Gaut, B.S.(2002).Evolutionary dynamics of grass genomes.New Phytol.154,15–28.
Gaut, B.S.,Morton, B.R.,McCaig, B.M.,and Clegg,M.T.(1996). Substitution rate comparisons between grasses and palms:Synony-mous rate differences in the nuclear gene Adh parallel rate differences at the plastid gene A93,10274–10279. Gealy,D.R.,Tai,T.H.,and Sneller,C.H.(2002).Identification of red rice,rice,and hybrid populations using microsatellite markers.Weed Sci.50,333–339.
Glahn,R.,Cheng,Z.,and Welch,R.(2002).Comparison of iron bioavailability from15rice genotypes:Studies using an in vitro digestion/caco-2cell culture model.J.Agric.Food Chem.50,3586–3591.
Goff,S.,Cone,K.,and Chandler,V.(1992).Functional analysis of the transcriptional activator encoded by the maize B gene:Evidence for a direct functional interaction between two classes of regulatory pro-teins.Genes Dev.6,864–875.
Grotewold,E.,Drummond,B.,Bowen,B.,and Peterson,T.(1994). The myb-homologous P gene controls phlobaphene pigmentation in maizefloral organs by directly activating aflavonoid biosynthetic gene subset.Cell76,543–553.
Gu,X.-Y.,Kianian,S.F.,Hareland,G.A.,Hoffer,B.L.,and Foley,M.E. (2005).Genetic analysis of adaptive syndromes interrelated with seed dormancy in weedy rice(Oryza sativa).Theor.Appl.Genet.110,1108–1118.
Hall,T.A.(1999).BioEdit:A user-friendly biological sequence alignment editor and analysis program for Windows95/98/NT.Nucleic Acids Symp.Ser.41,95–98.
Hartmann,U.,Sagasser,M.,Mehrtens, F.,Stracke,R.,and Weisshaar,B.(2005).Differential combinatorial interactions of cis-acting elements recognized by R2R3-MYB,BZIP,and BHLH factors control light-responsive and tissue-specific activation of phenylpro-panoid biosynthesis genes.Plant Mol.Biol.57,155–171.
Heim,M.A.,Jakoby,M.,Werber,M.,Martin,C.,Weisshaar,B.,and Bailey,P.C.(2003).The basic helix-loop-helix transcription factor family in plants:A genome-wide study of protein structure and functional diversity.Mol.Biol.Evol.20,735–747.
Hernandez,J.M.,Heine,G.F.,Irani,N.G.,Feller, A.,Kim,M.-G., Matulnik,T.,Chandler,V.L.,and Grotewold,E.(2004).Different mechanisms participate in the R-dependent activity of the R2R3MYB transcription factor C1.J.Biol.Chem.279,48205–48213.
Hu,J.,Beth,A.,and Wessler,S.R.(1996).Isolation and characteriza-tion of rice R genes:Evidence for distinct evolutionary paths in rice and maize.Genetics142,1021–1031.
Huelsenbeck,J.P.,and Ronquist, F.(2001).Mr Bayes:Bayesian inference of phylogeny.Bioinformatics17,754–755.
Ithal,N.,and Reddy, A.R.(2004).Riceflavonoid pathway genes, OsDfr and OsAns,are induced by dehydration,high salt and ABA, and contain stress responsive promoter elements that interact with the transcription activator,OsC1-MYB.Plant Sci.166,1505–1513.
Kato,S.,and Ishikawa,J.(1921).On the inheritance of the pigment of red rice.Jpn.J.Genet.1,1–7.
Kinoshita,T.(1998).Linkage mapping using mutant genes in rice.Rice Genet.Newsl.15,13–74.
Kubo,H.,Peeters, A.J.M.,Aarts,M.G.M.,Pereira, A.,and Koornneef,M.(1999).ANTHOCYANINLESS2,a homeobox gene affecting anthocyanin distribution and root development in Arabi-dopsis.Plant Cell11,1217–1226.
Ling,W.H.,Cheng,Q.X.,Ma,J.,and Wang,T.(2001).Red and black rice decrease atherosclerotic plaque formation and increase antiox-idant status in rabbits.J.Nutr.131,1421–1426.
Liu,Y.,Wang,L.,Kermicle,J.,and Wessler,S.R.(1998).Molecular
consequences of Ds insertion into and excision from the helix-loop-helix domain of the maize R gene.Genetics150,1639–1648. McCouch,S.R.,et al.(2002).Development and mapping of2240new SSR markers for rice(Oryza sativa L.).DNA Res.9,199–207. Myers,S.,Bottolo,L.,Freeman,C.,McVean,G.,and Donnelly,P. (2005).Afine-scale map of recombination rates and hotspots across the human genome.Science310,321–324.
Nesi,N.,Clarisse,J.,Debeaujon,I.,Caboche,M.,and Lepinec,L. (2001).The Arabidopsis TT2gene encodes an R2R3MYB domain protein that acts as a key determinant for proanthocyanidin accumu-lation in developing seed.Plant Cell13,2099–2114.
Nesi,N.,Debeaujon,I.,Jond,C.,Pelletier,G.,Caboche,M.,and Lepiniec,L.(2000).The TT8gene encodes a basic helix-loop-helix domain protein required for expression of DFR and BAN genes in Arabidopsis siliques.Plant Cell12,1863–1878.
Oki,T.,Masuda,M.,Kobayashi,M.,Nishiba,Y.,Furuta,S.,Suda,I., and Sato,T.(2002).Polymeric procyanidins as radical-scavenging components in red-hulled rice.J.Agric.Food Chem.50,7524–7529. Panaud,O.,Chen,X.,and McCouch,S.R.(1995).Frequency of microsatellite sequences in rice(Oryza sativa L.).Genome38,1170–1176.
Paris,M.,and Carter,M.(2000).Cereal DNA:A rapid high-throughput extraction method for marker assisted selection.Plant Mol.Biol.Rep. 18,357–360.
Payne,C.T.,Zhang,F.,and Lloyd,A.M.(2000).GL3encodes a bHLH protein that regulates trichome development in Arabidopsis through interaction with GL1and TTG1.Genetics156,1349–1362.
Puget,N.,Gad,S.,Perrin-Vidoz,L.,Sinilnikova,O.M.,Stoppa-Lyonnet, D.,Lenoir,G.M.,and Mazoyer,S.(2002).Distinct BRCA1rearrangements involving the BRCA1pseudogene suggest the existence of a recombination hot spot.Am.J.Hum.Genet.70, 858–865.
Sagasser,M.,Lu,G.-H.,Hahlbrock,K.,and Weisshaar,B.(2002).A. thaliana TRANSPARENT TESTA1is involved in seed coat develop-ment and defines the WIP subfamily of plant zincfinger proteins. Genes Dev.16,138–149.
Saitoh,K.,Onishi,K.,Mikami,I.,Thidar,K.,and Sano,Y.(2004). Allelic diversification at the C(OsC1)locus of wild and cultivated rice: Nucleotide changes associated with phenotypes.Genetics168,997–1007.
Sakamoto,W.,Ohmori,T.,Kageyama,K.,Miyzaki,C.,Saito,A., Murata,M.,Noda,K.,and Maekawa,M.(2001).The purple leaf(pl) locus of rice:The Pl w allele has a complex organization and includes two genes encoding basic helix-loop-helix proteins involved in an-thocyanin biosynthesis.Plant Cell Physiol.42,982–991. Schlueter,J.A.,Dixon,P.,Granger,C.,Grant,D.,Clark,L.,Doyle, J.J.,and Shoemaker,R.C.(2004).Mining the EST databases to resolve evolutionary events in major crop species.Genome47, 868–876.
Septiningsih, E.M.,Trijatmiko,K.R.,Moeljopawiro,S.,and McCouch,S.R.(2003).Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64and the wild relative O.rufipogon.Theor.Appl. Genet.107,1433–1441.
Shah,M.M.,and Hassan,A.(2005).Distribution of genes and recom-bination on wheat homoeologous group6chromosomes:A synthesis of available information.Mol.Breed.15,45–53.
Shirley,B.(1998).Flavonoids in seeds and grains:Physiological func-tion,agronomic importance and the genetics of biosynthesis.Seed Sci.Res.8,415–422.
Sompornpailin,K.,Makita,Y.,Yamazaki,M.,and Saito,K.(2002).
A WD-repeat-containing putative regulatory protein in anthocyanin biosynthesis in Perilla frutescens.Plant Mol.Biol.50,485–495.
Rc Encodes bHLH Protein Red Rice293