title: Comparisons of maize pericarp color1 alleles reveal paralogous gene recombination and an organ-specific enhancer region.
abstract: The maize (Zea mays) p1 (for pericarp color1) gene encodes an R2R3 Myb-like transcription factor that regulates the flavonoid biosynthetic pathway in floral organs, most notably kernel pericarp and cob. Alleles of the p1 gene condition distinct tissue-specific pigmentation patterns; to elucidate the molecular basis of these allele-specific expression patterns, we characterized two novel P1-rw (for red pericarp/white cob) alleles, P1-rw1077 and P1-rw751Ac. Structural analysis of P1-rw1077 indicated that this allele was generated by recombination between p1 and the tightly linked paralogous gene, p2. In the resulting gene, the p1 coding sequence was replaced by the p2 coding sequence, whereas the flanking p1 regulatory sequences remained largely preserved. The red pericarp color specified by P1-rw1077 suggests that the p1- and p2-encoded proteins are functionally equivalent as regulatory factors in the flavonoid biosynthesis pathway. Sequence analysis shows that the P1-rw1077 allele lacks a 386-bp sequence in a distal enhancer region 5 kb upstream of the transcription start site. An independently derived P1-rw allele contains an Ac insertion into the same sequence, indicating that this site likely contains cob glume-specific regulatory elements.
authors.affiliation: Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50010, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Zhang
authors.forename: Thomas
authors.initials: T
authors.lastname: Peterson
mesh_terms: D000483:Alleles; D001483:Base Sequence; D018744:DNA, Plant / Q000235:genetics; D004742:Enhancer Elements, Genetic; D005419:Flavonoids / Q000096:biosynthesis; D020869:Gene Expression Profiling; D017343:Genes, Plant; D005809:Genes, Regulator; D008969:Molecular Sequence Data; D009928:Organ Specificity; D010641:Phenotype; D010858:Pigmentation / Q000235:genetics; D011995:Recombination, Genetic; D012689:Sequence Homology, Nucleic Acid; D014158:Transcription, Genetic; D003313:Zea mays / Q000235:genetics* / Q000378:metabolism
chemical_list: D018744:DNA, Plant; D005419:Flavonoids; C091603:phlobaphene
references.citation: Proc Natl Acad Sci U S A. 1999 Dec 21;96(26):15330-5
references.pmid: 10611384
references.citation: Plant Cell. 2003 Feb;15(2):425-38
references.pmid: 12566582
references.citation: Plant J. 2003 Mar;33(5):853-66
references.pmid: 12609027
references.citation: Genetics. 1992 May;131(1):199-209
references.pmid: 1317315
references.citation: Plant Cell. 1995 Sep;7(9):1511-8
references.pmid: 8589631
references.citation: Eur J Biochem. 2001 Nov;268(22):5655-66
references.pmid: 11722549
references.citation: Plant J. 2001 Sep;27(5):467-78
references.pmid: 11576430
references.citation: Genetics. 2001 Dec;159(4):1727-40
references.pmid: 11779810
references.citation: J Mol Evol. 2000 Oct;51(4):305-17
references.pmid: 11040282
references.citation: Mol Gen Genet. 1994 Jan;242(1):40-8
references.pmid: 7904044
references.citation: Plant Mol Biol. 2003 May;52(1):1-15
references.pmid: 12825685
references.citation: Mutat Res. 1994 May;314(3):199-208
references.pmid: 7513053
references.citation: Plant Physiol. 1998 Dec;118(4):1111-20
references.pmid: 9847085
references.citation: Genetics. 2004 Feb;166(2):947-57
references.pmid: 15020479
references.citation: J Biol Chem. 1996 Feb 16;271(7):3366-74
references.pmid: 8631935
references.citation: Genetics. 1998 Jan;148(1):457-69
references.pmid: 9475755
references.citation: Genetics. 1991 May;128(1):163-73
references.pmid: 1648001
references.citation: Nucleic Acids Res. 2002 Jan 1;30(1):325-7
references.pmid: 11752327
references.citation: Plant Cell. 2000 Dec;12(12):2311-2322
references.pmid: 11148280
references.citation: Genes Dev. 2002 Aug 1;16(15):1906-18
references.pmid: 12154122
references.citation: Plant Mol Biol. 1999 Jul;40(4):699-709
references.pmid: 10480393
references.citation: Proc Natl Acad Sci U S A. 1991 Jun 1;88(11):4587-91
references.pmid: 2052542
references.citation: Cell. 2002 May 3;109(3):267-70
references.pmid: 12015975
references.citation: Plant J. 2000 Jun;22(6):471-82
references.pmid: 10886767
references.citation: Nature. 2004 Jul 22;430(6998):471-6
references.pmid: 15269773
references.citation: Proc Natl Acad Sci U S A. 1996 May 14;93(10):5055-60
references.pmid: 8643528
references.citation: Plant Mol Biol. 1999 Jan;39(1):11-9
references.pmid: 10080705
references.citation: Mol Gen Genet. 1989 Oct;219(1-2):225-34
references.pmid: 2559311
references.citation: Plant J. 2000 Mar;21(5):401-8
references.pmid: 10758492
references.citation: Proc Natl Acad Sci U S A. 1991 Apr 15;88(8):3502-6
references.pmid: 1849660
references.citation: Genetics. 2002 Oct;162(2):917-30
references.pmid: 12399399
references.citation: Mol Gen Genet. 1998 Nov;260(4):372-80
references.pmid: 9870702
references.citation: Dev Genet. 1999;25(4):291-6
references.pmid: 10570460
references.citation: J Biol Chem. 1994 Apr 1;269(13):9974-85
references.pmid: 8144592
references.citation: Plant Cell. 1996 Jul;8(7):1171-9
references.pmid: 8768375
references.citation: Science. 1996 Nov 1;274(5288):765-8
references.pmid: 8864112
references.citation: Genetics. 1995 Sep;141(1):347-60
references.pmid: 8536982
references.citation: Plant Cell. 2001 Feb;13(2):319-35
references.pmid: 11226188
references.citation: Genetics. 1990 Oct;126(2):469-76
references.pmid: 1700963
references.citation: Genetics. 1924 Sep;9(5):442-53
references.pmid: 17246050
references.citation: Genetics. 1987 Sep;117(1):117-37
references.pmid: 2822531
references.citation: Genetics. 2003 Mar;163(3):1135-46
references.pmid: 12663550
references.citation: Plant J. 2003 Nov;36(4):510-21
references.pmid: 14617081
references.citation: Proc Natl Acad Sci U S A. 1999 Dec 21;96(26):15348-53
references.pmid: 10611387
references.citation: Genetics. 2003 Jan;163(1):181-94
references.pmid: 12586706
references.citation: Genetics. 1992 Aug;131(4):939-56
references.pmid: 1325389
references.citation: Genes Dev. 1992 Nov;6(11):2152-64
references.pmid: 1427078
references.citation: Plant J. 1993 Feb;3(2):335-46
references.pmid: 8220447
references.citation: Plant Cell. 1997 May;9(5):799-807
references.pmid: 9165754
references.citation: Plant Cell. 1996 Jul;8(7):1149-58
references.pmid: 8768374
references.citation: Cell. 1994 Feb 11;76(3):543-53
references.pmid: 8313474