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Albar L, Bangratz-Reyser M, Hèbrard E, Ndjiondjop MN, Jones M, Ghesquiére A (2006) A single nucleotide polymorphism in the translation initiation factor eIF(iso)4G confers resistance of rice to Rice Yellow Mottle Virus. Plant J 47:417–426
Ammiraju JSS, Luo M, Goicoechea JL, Wang W, Kudrna D, Mueller C, Talag J, Kim HR, Sisneros NB, Blackmon B, Tomkins JB, Brar D, MacKill D, McCouch S, Kurata N, Lambert G, Galbraith DW, Arumuganathan K, Rao K, Walling JG, Gill N, Yu Y, SanMiguel P, Soderlund C, Jackson S, Wing RA (2006) The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Res 16:140–147
Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J (2004) Biomercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics 20:2324–2326
Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005) Cytokinin-oxidase regulates rice grain production. Science 309:741–745
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanisms and function. Cell:116:281–297
Bedell JA, Budiman MA, Nunberg A, Citek RW, Robbins D, Jones J, Flick E, Rholfing T, Fries J, Bradford K, McMenamy J, Smith M, Holeman H, Roe BA, Wiley G, Korf IF, Rabinowicz PD, Lakey N, McCombie WR, Jeddeloh JA, Martienssen RA (2005) Sorghum genome sequencing by methylation filtration. PLoS Biol 3(1):e13 (DOI: 10.1371/journal.pbio.0030013)
Bennetzen JL, Ma J (2003) The genetic collinearity of rice and other cereals on the basis of genomic sequence analysis. Curr Opin Plant Biol 6:128–133
Bennetzen JL, Ramakrishna W (2002) Numerous small rearrangements of gene content, order and orientation differentiates grass genomes. Plant Mol Biol 48:821–827
Bennetzen JL, Coleman C, Liu R, Ma J, Ramakrishna W (2004) Consistent over-estimation of gene number in complex plant genomes. Curr Opin Plant Biol 7:732–736
Berardini TZ, Mundodi S, Reiser L, Huala E, Garcia-Hernandez M, Zhang P, Mueller LA, Yoon J, Doyle A, Lander G, Moseyko N, Yoo D, Xu I, Zoeckler B, Montoya M, Miller N, Weems D, Rhee SY (2004) Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol 135:745–755
Blanc G, Wolfe KH (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667–1678
Blanc G, Barakat A, Guyot R, Cooke R, Delseny M (2000) Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12:1093–1101
Bomblies K, Doebley JF (2006) Pleiotropic effects of the duplicate maize FLORICAULA/LEAFY genes Zfl1 and Zfl2on traits under selection during maize domestication. Genetics 172:519–531
Bommert PB, Lunde C, Nardmann J, Vollbrecht E, Running MP, Jackson D, Hake S, Werr W (2005) thick tassel dwarf 1 encodes a putative maize orthologue of the ArabidopsisCLAVATA 1 leucine-rich receptor-like kinase. Development 132:1235–1245
Bonnet E, Wuyts J, Rouze P, van dePeer Y (2004) Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci USA 101:11511–11516
Bortiri E, Chuck G, Vollbrecht E, Rocheford T, Martienssen R, Hake S (2006a) ramosa2encodes a LARERAL ORGAN BOUNDARY domain protein that determines the fate of stem cells in branch meristem of maize. Plant Cell 18:574–585
Bortiri E, Jackson D, Hake S (2006b) Advances in maize genomics: the emergence of positional cloning. Curr Opin Plant Biol 9:164–171
Bowers JE, Arias MA, Asher R, Avise JA, Ball RT, Brewer GA, Buss RYW, Chen AH, Edwards TM, Estill JC, Exum HE, Goff VH, Herrick KL, James Steele CL, Karunakaran S, Lafayette GK, Lemke C, Marler BS, Master SL, McMillan JM, Nelson LK, Newsome GA, Nwakanma CC, Odeh RN, Phelps CA, Rarick EA, Rogers, CJ, Ryan SP, Slaughter KA, Soderlund CA, Tang H, Wing RA, Paterson AH (2005) Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Proc Natl Acad Sci USA 102:13206–13211
Bradbury LMT, Fitzgerald TL, Henry RJ, Jin Q, Waters DLE (2005) The gene for fragrance in rice. Plant Biotech J 3:363–370
Brueggeman R, Rostoks N, Kudrna D, Kilian A, Han F, Chen J, Druka A, Steffenson B, Kleinhofs A (2002) The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases. Proc Natl Acad Sci USA 99:9328–9333
Brunner S, Keller B, Feuillet C (2003) A large rearrangement involving genes and low-copy DNA interrupts the microcollinearity between rice and barley at the rph7 locus. Genetics 164:673–683
Brunner S, Fengler K, Morgante M, Tingey S, Rafalski A (2005) Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17:343–360
Buchanan CD, Lim S, Salzman R, Kagiampakis I, Morishige DT, Weers BD, Klein RR, Pratt LH, Cordonnier-Pratt MM, Klein PE, Mullet JE (2005) Sorghum bicolor’s transcriptome response to dehydration, high salinity and ABA. Plant Mol Biol 58:699–720
Caldwell KS, Langridge P, Powell W (2004) Comparative sequence analysis of the region harboring the hardness locus in barley and its colinear region in rice. Plant Physiol 136:3177–3190
Causier B, Castillo R, Zhou J, Ingram R, Xue Y, Schwarz-Sommer Z, Davies B (2005) Evolution in action: following function in duplicated floral homeotic genes. Curr Biol 15:1508–1512
Chantret N, Salse J, Sabot F, Rahman S, Bellec A, Laubin F, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier MF, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Bernard M, Leroy P, Chaloub B (2005) Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploidy wheat species (Triticum and Aegilops) Plant Cell 17:1033–1045
Chardon F, Virlon B, Moreau L, Falque M, Joets J, Decousset L, Murigneux A, Charcosset A (2004) Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genetics 168:2169–2185
Chardon F, Hourcade D, Combes V, Charcosset A (2005) Mapping of a spontaneous mutation for early flowering time in maize highlights contrasting allelic series at two-linked QTL on chromosome 8. Theor Appl Genet 112:1–11
Chen H, Wang S, Xing Y, Xu C, Hayes PM, Zhang Q (2005) Comparative analyses of genomic locations and race specificities of loci for quantitative resistance to Pyricularia grisea in rice and barley. Proc Natl Acad Sci USA 100:2544–2549
Clark RM, Linton E, Messing J, Doebley J (2004) Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc Natl Acad Sci USA 101:700–707
Collins NC, Lahaye T, Peterhansel C, Freialdenhoven A, Corbitt M, Schulze-Lefert P (2001) Sequence haplotypes revealed by sequence-tagged site fine mapping of the Ror1 gene in the centromeric region of barley chromosome 1H. Plant Physiol 125:1236–1247
Collins NC, Thordal-Christensen H, Lipka V, Bau S, Kombrink E, Qiu JL, Huckelhoven R, Stein M, Freialdenhoven A, Somerville SC, Schulze-Lefert P (2003) SNARE-protein-mediated disease resistance at the plant cell wall. Nature 425:973–977
Dardick C, Ronald P (2006) Plant and animal pathogen recognition receptors signal through non-RD kinases. PLoS Pathogens 2:14–28
Devos KM (2005) Updating the ‘crop circle’. Curr Opin Plant Biol 8:155–162
Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Yoshimura A (2004) Edh1, a B type response regulator in rice, confers short day promoting of flowering and controls FT-like gene expression independently of Hd1. Genes Dev 18:926–936
Dong Q, Lawrence CJ, Schlueter SD, Wilkerson MD, Kurtz S, Lushbough C, Brendel V (2005) Comparative plant genomics resources at plant GDB. Plant Physiol 139:610–618
Doust AN, Devos KM, Gadberry MD, Gale MD, Kellog EA (2005) The genetic basis for inflorescence variation between foxtail and green millet (Poaceae) Genetics 169:1659–1672
Draper J, Mur LAJ, Jenkins G, Ghosh-Biswas C, Bablak P, Hasterok R, Routledge APM (2001) Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiol 127:1539–1555
Duan M, Sun SS (2005) Profiling the expression of genes controlling rice grain quality. Plant Mol Biol 59:165–178
Duan K, Luo YH, Luo D, Xu ZH, Xue HW (2005) New insights into the complex and coordinated transcriptional regulation networks underlying rice seed development through cDNA chip-based analysis. Plant Mol Biol 57:785–804
Dugas DV, Bartel B (2004) MicroRNA regulation of gene expression in plants. Curr Opin Plant Biol 7:512–520
Dunford RP, Yano M, Kurata N, Sasaki T, Huestis G, Rocheford T, Laure DA (2002) Comparative mapping of the barley Ppd-H1 photoperiod response gene region, which lies close to a junction between two rice linkage segments. Genetics 161:825–834
Emberton J, Ma J, Yuan Y, SanMiguel P, Bennetzen JL (2005) Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries. Genome Res 15:1441–1446
Etzel CJ, Guerra R (2002) Meta-analysis of genetic-linkage analysis of quantitative-trait loci. Am J Hum. Genet 71:56–65
Feltus FA, Wa NJ, Schultze SR, Estill JC, Jiang N, Paterson AH (2004) An SNP resource for rice genetics and breeding based on subspeciesindicaand japonica genome alignments. Genome Res 14:1812–1819
Feuillet C, Keller B (2002) Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann Bot 89:3–10
Fritz-Laylin LK, Krishnamurthy N, Tör M, Sjölander KV, Jones JD (2005) Phylogenomic analysis of the receptor-like proteins of rice and Arabidopsis. Plant Physiol 138:611–623
Fu H, Dooner HK (2002) Intraspecific violation of genetic colinearity and its implications in maize. Proc Natl Acad Sci USA 99:9573–9578
Gallavotti A, Zhao Q, Kyozuka J, Meeley RB, Ritter MK, Doebley JF, Pe ME, Schmidt RJ (2004) The role of barren stalk1 in the architecture of maize. Nature 432:630–635
Gaut BS, Doebley JF (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci USA 94:6809–6814
Gaut BS, Peek AS, Morton BR, Clegg MT (1999) Patterns of genetic diversification within the Adh gene family in the grasses (Poaceae) Mol Biol Evol 16:1086–1097
Ge S, Sang T, Lu BR, Hong DY (1999) Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc Natl Acad Sci USA 96:14400–14405
Goff, SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica) Science 296:92–100
Goffinet B, Gerber S (2000) Quantitative trait loci: a meta-analysis. Genetics 155:463–473
Gottwald S, Stein N, Borner A, Sasaki T, Graner A (2004) The gibberellic-acid insensitive dwarfing gene sdw3 of barley is located on chromosome 2HS in a region that shows high colinearity with rice chromosome 7L. Mol Gen Genomics 271:426–436
Griffiths S, Dunford RP, Coupland G, Laurie DA (2003) The evolution of CONSTANS-likegene families in barley, rice and Arabidopsis. Plant Physiol 131:1855–1867
Griffiths S, Sharp R, Foote TN, Bertin I, Wanous M, Reader S, Colas I, Moore G (2006) Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature 439:749–752
Gu YQ, Coleman-Derr D, Kong X, Anderson OD (2004) Rapid genome evolution revealed by comparative sequence analysis of orthologous regions from four triticeae genomes. Plant Physiol 135:459–470
Gualtieri G, Conner JA, Morishige DT, Moore D, Mullet JE, Ozias-Akins P (2006) A segment of the apospory-specific genomic region is highly microsyntenic not only between the apomicts Pennisetum squamulatum and buffelgrass, but also with a rice chromosome 11 centromeric-proximal genomic region. Plant Physiol 140:963–971
Guo H, Moose SP (2003) Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell 15:1143–1158
Guyot R, Keller B (2004) Ancestral genome duplication in rice. Genome 47: 610–614
Guyot R, Yahiaoui N, Feuillet C, Keller B (2004) In silico comparative analysis reveals a mosaic conservation of genes within a novel colinear region in wheat chromosome 1AS and rice chromosome 5S. Funct Integr Genomics 4:47–58
Haberer G, Young S, Bharti AK, Gundlach H, Raymond C, Fuks G, Butler E, Wing RA, Rounsley S, Birren B, Nusbaum C, Mayer KF, Messing J (2005) Structure and architecture of the maize genome. Plant Physiol 139:1612–1624
Hamel LP, Nicole MC, Sritubtim S, Morency MJ, Ellis M, Ehlting J, Beaudoin N, Barbazuk B, Klessig D, Lee J, Martin G, Mundy J, Ohashi Y, Scheel D, Sheen J, Xing T, Zhang S, Seguin A, Ellis BE (2006) Ancient signals: comparative genomics of plant MAPK and MAPKK gene families. Trends Plant Sci 11:192–198
Hampson S, McLysaght A, Gaut B, Baldi P (2003) LineUp: statistical detection of chromosomal homology with application to plant comparative genomics. Genome Res 13:1–12
Han B, Xue Y (2003) Genome-wide intraspecific DNA sequence variations in rice. Curr Opin Plant Biol 6:134–138
Harlan JR (1992) Crops and Man. 2nd Ed. CSSA and ASA, Madison, WI.
Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R (2004) The Gene Ontology (GO) database and informatics resource. Nucl Acids Res 32:258–261
Hayama R, Coupland G (2004) The molecular basis of diversity in the photoperiodic flowering responses of Arabidopsis and rice. Plant Physiol 135:677–684
Hu FY, Tao DY, Sacks E, Fu BY, Xu P, Li J, Yang Y, McNally K, Khush GS, Paterson AH, Li ZK (2003) Convergent evolution of perenniality in rice and sorghum. Proc Natl Acad Sci USA 100:4050–4054
Huang LS, Brooks SA, Fellers JP, Gill BS (2003) Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploid genome of bread wheat. Genetics 164:655–664
Ilic K, SanMiguel PJ, Bennetzen JL (2003) A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes. Proc Natl Acad Sci USA 100:12265–12270
Ikeda A, Ueguchi-Tanaka M, Sonoda Y, Kitano H, Koshioka M, Futsuhara Y, Matsuoka M, Yamaguchi J. (2001) slender rice, a constitutive gibberellin response mutant is caused by a null mutation of the SLR1 gene, an orthologue of the height-regulating gene GAI/RGA/RHT/$D8$. Plant Cell 13:999–1010
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800
Isidore E, Scherrer B, Chaloub B, Feuillet C, Keller B (2005) Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levels. Genome Res 15:526–536
Izawa T, Takahashi Y, Yano M (2003) Comparative biology comes into bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis. Curr Opin Plant Biol 6:113–120
Jackson S, Rounsley S, Purugganan M (2006) Comparative sequencing: choices to make. Plant Cell 18:1100–1104
Jain M, Kaur N, Tyagi A, Khurana J (2006) The auxin-responsive GH3gene family in rice Oryza sativa. Funct Integr Genomics 6:36–46
Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S (2006) Gramene: a bird’s eye view of cereal genomes. Nucl Acids Res 34:717–723
Jeon JS, Jang S, Lee S, Nam J, Kim C, Lee SH, Chung YY, Kim SR, Lee YH, Cho YG, An G (2000) leafy hull sterile 1 is a homeotic mutation in a rice MADS box gene affecting rice flower development. Plant Cell 12:871–884
Jiao Y, Ma L, Strickland E, Deng XW (2005) Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. Plant Cell 17:3239–3256
Juarez MT, Kui JS, Thomas J, Heller BA, Timmermans MC (2004) MicroRNA-mediated repression of rolled leaf 1 specifies maize leaf polarity. Nature 428:84–88
Katagiri S, Wu J, Ito Y, Karasawa W, Shibata M, Kanamori H, Katayose Y, Namiki N, Matsumoto T, Sasaki T (2004) End sequencing and chromosomal in silico mapping of BAC clones derived from an indica rice cultivar, Kasalath. Breeding Sci 54:273–279
Katari MS, Balija V, Wilson R K, Martienssen RA, McCombie WR (2005) Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. Genome Res 15:496–504
Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, Galbraith D, Bohnert HJ (2001) Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13:889–905
Kellogg EA (2001) Evolutionary history of the grasses. Plant Physiol 125:1198–1205
Kellogg EA (2004) Evolution of developmental traits. Curr Opin Plant Biol 7:92–98
Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T, Otomo Y, Murakami K, Iida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, Xie Q, Lu M, Narikawa R, Sugiyama A, Mizuno K, Yokomizo S, Niikura J, Ikeda R, Ishibiki J, Kawamata M, Yoshimura A, Miura J, Kusumegi T, Oka M, Ryu R, Ueda M, Matsubara K, Kawai J, Carninci P, Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Hayatsu N, Imotani K, Ishii Y, Itoh M, Kagawa I, Kondo S, Konno H, Miyazaki A, Osato N, Ota Y, Saito R, Sasaki D, Sato K, Shibata K, Shinagawa A, Shiraki T, Yoshino M, Hayashizaki Y, Yasunishi A (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301:376–379
Kim JS, Islam-Faridi MN, Klein PE, Stelly DM, Price HJ, Klein RR, Mullet JE (2005) Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice. Genetics 171:1963–1976
Klein PE, Klein RR, Vrebalov J, Mullet JE (2003) Sequence-based alignment of sorghum chromosome 3 and rice chromosome 1 reveals extensive conservation of gene order and one major chromosomal rearrangement. Plant J 34:605–621
Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T, Yano M (2002) Hd3a, a rice orhtolog of the Arabidopsis FT gene, promotes transition to flowering downstream ofHd1 under short day condition. Plant Cell Physiol 43:1096–1105
Komatsu K, Maekawa M, Ujiie S, Satake Y, Furutani I, Okamoto H, Shimamoto K, Kyozuka J (2003) LAX and SPA: major regulators of shoot branching in rice. Proc Natl Acad Sci USA 100:11765–11770
Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M (2006) An SNP caused loss of seed shattering during rice domestication. Science 312:1392–1396
Kramer EM, Jaramillo MA, DiStilio VS (2004) Patterns of gene duplication and functional evolution during the diversification of the AGAMOUSsubfamily of MADS box genes in angiosperms. Genetics 166:1011–1023
Kresovich S, Barbazuk B, Bedell JA, Borell A, Buell CR, Clifton S, Cordonnier-Pratt MM, Cox S, Dahlberg J, Erpelding J, Fulton TM, Fulton B, Fulton L, Gingle AR, Hash CT, Huang Y, Jordan D, Klein PE, Klein RR, Magalhaes J, McCombie R, Moore P, Mullet JE, Ozias-Akins P, Paterson AH, Porter K, Pratt L, Roe B, Rooney W, Schnable PS, Stelly DM, Tuinstra M, Ware D, Warek U (2005) Towards sequencing the sorghum genome: a US National Science Foundation-sponsored workshop report. Plant Physiol 138:1898–1902
Kurata N, Yamazaki Y (2006) Oryzabase. An integrated biological and genome information database for rice. Plant Physiol 140:12–17
Lahaye T, Shirazu K, Schulze-Lefert P (1998) Chromosome landing at the barley Rar1 locus. Mol Gen Genomics 260:92–101
Lai J, Ma J, Swigonova Z, Ramakrishna W, Linton E, Llaca V, Tanyolac B, Park Y-J, Jeong O-Y, Bennetzen JL, Messing J (2004) Gene loss and movement in the maize genome. Genome Res 14:1924–1931
Lai J, Li Y, Messing J, Dooner HK (2005) Gene movement by helitron transposons contributes to the haplotype variability of maize. Proc Natl Acad Sci USA 102:9068–9073
Langham RJ, Walsh J, Dunn M, Ko C, Goff SA, Freeling M (2004) Genomic duplication, fractionalization and the origin of regulatory novelty. Genetics 166:935–945
La Rota M, Sorrells ME (2004) Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat. Funct Integr Genomics 4:34–46
Le Cunff L, Garsmeur O, Telismart H, Begum D, Deu M, Wing R, Glaszmann JC, Raboin LM, D’Hont A (2007) Exploitation of sorghum genetic and physical maps for fine gene mapping of the rust resistance gene Bru 1 in the high polyploid sugarcane. Theor Appl Genet (In Press)
Lee JH, Cho YS, Yoon HS, Suh MC, Moon J, Lee I, Weigl D, Yun CH, Kim JK (2005) Conservation and divergence of FCA function between Arabidopsisand rice. Plant Mol Biol 58:823–838
Levy AA, Feldman M (2002) The impact of polyploidy on grass genome evolution. Plant Physiol 130:1587–1593
Li C, Ni P, Francki M, Hunter A, Zhang Y, Schibeci D, Li H, Tarr A, Wang J, Cakir M, Yu J, Bellgard M, Lance R, Appels R (2004) Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison. Funct Integr Genomics 4:84–93
Li C, Zhou A, Sang T (2006a) Rice domestication by reducing shattering. Science 311:1936–1939
Li L, Wang X, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J, Deng XW (2006b) Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 38:124–129
Lijavetzky D, Carbonero P, Vicente-Carbajosa J (2003) Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families. BMC Evol Biol 3:17–27
Lim J, Jung JW, Lim CE, Lee MH, Kim BJ, Kim M, Bruce WB, Benfey PN (2005) Conservation and diversification of SCARECROW in maize. Plant Mol Biol 59:619–630
Linkiewicz AM, Qi LL, Gill BS, Ratnasiri A, Echalier B, Chao S, Lazo GR, Hummel DD, Anderson OD, Akhunov ED, Dvorak J, Pathan MS, Nguyen HT, Peng JH, Lapitan NL, Miftahudin, Gustafson JP, La Rota CM, Sorrells ME, Hossain KG, Kalavacharla V, Kianian SF, Sandhu D, Bondareva SN, Gill KS, Conley EJ, Anderson JA, Fenton RD, Close TJ, McGuire PF, Qualset CO, Dubcovsky J (2004) A 2500 locus bin map of wheat homeologous group 5 provides insights on gene distribution and colinearity with rice. Genetics 168:665–676
Lockton S, Gaut BS (2005) Plant conserved non-coding sequences and paralogue evolution. Trends Genet 21:60–65
Lukens L, Doebley J (2001) Molecular evolution of the teosinte branched gene among maize and related grasses. Mol Biol Evol 118:627–638
Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101:12404–12410
Ma J, SanMiguel P, Lai J, Messing J, Bennetzen JL (2005a) DNA rearrangement in orthologous orpregions of the maize, rice and sorghum genomes. Genetics 170:1209–1220
Ma L, Chen C, Liu X, Jiao Y, Su N, Li L, Wang X, Cao M, Sun N, Bao J, Li J, Pedersen S, Bolund L, Zhao H, Yuan L, Wong GK-S, Wang J, Deng XW, Wang J (2005b) A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res 15:1274–1283
Magalhaes JV, Garvin DF, Wang Y, Sorells ME, Klein PE, Schaffert RE, Li L, Kochian LV (2004) Comparative mapping of a major aluminium tolerance gene in sorghum and other species in the poaceae. Genetics 167:1905–1914
Malcomber ST, Kellogg EA (2004) Heterogenous expression patterns and separate roles of the SEPALLATA gene LEAFY HULL STERILE 1in grasses. Plant Cell 16:1692–1706
Mallory AC, Vaucheret H (2004) MicroRNAs: something important between the genes. Curr Opin Plant Biol 7:120–125
McCough SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Scheider D, Carthinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.) DNA Res 9:99–207
McLaren CG, Bruskiewich RM, Portugal AM, Cosico AB (2005) The international rice information system. A platform for meta-analysis of rice crop data. Plant Physiol 139:637–642
McSteen P (2006) Branching out: theramosa pathway and the evolution of grass inflorescence morphology. Plant Cell 18:518–522
Messing J, Dooner HK (2006) Organization and variability of the maize genome. Curr Opin Plant Biol 9:157–163
Mester DI, Ronin YI, Korostishevsky MA, Pikus VL, Glazman AE, Korol AB (2006) Multilocus consensus genetic maps (MCGM): formulation, algorithms, and results. Comput Biol Chem 30:12–20
Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, Maehara Y, Tanji M, Sato M, Nasu S, Minobe Y (2002) Positional cloning of rice semidwarfing gene, sd1: rice “green revolution gene” encodes a mutant enzyme involved in gibberellin synthesis. DNA Res 9:11–17
Moore G, Devos KM, Wang Z, Gale MD (1995) Cereal genome evolution: grasses, line up and form a circle. Curr Biol 5:737–739
Moore RC, Purugganan MD (2005) The evolutionary dynamics of plant duplicate genes. Curr Opin Plant Biol 8:122–128
Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, Rafalski A (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37:997–1002
Munkvold JD, Greene RA, Bermudez Kandianis CE, La Rota CM, Edwards H, Sorrells SF, Dake T, Kantety R, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorak J, Miftahudin, Gustafson JP, Pathan MS, Nguyen HT, Mathews DE, Chao S, Lazo GR, Hummel DD, Anderson OD, Anderson JA, Gonzalez-Hernandez JL, Peng JH, Lapitan N, Qi LL, Echalier B, Gill BS, Hossain KG, Kalavacharla V, Kianian SF, Sandhu D, Erayman M, Gill KS, McGuire PE, Qualset CO, Sorrells ME (2004) Group 3 chromosome bin maps of wheat and their relationship to rice chromosome 1. Genetics 168:639–650
Nagano H, Onishi K, Ogasawara M, Horiuchi Y, Sano Y (2005) Genealogy of the “Green Revolution” gene in rice. Gene Genet Syst 80:351–356
Nam J, De Pamphilis CW, Ma H, Nei M (2003) Antiquity and evolution of the MADS-box gene family controlling flower development in plants. Mol Biol Evol 20:1435–1447
Nelson DR, Schuler MA, Paquette SM, Werck-Reichhart D, Bak S (2004) Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot. Plant Physiol 135: 756–772
Nelson WM, Bharti AK, Butler E, Wei F, Fuks G, Kim H, Wing RA, Messing J, Soderlund C (2005) Whole-genome validation of high information-content fingerprinting. Plant Physiol 139:27–38
Nogueira FTS, De Rosa VE, Menossi M, Ulian EC, Arruda P (2003) RNA expression profiles and data mining of sugarcane response to low temperature. Plant Physiol 132:1811–1824
Ohyanagi H, Tanaka T, Sakai H, Shigemoto Y, Yamaguchi K. Habara T, Fujii Y, Antonio BA, Nagamura Y, Imanishi T, Ikeo K, Itoh T, Gojobori T, Sasaki T (2006) The rice annotation project database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucl Acids Res 34:741–744
Olsen AN, Ernst HA, Lo Leggio L, Skriver K (2005) NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci 10:79–87
Ozturk ZN, Talame V, Deyholos M, Michalowski CB, Galbraith DW, Gozurkirmizi N, Tuberosa R, Bonhert HJ (2002) Monitoring large scale changes in transcript abundance in drought- and salt-stressed barley. Plant Mol Biol 48:551–573
Paterson AH (2006) Leafing through the genomes of our major crop plants: strategies for capturing unique information. Nat Rev Genet 7:174–184
Paterson AH, Lin RY, Li ZK, Schertz KF, Doebley JF, Pinson SRM, Liu S-C, Stansel JW, Irvine JE (1995) Convergent domestication of cereal crops by independant mutations at corresponding genetic loci. Science 269:1714–1718
Paterson AH, Bowers JE, Chapman BA (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci USA 101:9903–9908
Paterson AH, Freeling M, Sazaki T (2005) Grains of knowledge: genomics of model cereals. Genome Res 15:1643–1650
Pellio B, Streng S, Bauer E, Stein N, Perovic D, Schiemann A, Friedt W, Ordon F, Graner A (2005) High resolution mapping of the Rym4/Rym5 locus conferring resistance to the barley yellow mosaic virus complex (BaMMV, BaYMV, BaYMV-2) in barley (Hordeum vulgare ssp. vulgare L) Theor Appl Genet 110:283–293
Peng JH, Zadeh H, Lazo GR, Gustafson JP, Chao S, Anderson OD, Qi LL, Echalier B, Gill BS, Dilbirligi M, Sandhu D, Gill KS, Greene RA, Sorrells ME, Akhunov ED, Dvorak J, Linkiewicz AM, Dubcovsky J, Hossain KG, Kalavacharla V, Kianian SF, Mahmoud AA, Miftahudin, Conley EJ, Anderson JA, Pathan MS, Nguyen HT, McGuire PE, Qualset CO, Lapitan N (2004) Chromosome bin map of expressed sequence tags in homeologous group 1 of hexaploid wheat and homeology with rice and Arabidopsis. Genetics 168:609–623
Peng JR, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, Beales J, Fish LJ, Worland AJ, Pelica F, Sudhakar D, Christou P, Snape JW, Gale MD, Harberd NP (1999) ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature 400:256–261
Prasad V, Stromberg CA, Alimohammadian H, Sahni A (2005) Dinosaur coprolites and the early evolution of grasses and grazers. Science 310:1177–1180
Pratt LH, Liang C, Shah M, Sun F, Wang H, Reid SP, Gingle AR, Paterson AH, Wing R, Dean R, Klein R, Nguyen HT, Ma HM, Zhao X, Morishige DT, Mullet JE, Cordonnier-Pratt MM (2005) Sorghum expressed sequence tags identify signature genes for drought, pathogenesis, and skotomorphogenesis from a milestone set of 16,801 unique transcripts. Plant Physiol 139:8869–8884
Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvorak J, Linkiewicz AM, Ratnasiri A, Dubcovsky J, Bermudez-Kandianis CE, Greene RA, Kantety R, La Rota CM, Munkvold JD, Sorrells SF, Sorrells ME, Dilbirligi M, Sidhu D, Erayman M, Randhawa HS, Sandhu D, Bondareva SN, Gill KS, Mahmoud AA, Ma X-F, Miftahudin, Gustafson JP, Conley EJ, Nduati V, Gonzalez-Hernandez JL, Anderson JA, Peng JH, Lapitan NLV, Hossain KG, Kalavacharla V, Kianian SF, Pathan MS, Zhang DS, Nguyen HT, Choi D-W, Fenton RD, Close TJ, McGuire PE, Qualset CO, Gill BS (2004) A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168:701–712
Rabbani M, Maruyama K, Abe H, Khan M, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, Yamaguchi-Sinozali K (2003) Monitoring expression profiles of rice genes under cold, drought, and high salinity stresses and abscisic acid application using cDNA microarrays and RNA-gel blot analyses. Plant Physiol 133:1755–1767
Rabinowicz PD, Bennetzen JL (2006) The maize genome as a model for efficient sequence analysis of large plant genomes. Curr Opin Plant Biol 9:149–156
Ramakrishna W, Emberton J, SanMiguel P, Ogden M, Llaca V, Messing J, Bennetzen JL (2002) Comparative sequence analysis of the sorghum Rph region and the maize Rp1 resistance gene complex. Plant Physiol 130:1728–1738
Rensink WA, Buell CR (2004) Arabidopsis to rice. Applying knowledge from a weed to enhance our understanding of a crop species. Plant Physiol 135:622–629
Reyes JC, Muro-Pastor MI, Florencio FJ (2004) The GATA family of transcription factors in Arabidopsis and rice. Plant Physiol 134:1718–1732
Salse J, Piegu B, Cooke R, Delseny M (2004) New in silico insight into the synteny between rice (Oryza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genome. Plant J 38:396–409
Salvi S, Tuberosa R, Chiapparino E, Maccaferri M, Veillet S, Van Beuningen L, Isaac P, Edwards K, Phillips RL (2002) Toward positional cloning of Vgt1, a QTL controlling the transition from the vegetative to reproductive phase in maize. Plant Mol Biol 48:601–613
Salzman RA, Brady JA, Finlayson SA, Buchanan CD, Sun F, Kein PE, Klein RR, Pratt LH, Cordonnier-Pratt MM, Mullet JE (2005) Transcriptional profiling of sorghum induced by methyl jasmonate, salicylic acid, and aminocyclopropane carboxylic acid reveals co-operative regulation and novel gene responses. Plant Physiol 138:352–368
SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposon of maize. Nat Genet 20:43–45
Satoh-Nagasawa N, Nagasawa N, Malcomber S, Sakai H, Jackson D (2006) A trehalose metabolic enzyme controls inflorescence architecture in maize. Nature 441:227–230
Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y, Muramatsu M, Hayashizaki Y, Kawai J, Carninci P, Itoh M, Ishii Y, Arakawa T, Shibata K, Shinagawa A, Shinozaki K (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296:141–145
Shen QH, Zhou F, Bieri S, Haizel T, Shirazu K, Schulze-Lefert P (2003) Recognition specificity and RAR1/SGT1 dependence in barley Mla disease resistance genes to the powdery mildew fungus. Plant Cell 15:732–744
Shen Y, Jiang H, Jin JP, Zhang ZB, Xi B, He YY, Wang C, Qian L, Li X, Yu QB, Liu HJ, Chen DH, Gao JH, Huang H, Shi TL, Yang ZN (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 135:1198–1205
Shiu SH, Karlowski WM, Pan R, Tzeng YH, Mayer KFX, Li WH (2004) Comparative analysis of the receptor like kinase family in Arabidopsis and rice. Plant Cell 16:1220–1234
Simons KJ, Fellers JP, Trick HN, Zhang Z, Tai YS, Gill B, Faris JD (2006) Molecular characterization of the major wheat domestication gene $Q$. Genetics 172:547–555
Skinner JS, Von Zitzewitz J, Szücs P, Marquez-Cedillo L, Filichkin T;, Amundsen K, Stockinger EJ, Thomashow MF, Chen THH, Hayes PM (2005) Structural, functional, and phylogenetic characterization of a large CBF gene family in barley. Plant Mol Biol 59:533–551
Song R, Llaca V, Messing J (2002) Mosaic organization of orthologous sequences in grass genomes. Genome Res 12:1549–1555
Springer NM, Kaeppler SM (2005) Evolutionary divergence of monocot and dicot methyl-CpG-binding domain proteins. Plant Physiol 138:92–104
Sterck L, Rombauts S, Jansson S, Sterky F, Rouze P, Van de Peer Y (2005) EST data suggest that poplar is an ancient polyploid. New Phytol 167:165–170
Sunkar R, Girke T, Kumar Jain P, Zhu JK (2005) Cloning and characterization of microRNA from rice. Plant Cell 17:1397–1411
Sutton T, Whitford R, Baumann U, Dong C, Able JA, Langridge P (2003) The Ph2 pairing homeologous locus of wheat (Triticum aestivum): identification of candidate meiotic genes using a comparative genomic approach. Plant J 36:443–456
Suzaki T, Sato M, Ashikari M, Miyoshi M, Nagato Y, Hirano HY (2004) The gene FLORAL ORGAN NUMBER1 regulates floral meristem size in rice and encodes a leucine-rich repeat receptor kinase orthologous to Arabidopsis CLAVATA1. Development 131:5649–5657
Swigonova Z, Bennetzen JL, Messing J (2005) Structure and evolution of the r/b chromosomal regions in rice maize and sorghum. Genetics 169:891–906
Takano M, Inagaki N, Xie X, Yuzurihara N, Hihara F, Ishizuka T, Yano M, Nishimura M, Miyao A, Hirochika H, Shimomura T (2005) Distinct and cooperative functions of Phytochromes A, B, and C in the control of deetiolation and flowering in rice. Plant Cell 17:3311–3325
Tanno KI, Wilcox G (2006) How fast was wild wheat domesticated? Science 311:1886
Tèrol J, Domingo C, Talon M (2006) The GH3 family in plants: genome wide analysis in rice and evolutionary history based on EST analysis. Gene 371:279–290
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
The Rice Chromosome 3 Sequencing Consortium (2005) Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res 15:1284–1291
The Rice Chromosomes 11 and 12 Sequencing Consortia (2005) The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biology 3:20 (http://www.biomedcentral.com/1741-7007/3/20)
Thomson MJ, Edwards JD, Septiningsih EM, Harrington SE, McCouch SR (2006) Substitution mapping ofdth1.1, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL. Genetics 172:2501–2514
Tian C, Wan P, Sun S, Li J, Chen M (2004) Genome-wide analysis of the GRAS gene family in rice and Arabidopsis. Plant Mol Biol 54:519–532
Turner, A, Beales J, Faure S, Dunford RP, and Laurie DA (2005) The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley. Science 310:1031–1034
Ueguchi-Tanaka M, Ashikari L, Nakajima M, Itoh H, Katoh E, Kobayashi M, Chow TY, Hsing YI, Kitano H, Yamaguchi I, Matsuoka M (2005) GIBBERELLIN INSENSITIVE DWARF 1 encodes a soluble receptor for gibberellin. Nature 437:693–698
Van de Poele K, Saeys Y, Simillion E, Raes J, Van dePeer Y (2002) The automatic detection of homologous regions (ADHoRE) and its application to microcolinearity between Arabidopsis and rice. Genome Res 12:1792–1801
Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–630
Vitte C, Ishii T, Lamy F, Brar D, Panaud O (2004) Genomic paleontology provides evidence for two distinct origin of Asian rice (Oryza sativa L) Mol Gen Genomics 272:504–511
Vollbrecht E, Springer PS, Goh L, Buckler ES, Martienssen R (2005) Architecture of floral branch systems in maize and related grasses. Nature 436:1119–1126
Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker SI, Mandal J, Xu J, Cui X, Close TJ (2005) Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol 139:822–835
Wang CJR, Harper L, Cande WZ (2006) High-resolution single copy gene fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome 9. Plant Cell 18:529–544
Wang G, Kong H, Sun Y, Zhang X, Zhang W, Altman N, De Pamphilis CW, Ma H (2004a) Genome-wide analysis of the cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclin-like proteins. Plant Physiol 135:1084–1089
Wang H, Yu L, Lai F, Liu L, Wang J (2005a) Molecular evidence for asymmetric evolution of sister duplicated blocks after cereal polyploidy. Plant Mol Biol 59:63–74
Wang H, Nussbaum-Wagler T, Li B, Zhao Q, Vigouroux Y, Faller M, Bomblies K, Lukens L, Doebley JF (2005b) The origin of naked grains of maize. Nature 436:714–719
Wang JF, Zhou H, Chen YQ, Luo QJ, Qu LH (2004b) Identification of 20 new miRNA from Oryza sativa. Nucl Acids Res 32:1688–1695
Wang RL, Dtec A, Hei J, Lukens L, Doebley J (1999) The limits of selection during maize domestication. Nature 398:236–239
Wang Z, Liang Y, Li C, Xu Y, Lan L, Zhao D, Chen C, Xu Z, Xue Y, Chong K (2005c) Microarray analysis of gene expression involved in anther development in rice (Oryza sativa L) Plant Mol Biol 58:721–737
Wessler SR (2006) Genome studies and molecular genetics: Part 2 Maize genomics The maize community welcomes the maize genome sequencing project. Curr Opinion in Plant Biology 9:147–148
Wicker T, Yahiaoui N, Guyot R, Schlagenhauf E, Liu ZD, Dubcovsky J, Keller B (2003) Rapid genome divergence at orthologous low molecular weight glutenin loci of the A and A$m$ genomes of wheat. Plant Cell 15:1187–1197
Wing R (2005) Unlocking the secrets of the rice genome. Plant Mol Biol (Special Issue) 59:1–219
Wu KL, Guo ZJ, Wang HH, Li J (2005) The WRKY family of transcription factors in rice and Arabidopsis and their origins. DNA Res 12:9–26
Xiong Y, Liu T, Tian C, Sun S, Li J, Chen M (2005) Transcription factor in rice: a genome-wide comparative analysis between monocots and eudicots. Plant Mol Biol 59:191–203
Xu Y, McCouch SR, Zhang Q (2005) How can we use genomics to improve cereals with rice as a reference genome? Plant Mol Biol 59:7–26
Yahiaoui N, Srichumpa P, Dudler R, Keller, B (2004) Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene Pm3b from hexaploid wheat. Plant J 37:528–538
Yan LL, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci USA 100:6263–6268
Yan LL, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W, San Miguel P, Echenique V, Dubcovsky J (2004) The wheat VRN2gene is a flowering repressor down-regulated by vernalization. Science 303:1640–1644
Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is a closely related to the Arabidopsis flowering gene CONSTANS. Plant Cell 12:2473–2484
Yap IV, Schneider D, Kleinberg J, Matthews D, Cartinhour S, McCouch SR (2003) A graph-theoretic approach to comparing and integrating genetic, physical and sequence-based maps. Genetics 165:2235–2247
Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp.indica). Science 296:79–92
Yu J, Wang J, LinW, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, LI R, Xu Z, Li S, Li X, Zheng H, Cong L, Lin L, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Wang J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Xiao Y, Bu D, Tan J, Yang L, Ye C, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Huang X, Su Z, Tong W, Tong Z, Ye J, Wang L, Lei T, Chen C, Chen H, Huang H, Zhang F, Li N, Zhao C, Huang Y, Li L, Xi Y, Qi Q, Li W, Hu W, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott J, Samudrala R, Wong G. K, Yang H (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3:266–281
Yuan Q, Ouyang S, Wang A, Zhu W, Maiti R, Lin H, Hamilton J, Haas B, Sultana R, Foo Cheung F, Wortman J, Buell CR (2005) The Institute for Genomic Research Osa1 rice genome annotation database. Plant Physiol 138:18–26
Yuan Y, SanMiguel P, Bennetzen JL (2002) Methylation spanning linker libraries link gene-rich regions and identify epigenetic boundaries in Zea mays. Genome Res 12:1345–1349
Yue B, Xue W, Xiong L, Yu X, Luo L, Cui K, Jin D, Xing Y, Zhang Q (2006) Genetic basis of drought resistance at reproductive stage in rice: separation of drought tolerance from drought avoidance. Genetics 172:1213–1228
Zahn LM, Kong H, Leebens-Mack JH, Kim S, Soltis PS, Landherr LL, Soltis DE, De Pamphilis CW, Ma H (2005) The evolution of the SEPALLATAsubfamily of MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm history. Genetics 169:2209–2223
Zhang S, Chen C, Li L, Meng L, Singh J, Jiang N, Deng XW, He ZH, Lemaux PG (2005) Evolutionary expansion, gene structure, and expression of the rice wall-associated kinase gene family. Plant Physiol 139:1107–1124
Zhang Y, Wang L (2005) The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol Biol 5:1 (http://www.biomedcentral.com/1471-2148/5/1)
Zhu T, Budworth P, Chen WQ, Provart N, Chang HS, Guimil S, Wu WP, Estes B, Zou GZ, Wang X (2003) Transcriptional control of nutrient partitioning during rice grain filling. Plant Biotechnol J 1:59–70
Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol 136:2621–2632
Zimmermann P, Schildknecht B, Craignan D, Garcia-Hernandez M, Gruissem W, May S, Mukherjee G, Parkinson H, Rhee S, Wagner U, Hennig L (2006) MIAME/Plant-adding value to plant microarray experiments. Plant Methods BMC 2:1 (http://www.plantmethods.com/content/2/1/1)
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Cooke, R. et al. (2007). From Rice to Other Cereals: Comparative Genomics. In: Rice Functional Genomics. Springer, New York, NY. https://doi.org/10.1007/0-387-48914-2_17
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