Methods and compositions for producing clonal, non-reduced, non-recombined gametes

1. A maize plant that produces clonal, non-reduced, non-recombined gametes, wherein the maize plant comprises:

a) eliminated Spo11 activity of an endogenous Spo11 polynucleotide or polypeptide, wherein the Spo11 polynucleotide is selected from the group consisting of:

i. a polynucleotide that encodes the polypeptide of SEQ ID NO:16;

ii. a polynucleotide comprising the sequence set forth in SEQ ID NO:13, and

iii. a polynucleotide having at least 95% sequence identity to SEQ ID NO: 13, wherein the Spo11 polypeptide is selected from the group consisting of:

i. a polypeptide that is encoded by a nucleic acid molecule comprising a nucleotide sequence that is at least 95% identical to SEQ ID NO: 13, wherein the Spo11 activity of the endogenous Spo11 polynucleotide or polypeptide is eliminated by introducing a nucleotide modification into the Spo11 polynucleotide sequence or nucleic acid molecule in part a) to knock-out the endogenous Spo11 polynucleotide;

b) eliminated Rec8 activity of an endogenous Rec8 polynucleotide or polypeptide, wherein Rec8 polynucleotide is selected from the group consisting of:

i. a polynucleotide comprising the sequence set forth in SEQ ID NO:9; and

ii. a polynucleotide having at least 95% sequence identity to SEQ ID NO: 9; wherein the Rec8 polypeptide is selected from the group consisting of:

i. a polypeptide that is encoded by a nucleic acid molecule comprising a nucleotide sequence that is at least 95% identical to SEQ ID NO:9, wherein the Rec8 activity of the endogenous Rec8 polynucleotide or polypeptide is eliminated by introducting a nucleotide modification into REC8 Polyculeotide sequence or nucleic acid molecule in part b) to knock-out the endogenour Rec8 polynucleotide;

c) eliminated OSD1-1A activity of an endogenous OSD1-1A poluynucleotide or polypeptide, wherein OSD1-1A polynuycleotide is selected from the group consisting of:

i. a polynucleotide that encodes the polypeptide of SEQ ID NO:4;

ii. a polynucleotide comprising the sequence set forth in SEQ ID NO:1; and

iii. a polynucleotide having at least 95% sequence identitiy of SEQ ID NO:1; wherein the OSD1-1A polypeptide is selected form the group consisting of:

i. a polypeptide that is encoded by a nucleic acid molecule comprising a nucleotide sequence that is at least 95% identical to SEQ ID NO:1,

wherein the OSD1-1A activity of the endogenous OSD1-1A polynucleotide or polypeptide is eliminated by introducing a nucleotide modification into the OSD1-1A polynucleotide sequence or nucleic acid molecule in part c) to knock-out the endogenous OSD1-1A polynucleotide;

and

d) eliminated OSD1-3A activity of an endogenous OSD1-3A polynucleotide or polypeptide, wherein OSD1-3A polynucleotide is selected from the group consisting of:

i. a polynucleotide that encodes the polypeptide of SEQ ID NO:8;

ii. a polynucleotide comprising the sequence set forth in SEQ ID NO:5; and

iii. a polynucleotide having at least 95% sequence identity to SEQ ID NO:5; wherein the OSD1-3A polypeptide is selected form the group consisting of:

i. a polypeptide that is encoded by a nucleic acid molecule comprising a nucleotide sequence that is at least 95% identical to SEQ ID NO: 5,

wherein the OSD1-3A activity of the endogenous OSD1-3A polynucleotide or polypeptide is eliminated by introducing a nucleotide modification into the OSD1-3A polynucleotide sequence of nucleic acid molecule in part d) to knock-out the endogenous OSD1-3A polynucleotide.

2. The maize plant of claim 1 , wherein the maize plant is a hybrid.

3. The maize plant of claim 1 , wherein the maize plant is a female parent.

4. The maize plant of claim 1 , wherein the introduced nucleotide modification is a deletion, addition, or substitution of one or more nucleotides.

5. The maize plant of claim 1 , wherein the introduced amino acid modification is a deletion, addition, or substitution of one or more amino acids.

6. The maize plant of claim 1 , wherein said the nucleotide modification is introduced by a nuclease selected from the group consisting of: a TALEN, a meganuclease, a zinc finger nuclease, and a CRISPR-associated nuclease.

7. The maize plant of claim 6 , wherein the nucleotide modification is introduced by a Cas9 endonuclease guided by at least one guide RNA.

8. A method for obtaining a maize plant producing clonal, non-reduced, non-recombined gametes, the method comprising:

a) eliminating in the maize plant the Spo11 activity of an endogenous Spo11 polynucleotide or polypeptide, wherein the Spo11 polynucleotide is selected from the group consisting of:

i. a polynucleotide that encodes the polypeptide of SEQ ID NO:16;

ii. a polynucleotide comprising the sequence set forth in SEQ ID NO:13; and

iii. a polynucleotide having at least 95% sequence identity to SEQ ID NO: 13;

wherein the Spo11 polypeptide is selected from the group consisting of:

i. a polypeptide that is encoded by a nucleic acid molecule comprising a nucleotide sequence that is at least 95% identical to SEQ ID NO:13;

b) eliminating in the maize plant the Rec8 activity of an endogenous Rec8 polynucleotide or polypeptide, wherein Rec8 polynucleotide is selected from the group consisting of:

i. a polynucleotide comprising the sequence set forth in SEQ ID NO:9; and

ii. a polynucleotide having at least 95% sequence identity to SEQ ID NO: 9;

wherein the Rec8 polypeptide is selected from the group consisting of:

i. a polypeptide that is encoded by a nucleic acid molecule comprising a nucleotide sequence that is at least 95% identical to SEQ ID NO:9;

c) eliminating in the maize plant the OSD1-1A activity of an endogenous OSD1-1A polynucleotide or polypeptide, wherein OSD1-1A polynucleotide is selected from the group consisting of:

i. a polynucleotide that encodes the polypeptide of SEQ ID NO:4;

ii. a polynucleotide comprising the sequence set forth in SEQ ID NO:1; and

iii. a polynucleotide having at least 95% sequence identity to SEQ ID NO: 1;

wherein the OSD1-1A polypeptide is selected from the group consisting of:

i. a polypeptide that is encoded by a nucleic acid molecule comprising a nucleotide sequence that is at least 95% identical to SEQ ID NO:1;

and

d) eliminating in the maize plant the OSD1-3A activity of an endogenous OSD1-3A polynucleotide or polypeptide, wherein OSD1-3A polynucleotide is selected from the group consisting of:

i. a polynucleotide that encodes the polypeptide of SEQ ID NO:8;

ii. a polynucleotide comprising the sequence set forth in SEQ ID NO:5; and

iii. a polynucleotide having at least 95% sequence identity to SEQ ID NO:5;

wherein the OSD1-3A polypeptide is selected from the group consisting of:

i. a polypeptide that is encoded by a nucleic acid molecule comprising a nucleotide sequence that is at least 95% identical to SEQ ID NO: 5;

wherein the Spo11 activity of the endogenous Spo11 polynucleotide or polypeptide, wherein the Rec8 activity of the endogenous Rec8 polynucleotide or polypeptide, wherein the OSD1-1A activity of the endogenous OSD1-1A polynucleotide or polypeptide, wherein the OSD1-3A activity of the endogenous OSD1-3A polynucleotide or polypeptide, is eliminated by introducing a nucleotide modification into the polynucleotide sequence or nucleic acid molecule in part a), b), c), and d) respectively.

9. The method of claim 8 , wherein the maize plant is a hybrid.

10. The method of claim 8 , wherein the maize plant is a female parent.

11. The method of claim 8 , wherein the nucleotide modification is a deletion, addition, or substitution of one or more nucleotides.

12. The method of claim 8 , wherein the amino acid modification is a deletion, addition, or substitution of one or more amino acids.

13. The method of claim 11 , wherein said the nucleotide modification is introduced by a nuclease selected from the group consisting of: a TALEN, a meganuclease, a zinc finger nuclease, and a CRISPR-associated nuclease.

14. The method of claim 13 , wherein the nucleotide modification is introduced by a Cas9 endonuclease guided by at least one guide RNA.

15. The method of claim 8 , wherein the maize plant is obtained by crossing maize plants that are heterozygous or homozygous for the eliminated endogenous Spo11, Rec8, OSD1-1A or OSD1-3A activity.

16. The method of claim 8 , further comprising obtaining gametes from the female parent, wherein the gametes are clonal, non-reduced, non-recombined.

17. Clonal, non-reduced, non-recombined gametes obtained from the method of claim 8 , wherein the introduced nucleotide modifications into the Spo11, Rec8, OSD1-1A, and OSD1-3A polynucleotide sequences in the maize plant render the gametes clonal, non-reduced, and non-recombined.

18. A maize plant comprising clonal, non-reduced, non-recombined gametes produced from the method of claim 8 .

19. The maize plant of claim 1 , wherein the nucleotide modification is introduced by chemical mutagenesis.

20. The method of claim 8 , wherein the nucleotide modification is introduced by chemical mutagenesis.