Abstract
Sequence characterization of the genomic region of sorghum yellow seed1 shows the presence of two genes that are arranged in a head to tail orientation. The two duplicated gene copies, y1 and y2 are separated by a 9.084 kbp intergenic region, which is largely composed of highly repetitive sequences. The y1 is the functional copy, while the y2 may represent a pseudogene; there are several sequence indels and rearrangements within the putative coding region of y2. The y1 gene encodes a R2R3 type of Myb domain protein that regulates the expression of chalcone synthase, chalcone isomerase and dihydroflavonol reductase genes required for the biosynthesis of 3-deoxyflavonoids. Expression of y1 can be observed throughout the plant and it represents a combination of expression patterns produced by different alleles of the maize p1. Comparative sequence analysis within the coding regions and flanking sequences of y1, y2 and their maize and teosinte orthologs show local rearrangements and insertions that may have created modified regulatory regions. These micro-colinearity modifications possibly are responsible for differential patterns of expression in maize and sorghum floral and vegetative tissues. Phylogenetic analysis indicates that sorghum y1 and y2 sequences may have arisen by gene duplication mechanisms and represent an evolutionarily parallel event to the duplication of maize p2 and p1 genes.
Similar content being viewed by others
References
Athma (1992) ArticleTitleInsertional mutagenesis of the maize P gene by intragenic transposition of Ac Genetics 131 199–209 Occurrence Handle1:CAS:528:DyaK3sXisVyksLw%3D Occurrence Handle1317315
Bennetzen (2002) ArticleTitleNumerous small rearrangements of gene content, order and orientation differentiate grass genomes Plant Mol. Biol. 48 821–827 Occurrence Handle1:CAS:528:DC%2BD38XjsFWrtL8%3D Occurrence Handle11999852 Occurrence Handle10.1023/A:1014841515249
J. Boddu C. Svabek R. Sekhon A. Gevens R. Nicholson A.D. Jones J. Pederson D. Gustine S. Chopra (2004) ArticleTitleExpression of a putative flavonoids 3’hydroxylase in sorghum mesocotyls synthesizing 3-deoxyanthocyanidin phytoalexins Physiol. Mol. Plant Pathol. 65 101–113 Occurrence Handle1:CAS:528:DC%2BD2MXktlOrsb0%3D Occurrence Handle10.1016/j.pmpp.2004.11.007
J. Boddu C. Svabek F. Ibraheem A. D. Jones S. Chopra (2005) ArticleTitleCharacterization of a deletion allele of a sorghum Myb gene yellow seed1 showing loss of 3-deoxyflavonoids Plant Sci. 169 542–552 Occurrence Handle1:CAS:528:DC%2BD2MXmsVOhsbk%3D Occurrence Handle10.1016/j.plantsci.2005.05.007
J.E. Bowers C. Abbey S. Anderson C. Chang X. Draye A.H. Hoppe R. Jessup C. Lemke J. Lennington Z. Li Y.R. Lin S.C. Liu L. Luo B.S. Marler R. Ming S.E. Mitchell D. Qiang K. Reischmann SR. Schulze DN. Skinner Y.W. Wang S. Kresovich K.F. Schertz A.H. Paterson (2003) ArticleTitleA high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses Genetics 165 367–386 Occurrence Handle1:CAS:528:DC%2BD3sXosFalur4%3D Occurrence Handle14504243
W. Bruce O. Folkert C. Garnaat O. Crasta B. Roth B. Bowen (2000) ArticleTitleExpression profiling of the maize flavonoid pathway genes controlled by the Estradiol-inducible transcription factors CRC and P Plant Cell 12 65–79 Occurrence Handle1:CAS:528:DC%2BD3cXhtVWqs7w%3D Occurrence Handle10634908 Occurrence Handle10.1105/tpc.12.1.65
C. Carvalho J. Boddu U. Zehr J. Axtell J. Pedersen S. Chopra (2005) ArticleTitleGenetic and molecular characterization of Candystripe1 transposition events in sorghum Genetica 124 201–212 Occurrence Handle16134333 Occurrence Handle10.1007/s10709-005-2268-8
S. Chopra P. Athma T. Peterson (1996) ArticleTitleAlleles of the maize P gene with distinct tissue specificities encode Myb-homologous proteins with C-terminal replacements Plant Cell 8 1149–1158 Occurrence Handle1:CAS:528:DyaK28XksFKkuro%3D Occurrence Handle8768374 Occurrence Handle10.1105/tpc.8.7.1149
S. Chopra P. Athma X. Li T. Peterson (1998) ArticleTitleA maize Myb homolog is encoded by a multicopy gene complex Mol. Gen. Genet. 260 372–380 Occurrence Handle1:CAS:528:DyaK1MXjtFWhsw%3D%3D Occurrence Handle9870702
S. Chopra V. Brendel J. Zhang J.D. Axtell T. Peterson (1999) ArticleTitleMolecular characterization of a mutable pigmentation phenotype and isolation of the first active transposable element from Sorghum bicolor Proc. Natl. Acad. Sci. USA. 96 15330–15335 Occurrence Handle1:CAS:528:DC%2BD3cXhtFehtg%3D%3D Occurrence Handle10611384 Occurrence Handle10.1073/pnas.96.26.15330
S. Chopra A. Gevens C. Svabek K.V. Wood T. Peterson R.L. Nicholson (2002) ArticleTitleExcision of the Candystrip1 transposon from a hyper-mutable Y1-cs allele shows that the sorghum y1 gene control the biosynthesis of both 3-deoxyanthocyanidin phytoalexins and phlobaphene pigments Physiol. Mol. Plant Pathol. 60 321–330 Occurrence Handle1:CAS:528:DC%2BD38XnslGrsLs%3D
S. Chopra S. Cocciolone S. Bushman V. Sangar M. McMullen T. Peterson (2003) ArticleTitleA maize Unstable factor for orange1 is a dominant epigenetic modifier of tissue specifically silent allele of pericarp color1 Genetics 163 1135–1146 Occurrence Handle1:CAS:528:DC%2BD3sXjtlOgsLo%3D Occurrence Handle12663550
S.M. Cocciolone L.V. Sidorenko S. Chopra P.M. Dixon T. Peterson (2000) ArticleTitleHierarchical patterns of transgene expression indicate involvement of developmental mechanisms in the regulation of the maize P1-rr promoter Genetics 156 839–846 Occurrence Handle1:CAS:528:DC%2BD3cXnvV2ns7k%3D Occurrence Handle11014829
S.M. Cocciolone S. Chopra S.A. Flint-Garcia M.D. McMullen T. Peterson (2001) ArticleTitleTissue-specific patterns of a maize Myb transcription factor are epigenetically regulated Plant J. 27 467–478 Occurrence Handle1:CAS:528:DC%2BD3MXnvVansrY%3D Occurrence Handle11576430 Occurrence Handle10.1046/j.1365-313X.2001.01124.x
K.C. Cone S.M. Cocciolone F.A. Burr B. Burr (1993) ArticleTitleMaize anthocyanin regulatory gene pl is a duplicate of c1 that functions in the plant Plant Cell 5 1795–1805 Occurrence Handle1:CAS:528:DyaK2cXlsFSgsLw%3D Occurrence Handle8305872
A.P. Dias E.L. Braun M.D. McMullen E. Grotewold (2003) ArticleTitleRecently duplicated maize R2R3 Myb genes provide evidence for distinct mechanism of evolutionary divergence after duplication Plant Physiol. 131 610–620 Occurrence Handle1:CAS:528:DC%2BD3sXhtlyjsrk%3D Occurrence Handle12586885 Occurrence Handle10.1104/pp.012047
J.F. Doebley M.M. Goodman C.W. Stuber (1984) ArticleTitleIsoenzymatic variation in Zea Syst. Bot. 9 203–218
C. Feuillet B. Keller (2002) ArticleTitleComparative genomics in grass family: Molecular characterization of grass genome structure and evolution Ann. Bot. 89 3–10 Occurrence Handle1:CAS:528:DC%2BD38XkslWjs7Y%3D Occurrence Handle12096816 Occurrence Handle10.1093/aob/mcf008
J. Felsenstein (1985) ArticleTitleConfidence limits on phylogenies: an approach using the bootstrap Evolution 39 783–791
H. Fu H. Dooner (2002) ArticleTitleIntraspecific violation of genetic colinearity and its implications in maize Proc. Natl. Acad. Sci. USA. 99 9573–9578 Occurrence Handle1:CAS:528:DC%2BD38XlsVGgtbs%3D Occurrence Handle12060715
B.S. Gaut (1998) ArticleTitleMolecular clocks and nucleotide substitution rates in higher plants Evol. Biol. 30 93–120 Occurrence Handle1:CAS:528:DyaK1cXks1ajsLY%3D
B.S. Gaut J.F. Doebley (1997) ArticleTitleDNA sequence evidence for the segmental allotetraploid origin of maize Proc. Natl. Acad. Sci. USA. 94 6809–6814 Occurrence Handle1:CAS:528:DyaK2sXktF2rur0%3D Occurrence Handle11038553 Occurrence Handle10.1073/pnas.94.13.6809
T. Gerik B. Bean R. Vanderlip (2003) Sorghum growth and development. Texas Cooperative Extension Service Texas A&M, Agricultural Research and Extension Center Amarillo, TX
S.A. Goff K.C. Cone V.L. Chandler (1992) ArticleTitleFunctional analysis of the transcriptional activator encoded by the maize B gene: Evidence for a direct functional interaction between two classes of regulatory proteins Genes Dev. 6 864–975 Occurrence Handle1:CAS:528:DyaK38Xkt1Wns7s%3D Occurrence Handle1577278
E. Grotewold P. Athma T. Peterson (1991) ArticleTitleAlternatively spliced products of the maize P gene encode proteins with homology to the DNA binding domain of Myb-like transcription factors Proc. Natl. Acad. Sci. USA. 88 4587–4591 Occurrence Handle1:CAS:528:DyaK38Xht1aht7Y%3D Occurrence Handle2052542
E. Grotewold T. Peterson (1994) ArticleTitleIsolation and characterization of a maize gene encoding chalcone flavonone isomerase Mol. Gen. Genet. 242 1–8 Occurrence Handle1:CAS:528:DyaK2cXkslCqsL0%3D Occurrence Handle8277939
E. Grotewold B. Drummond B. Bowen T. Peterson (1994) ArticleTitleThe myb-homologous P gene controls phlobaphene pigmentation in maize floral organs by directly activating a flavonoid biosynthetic gene subset Cell 76 543–553 Occurrence Handle1:CAS:528:DyaK2cXitlOntb4%3D Occurrence Handle8313474 Occurrence Handle10.1016/0092-8674(94)90117-1
E. Grotewold M. Chamberlin M. Snook B. Siame L. Butler J. Swenson S. Maddock G. Clair B. Bowen (1998) ArticleTitleEngineering secondary metabolism in maize cells by ectopic expression of transcription factor Plant Cell 10 721–740 Occurrence Handle1:CAS:528:DyaK1cXjs1ehsb8%3D Occurrence Handle9596632 Occurrence Handle10.1105/tpc.10.5.721
M.A. Hanson B.S. Gaut A.O. Stec S.I. Fuerstenberg M.J. Goodman E.H. Coe J.F. Doebly (1996) ArticleTitleEvolution of anthocyanin biosynthesis in maize kernels: the role of regulatory and enzymatic loci Genetics 143 1395–1407 Occurrence Handle1:CAS:528:DyaK28XksFentLo%3D Occurrence Handle8807310
G. Hu K.D. Kofoid G.H. Liang (1991) ArticleTitleAn unstable mutation for pigmentation in kernels of “Calico” sorghum Hereditas 115 163–167
K. Ilic P.J. SanMiguel J.L. Bennetzen (2003) ArticleTitleA complex history of rearrangements in an orthologous region of the maize, sorghum and rice genomes Proc. Natl. Acad. Sci. USA. 100 12265–12270 Occurrence Handle1:CAS:528:DC%2BD3sXotlGks7w%3D Occurrence Handle14530400 Occurrence Handle10.1073/pnas.1434476100
H. Iltis (1983) ArticleTitleFrom teosinte to maize: The catastrophic sexual transmutation Science 222 886–894
C. Jiang J. Gu S. Chopra X. Gu T. Peterson (2004a) ArticleTitleOrdered origin of the typical two and three-repeat Myb genes Gene 326 13–22 Occurrence Handle1:CAS:528:DC%2BD2cXit1KltA%3D%3D Occurrence Handle10.1016/j.gene.2003.09.049
C. Jiang X. Gu T. Peterson (2004b) ArticleTitleIdentification of conserved Gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. Indica Genome Biol. 5 R46
A.E. Kambal E.C. Bate-Smith (1976) ArticleTitleA genetic and biochemical study on pericarp pigmentation in a cross between two cultivars of grain sorghum, Sorghum bicolor Heredity 37 417–421
S. Kumar K. Tamura I.B. Jakobsen M. Neim (2001) ArticleTitleMEGA2: Molecular Evolutionary Genetics Analysis software Bioinformatics 17 1244–1245 Occurrence Handle1:CAS:528:DC%2BD38XmtVCktQ%3D%3D Occurrence Handle11751241 Occurrence Handle10.1093/bioinformatics/17.12.1244
C. Lechelt T. Peterson A. Laird J. Chen S. Dellaporta E. Dennis W.J. Peacock P. Starlinger (1989) ArticleTitleIsolation and Molecular Analysis of the Maize P Locus Mol. Gen. Genet. 219 225–234 Occurrence Handle1:CAS:528:DyaK3cXpt12htA%3D%3D Occurrence Handle2559311 Occurrence Handle10.1007/BF00261181
W. Li D. Graur (1991) Fundamentals of Molecular Evolution Sinauer Associates Suderland, MA
S-C. Lo R.L. Nicholson (1998) ArticleTitleReduction of light-induced anthocyanin accumulation in inoculated sorghum mesocotyls. Implications for a compensatory role in the defense response Plant Physiol. 116 979–989 Occurrence Handle1:CAS:528:DyaK1cXitVOjsr4%3D Occurrence Handle9501130 Occurrence Handle10.1104/pp.116.3.979
S-C. Lo R. Coolbaugh R.L. Nicholson (2002) ArticleTitleMolecular characterization and in silico expression analysis of a chalcone synthase gene family in sorghum bicolor Physiol. Mol. Plant Pathol. 61 179–188 Occurrence Handle1:CAS:528:DC%2BD38Xps1Sjtrk%3D Occurrence Handle10.1006/pmpp.2002.0428
S.E. Ludwig S.R. Wessler (1990) ArticleTitleMaize R gene family: Tissue specific helix-loop-helix proteins Cell 62 849–851 Occurrence Handle1:CAS:528:DyaK3cXls1KitL0%3D Occurrence Handle2203535 Occurrence Handle10.1016/0092-8674(90)90259-H
M.D. McMullen M. Snook E.A. Lee P. Byrne H. Kross T. Musket K. Houchin E.H. Coe (2001) ArticleTitleThe biological basis of epistasis between quantitative trait loci for flavone and 3-deoxyanthocyanin synthesis in maize (Zea mays L.) Genome 44 667–676 Occurrence Handle1:CAS:528:DC%2BD3MXntVKqt7s%3D Occurrence Handle11550903 Occurrence Handle10.1139/gen-44-4-667
G. Moore K.M. Devos Z. Wang M.D. Gale (1995) ArticleTitleCereal Genome Evolution: Grasses, line up and form a circle Curr. Biol. 5 737–739 Occurrence Handle1:CAS:528:DyaK2MXnt1agsrg%3D Occurrence Handle7583118
D.T. Morishige K.L. Childs L.D. Moore J.E. Mullet (2002) ArticleTitleTargeted analysis of orthologous Phytochrome A regions of the sorghum, maize and rice genomes using comparative gene-island sequencing Plant Physiol. 130 1614–1625 Occurrence Handle1:CAS:528:DC%2BD3sXktlei Occurrence Handle12481045 Occurrence Handle10.1104/pp.012567
M. Nei T. Gojobori (1986) ArticleTitleSimple methods for estimating the number of synonymous and non-synonymous nucleotide substitutions Mol. Biol. Evol. 3 418–426 Occurrence Handle1:CAS:528:DyaL28Xmt1aisbs%3D Occurrence Handle3444411
A.H. Paterson J.E. Bowers B.A. Chapman (2004) ArticleTitleAncient polyploidization predating divergence of the cereals, and its consequences for comparative genomics Proc. Natl. Acad. Sci. USA. 101 9903–9908 Occurrence Handle1:CAS:528:DC%2BD2cXlvVahtbY%3D Occurrence Handle15161969
J.P. Radicella D. Brown L.A. Tolar V.L. Chandler (1992) ArticleTitleAllelic diversity of the maize B regulatory gene: Different leader and promoter sequences of two alleles determine distinct tissue specificities of anthocyanin production Genes Dev. 6 2152–2164 Occurrence Handle1:CAS:528:DyaK3sXhvFCm Occurrence Handle1427078
W. Ramakrishna J. Emberton P. SanMiguel M. Ogden V. Llaca J. Messing J.L. Bennetzen (2002) ArticleTitleComparative sequence analysis of the sorghum Rph region and maize Rp1 resistance gene complex Plant Physiol. 130 1728–1738 Occurrence Handle1:CAS:528:DC%2BD3sXktlCi Occurrence Handle12481055 Occurrence Handle10.1104/pp.014951
M.A. Saghai-Maroof K.M. Soliman R.A. Jorgensen R.W. Allard (1984) ArticleTitleRibosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics Proc. Natl. Acad. Sci. USA. 81 8014–8018 Occurrence Handle1:CAS:528:DyaL2MXptlWitg%3D%3D Occurrence Handle6096873
J. Sambrook D.W. Russell (2001) Molecular Cloning: A Laboratory Manual Cold Spring Harbor Laboratory Press New York
Z. Schwarz-Sommer N. Shepherd E. Tacke A. Gierl W. Rohde et al. (1987) ArticleTitleInfluence of transposable elements on the structure and function of the A1 gene of Zea mays EMBO J. 6 287–294 Occurrence Handle1:CAS:528:DyaL2sXktVWktL0%3D Occurrence Handle15981326
D.A. Selinger D. Lisch V.L. Chandler (1998) ArticleTitleThe maize regulatory gene B-Peru contains a DNA rearrangement that specifies tissue-specific expression through both positive and negative promoter elements Genetics 149 1125–1138 Occurrence Handle1:CAS:528:DyaK1cXks1eht7Y%3D Occurrence Handle9611220
L.V. Sidorenko X. Li S.M. Cocciolone S. Chopra L. Tagliani B. Bowen M. Daniels T. Peterson (2000) ArticleTitleComplex structure of a maize Myb gene promoter: functional analysis in transgenic plants Plant J. 22 471–482 Occurrence Handle1:CAS:528:DC%2BD3cXltFKksLg%3D Occurrence Handle10886767 Occurrence Handle10.1046/j.1365-313x.2000.00750.x
B.A. Snyder R.L. Nicholson (1990) ArticleTitleSynthesis of phtyoalexins in sorghum as a site-specific response to fungal ingress Science 248 1637–1639 Occurrence Handle1:CAS:528:DyaK3cXkslGju7o%3D
R. Song V. Llaca J. Messing (2001) ArticleTitleSequence, regulation and evolution of the maize 22-kD α zein gene family Genome Res. 11 1817–1825 Occurrence Handle1:CAS:528:DC%2BD3MXotlajur8%3D Occurrence Handle11691845
E.D. Styles O. Ceska (1977) ArticleTitleThe genetic control of flavonoid synthesis in maize Can J. Genet. Cytol .19 289–302
E.D. Styles O. Ceska (1989) ArticleTitlePericarp flavonoids in genetic strains of Zea mays Maydica 34 227–237
J.D. Thompson T.J. Gibson F. Plewniak F. Jeanmougin D.G. Higgins (1997) ArticleTitleThe ClustalX windows interface: flexible strategies for multiple sequencealignment aided by quality analysis tools Nucleic Acids Res. 25 4876–4882 Occurrence Handle1:CAS:528:DyaK1cXntFyntQ%3D%3D Occurrence Handle9396791 Occurrence Handle10.1093/nar/25.24.4876
C.A. Zanta X. Yang J.D. Axtell J.L. Bennetzen (1994) ArticleTitleThe Candystripe locus, y-cs, determines mutable pigmentation of the sorghum leaf, flower, and pericarp J. Hered. 85 23–29
P. Zhang S. Chopra T. Peterson (2000) ArticleTitleA segmental gene duplication generated differentially expressed myb-homologous genes in maize Plant Cell 12 2311–2322 Occurrence Handle1:CAS:528:DC%2BD3MXns1ShsA%3D%3D Occurrence Handle11148280
P. Zhang Y. Wang J. Zhang S. Maddock M. Snook T. Peterson (2003) ArticleTitleA maize QTL for silk maysin levels contains duplicated Myb-homologous genes which jointly regulate flavone biosynthesis Plant Mol. Biol. 52 1–15 Occurrence Handle1:CAS:528:DC%2BD3sXktFSntb4%3D Occurrence Handle12825685
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Boddu, J., Jiang, C., Sangar, V. et al. Comparative Structural and Functional Characterization of Sorghum and Maize Duplications Containing Orthologous Myb Transcription Regulators of 3-Deoxyflavonoid Biosynthesis. Plant Mol Biol 60, 185–199 (2006). https://doi.org/10.1007/s11103-005-3568-1
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/s11103-005-3568-1