Phenylpropanoid related regulatory protein-regulatory region associations

1. A method of producing a plant, said method comprising growing a plant cell comprising an exogenous nucleic acid, said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence encoding a polypeptide having 95% or greater sequence identity to a polypeptide having the amino acid sequence set forth in SEQ ID NO:2133, wherein a tissue of a plant produced from said plant cell has a difference in the level of lignin as compared to the corresponding level in lignin of a control plant that does not comprise said nucleic acid.

2. A plant cell comprising an exogenous nucleic acid, said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence encoding a polypeptide having 95% or greater sequence identity to a polypeptide sequence set forth in SEQ ID NO:2133, where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.

3. The plant cell of claim 2 , wherein said regulatory region is involved in lignin or cellulose biosynthesis.

4. The plant cell of claim 3 , wherein said regulatory region has a nucleotide sequence selected from the group consisting of SEQ ID NOs:1909-1918.

5. The plant cell of claim 2 , wherein said regulatory region is not associated with said polypeptide.

6. The plant cell of claim 2 , wherein said regulatory region is a promoter.

7. The plant cell of claim 6 , wherein said promoter is a tissue-preferential promoter.

8. The plant cell of claim 7 , wherein said tissue is vascular, stem, pith, xylem, phloem, fruit, seed, seed pod, root, tuber, inflorescence, or leaf tissue.

9. The plant cell of claim 6 , wherein said promoter is a cell type-preferential promoter.

10. The plant cell of claim 9 , wherein said cell is a sieve, laticifer, companion, sclerenchyma, xylem, or trichome cell.

11. The plant cell of claim 6 , wherein said promoter is an inducible promoter.

12. A method of expressing a sequence of interest in a plant cell, said method comprising growing a plant cell comprising:

1) an exogenous nucleic acid comprising a regulatory region operably linked to a sequence of interest, said regulatory region comprising a nucleic acid having 95% or greater sequence identity to a regulatory region having a nucleotide sequence selected from the group consisting of SEQ ID NOs:1909-1918; and

2) an exogenous nucleic acid comprising a nucleic acid encoding a polypeptide having 95% or greater sequence identity to a polypeptide sequence set forth in SEQ ID NO:2133;

wherein said regulatory region and said polypeptide are associated, wherein said plant cell is grown under conditions effective for expression of said regulatory protein, and wherein said plant cell expresses said sequence of interest.

13. The method of claim 12 , wherein said exogenous nucleic acid comprising a regulatory region operably linked to a sequence of interest and said exogenous nucleic acid comprising a nucleic acid encoding a polypeptide are included in the same nucleic acid construct or in separate nucleic acid constructs.

14. A method of expressing a sequence of interest in a plant cell, said method comprising growing a plant cell comprising an exogenous nucleic acid encoding a polypeptide sequence having 95% or greater sequence identity to a polypeptide sequence set forth in SEQ ID NO:2133, said plant cell having an endogenous gene involved in lignin biosynthesis, said endogenous gene comprising a regulatory region and said sequence of interest, wherein said polypeptide and said endogenous regulatory region are associated, wherein said plant cell is grown under conditions effective for expression of said polypeptide, and wherein said plant cell expresses said sequence of interest.

15. The method of claim 12 or 13 , wherein said sequence of interest comprises a coding sequence for a polypeptide involved in lignin biosynthesis.

16. The method of claim 12 or 13 , wherein said sequence of interest is in an antisense orientation relative to said regulatory region.

17. The method of claim 12 or 13 , wherein said sequence of interest is transcribed into an interfering RNA.

18. The method of claim 14 , wherein said endogenous gene comprises a coding sequence for a polypeptide involved in lignin biosynthesis.

19. The method of claim 14 , wherein said exogenous nucleic acid encoding said polypeptide is operably linked to a regulatory region capable of modulating expression of said polypeptide in said plant cell.

20. The method of claim 19 , wherein said regulatory region capable of modulating expression of said polypeptide in said plant cell is a tissue-preferential, cell type-preferential, organ-preferential, or inducible promoter.

21. A plant cell comprising an exogenous nucleic acid, said exogenous nucleic acid comprising a regulatory region operably linked to a polynucleotide that is transcribed into an interfering RNA effective for inhibiting expression of a polypeptide having 95% or greater sequence identity to a polypeptide sequence set forth in SEQ ID NO:2133; wherein said regulatory region modulates transcription of said polynucleotide in said plant cell.

22. The plant cell of claim 21 , wherein said exogenous nucleic acid further comprises a 3′UTR operably linked to said polynucleotide.

23. The plant cell of claim 22 , wherein said polynucleotide is transcribed into an interfering RNA comprising a stem-loop structure.

24. The plant cell of claim 22 , wherein said stem-loop structure comprises an inverted repeat of said 3′ UTR.

25. An isolated nucleic acid molecule comprising a nucleotide sequence having 95% or greater sequence identity to the nucleotide sequence set forth in SEQ ID NO:2132.

26. An isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide having 95% or greater sequence identity to the amino acid sequence set forth in SEQ ID NO:2133.