Targeted genome engineering in plants

1. A method for modifying the nuclear genome of a cotton plant cell at a preselected site, comprising the steps of:

a. contacting a cotton plant cell with a bacterium capable of directing the transfer of T-DNA molecules from said bacterium into the nuclear genome of said plant cell, said bacterium comprising

i. a first T-DNA molecule comprising between a first pair of T-DNA borders a chimeric gene encoding a plant-functional double stranded DNA break inducing (DSBI) enzyme, said DSBI enzyme being capable of recognizing and inducing a double stranded DNA break at a recognition site located at or within 1 kb of said preselected site, said chimeric gene comprising the following operably linked elements:

1. A plant expressible promoter;

2. a DNA region encoding a DSBI enzyme;

3. a plant-functional 3′ termination and polyadenylation region; and

ii. a second T-DNA molecule comprising between a second pair of T-DNA borders a repair DNA molecule for use as a template for repair of said double stranded DNA break, wherein said repair DNA molecule comprises one or two flanking nucleotide sequences flanking the DNA molecule of interest, said flanking nucleotide sequence or sequences having at least 80% sequence identity over at least 50 nucleotides of the genomic DNA upstream and/or downstream of said preselected site to allow homologous recombination with said upstream and/or downstream DNA region, wherein said two T-DNA molecules are comprised within the same vector,

b. selecting a cotton plant cell wherein said repair DNA has been used as a template for repair of the double stranded DNA break, said repair of said double stranded DNA break resulting in a modification of said nuclear genome at said preselected site, wherein said modification is selected from

i. a replacement of at least one nucleotide;

ii. a deletion of at least one nucleotide;

iii. an insertion of at least one nucleotide; or

iv. any combination of i.-iii

wherein said bacterium is an Agrobacterium spp.

wherein frequency of correctly targeted genome modification is increased compared to when two T-DNA molecules are in different vectors.

2. The method of claim 1 , wherein said bacterium is Agrobacterium tumefaciens.

3. The method of claim 1 , wherein said DSBI enzyme is non-naturally occurring.

4. The method of claim 1 , wherein said repair DNA molecule comprises a DNA molecule of interest.

5. The method of claim 4 , wherein said DNA molecule of interest comprises one or more plant expressible gene(s) of interest.

6. The method of claim 1 , wherein said repair DNA molecule consists of two flanking nucleotide sequences, one of said flanking nucleotide sequence having at least 80% sequence identity over at least 50 nucleotides of the DNA region upstream of said predefined site, the other flanking nucleotide sequence having at least 80% sequence identity over at least 50 nucleotides of the DNA region downstream of said predefined site to allow homologous recombination between said flanking nucleotide sequences and said upstream and downstream DNA regions.

7. The method of claim 1 , comprising the further step of growing said selected cotton plant cell into a cotton plant.

8. The method of claim 1 , wherein said DSBI enzyme encoding gene and said modification genetically segregate in progeny of a cotton plant regenerated from said selected cotton plant cell.

9. A DNA vector comprising a first and a second T-DNA molecule as described in claim 1 .

10. A bacterium capable of directing the transfer of T-DNA molecules from said bacterium into the nuclear genome of a cotton plant cell, said bacterium comprising the first and second T-DNA molecules as described in claim 1 or the DNA vector as described in claim 9 , wherein said bacterium is an Agrobacterium spp.

11. The bacterium of claim 10 , which is Agrobacterium tumefaciens.

12. The method of claim 5 , wherein said plant expressible gene of interest is an herbicide tolerance gene, a gene encoding an enzyme involved in oil biosynthesis—or carbohydrate biosynthesis, a gene encoding an enzyme involved in fiber strength or fiber length, a gene encoding an enzyme involved in biosynthesis of secondary metabolites, insect resistance gene, a disease resistance gene, or an abiotic stress resistance gene.

13. A method for modifying the nuclear genome of a plant cell at a preselected site, comprising the steps of:

a. contacting a plant cell with a bacterium capable of directing the transfer of T-DNA molecules from said bacterium into the nuclear genome of said plant cell, said bacterium comprising

i. a first T-DNA molecule comprising between a first pair of T-DNA borders a chimeric gene encoding a plant-functional double stranded DNA break inducing (DSBI) enzyme, said DSBI enzyme being capable of recognizing and inducing a double stranded DNA break at a recognition site located at or within 1 kb of said preselected site, said chimeric gene comprising the following operably linked elements:

1. A plant expressible promoter;

2. a DNA region encoding a DSBI enzyme;

3. a plant-functional 3′ termination and polyadenylation region; and

ii. a second T-DNA molecule comprising between a second pair of T-DNA borders a repair DNA molecule for use as a template for repair of said double stranded DNA break, wherein said repair DNA molecule comprises one or two flanking nucleotide sequences flanking the DNA molecule of interest, said flanking nucleotide sequence or sequences having at least 80% sequence identity over at least 50 nucleotides of the genomic DNA upstream and/or downstream of said preselected site to allow homologous recombination with said upstream and/or downstream DNA region, wherein said two T-DNA molecules are comprised within the same vector,

b. selecting a plant cell wherein said repair DNA has been used as a template for repair of the double stranded DNA break, said repair of said double stranded DNA break resulting in a modification of said nuclear genome at said preselected site, wherein said modification is selected from

i. a replacement of at least one nucleotide;

ii. a deletion of at least one nucleotide;

iii. an insertion of at least one nucleotide; or

iv. any combination of i.-iii

wherein said bacterium is an Agrobacterium spp.

wherein frequency of correctly targeted genome modification is increased compared to when two T-DNA molecules are in different vectors.