomal segment compared to a control crop plant.

A method for high-efficiency introgression or translocation of a trait of interest or a quantitative trait locus (QTL) of interest in an elite genotype, the method comprising:

• generating a first translocation event of a trait or a QTL from a first chromosome to a second chromosome, wherein the chromosomal segments are translocated between the first and the second chromosomes resulting in the second chromosome having the trait or QTL of interest along with a non-trait or a non-QTL segment from the first chromosome;
• generating a second translocation event such that the non-trait or the non-QTL segment of the first chromosome that is present in the second chromosome is translocated back to the first chromosome such that the non-trait or the non-QTL segment without the trait or the QTL of interest is present in the first chromosome as a result of the second translocation event;
• and
• generating a plant cell that contains homozygous copies of the restored first chromosome and the second chromosome having the trait or the QTL segment translocated from the first chromosome;
• wherein the first and the second translocation events are performed by introducing targeted double strand or single strand DNA breaks in the chromosomal regions of the donor and/or the recipient plant species between the QTL and the centromere of the chromosome, wherein the DNA breaks are introduced by (i) providing one or more oligonucleotides with substantial sequence similarity to one or more chromosomal ends at two different or distinct double strand break regions and/or (ii) increasing the incubation temperature to greater than 28° C., thereby cleaving the chromosome homologous to the chromosome comprising the QTL at the corresponding target site.