Ji, H-S, Chu, S-H, Jiang, W, Cho, Y-I, Hahn, J-H, Eun, M-Y, McCouch, S, Koh, H-J (2006) Characterization and mapping of a shattering mutant in rice that corresponds to a block of domestication genes.
Genetics (doi: 10.1534/genetics.105.054031)

Thomson M, Edwards J, Septiningsih E, Harrington S, McCouch S (2006) Substitution mapping of dth1.1, a flowering time QTL associated with transgressive variation in rice, reveals a cluster of QTLs.
Genetics (doi: 10.1534/genetics.105.050500)

Sweeney M, Pfeil B, McCouch S (2006) Rc, a bHLH protein conditioning red pericarp in rice, is orthologous to the maize intensifier1.
Plant Cell 18:283-294

Jaiswal P, Avaraham S, Ilic K, Kellogg E, McCouch S, Pujar A, Reiser L, Rhee S, Sachs M, Schaeffer M, Stein L, Stevens P, Leszek V, Ware D, Zapata F (2006) Plant Ontology (PO): A controlled vocabulary of plant structures and growth stages.
Comp Func Gen 6:388-397 (DOI:10.1002/cfg.496)

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 T, Buckler E, Stein L, McCouch S (2006) Gramene: A bird's eye view.
Nucleic Acids Research 34: D717-D723; doi: 10.1093/nar/gkj154

Ammiraju J, Luo M, Goicoechea JL, Wang W, Kudrna D, Mueller C, Talag J, Kim H, Sisneros NB, Blackmon B, Fang E, Tomkins JB, Brar D, MacKill D, McCouch SR, Kurata N, Lambert G, Galbraith DW, Arumuganathan K, Rao K, Walling JG, Gill N, Yu Y, SanMiguel P, Soderlund C, Jackson S and Wing RA (2005) The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genomes types of the genus Oryza.
Genome Research 16: 140-147

Comstock J, McCouch S, Martin B, Tauer C, Vision T, Xu Y, Pausch R (2005) The effects of resource availability and environmental conditions on genetic ranking for carbon isotope discrimination during growth in tomato and rice.
Func Pl Biol 32: 1089-1105

Xu Y, McCouch S, Zhang Q (2005) How can we use genomics to improve cereals with rice as a reference genome?
Pl Mol Biol 59: 7-26

International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome.
Nature 436: 793-800.
Supplemental Files

Zhang N, Xu Y, Akash M, McCouch S, Oard J (2005) Identification of candidate markers associated with agronomic traits in rice using discriminant analysis.
Theor Appl Genet 110: 721-729

Lee S-J, Oh C-S, Suh J-P, McCouch, S R, Ahn S-N (2005) Identification of QTLs for domestication-related and agronomic traits in an Oryza sativa x O. rufipogon BC1F7 population.
Pl Breed 124: 209-219

Lu H, Redus M, Coburn J, Rutger N, McCouch S, Tai T (2005) Population structure and breeding patterns of 145 U.S. rice cultivars based on SSR marker analysis.
Crop Sci 45: 66-76
Supplemental Files

Garris A, Tai T, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L.
Genetics: http://www.genetics.org/cgi/rapidpdf/genetics.104.035642v1
Supplemental Files

Semon M, Nielsen R, Jones M, McCouch S (2004) The population structure of African cultivated rice Oryza Glaberrima (Steud.): evidence for elevated levels of LD caused by admixture with O. sativa and ecological adaptation.
Genetics: DOI 1010.1534/genetics.104.033175
Supplemental Files

Fraker E, Li J, McCouch S (2004) SSR Mapping of Minute, a major gene for grain size, on rice chromosome 3.
Rice Genet Newsl 21: 21-23

Cho, Y-I, Park C-W, Kwon, S-W, Chin J-H, Ji, H-S, Park K-J, McCouch S, Koh, H-J (2004) Key DNA markers for predicting heterosis in F1 hybrids of japonica rice.
Breed Sci 54: 389-397
Supplemental Files

Semon M, Nielsen R, Jones M, McCouch S (2004) The population structure of African cultivated rice Oryza Glaberrima (Steud.): evidence for elevated levels of LD caused by admixture with O. sativa and ecological adaptation.
Genetics: DOI 1010.1534/genetics.104.033175
Supplemental Files

Li J, Thomson M, McCouch S (2004) Fine mapping of a grain weight QTL in the peri-centromeric region of rice chromosome 3.
Genetics 168: 2187-2195

McCouch S (2004) Diversifying Selection in Plant Breeding.
PLoS Biol 2(10): e347 (DOI: 10.1371/journal.pbio.0020347)

Iyer A and McCouch S (2004) The rice disease resistance gene xa5 encodes a novel form of disease resistance.
MPMI 17: 1348-1354

Li J, Xiao J, Grandillo S, Jiang L, Wan Y, Deng Q, Yuan L, McCouch S (2004) QTL detection for rice grain quality traits using an interspecific backcross population derived from cultivated Asian (O. sativa L.) and African (O. glaberrima S.) rice.
Genome 47: 697-704

Jain S, Jain R, McCouch S (2004) Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers.
Theor Appl Genet: 109: 965-977 (DOI: 10.1007/s00122-004-1700-2)
Supplemental Files

Edwards J, Lee VM, McCouch SR (2004) Sources and predictors of detectable indel polymorphism using rice as a model.
Mol Gen Genomics 271: 298-307

Moncada P and McCouch S (2004) Simple Sequence Repeat (SSR) diversity in diploid and tetraploid Coffea species.
Genome 47: 501-509

Xu Y, Beachell H, McCouch SR (2004) A marker-based approach to broadening the genetic base of rice (Oryza sativa L.) in the U.S.
Crop Science 44: 1947-1959
Supplemental Files

Yap I, Cartinhour S, Kleinberg J, Matthews D, Schneider D, McCouch S (2003) A graph-theoretic approach to integrating genetic linkage maps.
Genetics 165: 2235-2247

Garris A, McCouch S, Kresovich S (2003) Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 165: 759-769

Septiningsih E, Prasetiyono J, Lubis E, Tai TH, Tjubaryat T, Moeljopawiro S, McCouch SR (2003a) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon Theor Appl Genet 107:1419-1432.

Septiningsih E, Trijatmiko KR, Moeljopawiro S, McCouch SR (2003b) Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O.rufipogon. Theor Appl Genet 107:1433-1441.

Thomson M, Tai T, McClung A, Xai X-H, Hinga M, Lobos K, Xu Y, Martinez P, McCouch S (2003) Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107:479-493 DOI 10.1007_s00122-003-1270-8

Blair M, Garris A, Iyer A, Chapman B, Kresovich S, McCouch S (2003) High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice (Oryza sativa L.). Theor Appl Genet 107:62-73

McCouch S, Teytelman L, Xu Y, Lobos K, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L. (2002) Development of 2,240 new SSR markers for rice (Oryza sativa L.) DNA Res.9:199-207

Ware D, Jaiswal P, Ni J, Yap I, Pan X, Clark K, Teytelman L, Schmidt S, Zhao W, Chang K, Cartinhour S, Stein L, McCouch S (2002) Gramene, a tool for Grass Genomics. Pl. Phys. 130: 1606-1613.
Supplemental Files

Jiang N, Bao Z, Zhang X, Hirochika H, Eddy SR, McCouch SR and Wessler SR (2002) An active transposon family in rice. Nature 421:163-167.

Chen X, Cho Y, McCouch SR (2002) Sequence divergence of rice microsatellites in Oryza and other plant species. Mol Gen Genet 268:331-343 (DOI.1007/s00438-002-0739-5)

Jiang N, Bao Z, Temnykh S, Cheng Z, Jiang J, Wing RA, McCouch SR, Wessler SR (2002) Dasheng: A recently amplified nonautonomous Ltr elelment that is a major component of pericentromeric regions in rice. Genetics 161: 1293-1305

Coburn J., S Temnykh, E Paul, SR McCouch (2002) Design and Application of Microsatellite Marker Panels for Semi-automated Genotyping of Rice (Oryza sativa L.). Crop Science 42: 2092-2099
Supplemental Files

Ho J, McCouch SR, Smith ME (2002) Improvement of hybrid yield by advanced backcross QTL analysis in elite maize. Theor Appl Genet 105:440-448 (DOI 10.1007/s00122-002-0945-x)

Blair MW, V Hedatale and SR McCouch (2002) Fluorescent-labeled microsatellite panels useful for detecting allelic diversity in cultivated rice (Oryza sativa L.) Theor Appl Genet DOI 10.1007/s00122-002-0921-5

Ware D, P Jaiswal, J Ni, X Pan, K Chang, K Clark, L Teytelman, S Schmidt, W Zhao, S Cartinhour, S McCouch, L Stein (2002) Gramene: A Resource for Comparative Grass Genomics. Nucl Acids Res 30:103-105

Jaiswal J, Ware D, Ni J, Chang, K, Zhao W, Schmidt S, Pan X, Clark K, Teytelman L, Cartinhour S, Stein L, McCouch S (2002) Gramene: development and integration of trait and gene ontologies for rice. Comp Funct Genom 3:132-136 (DOI: 10.1002/cfg.156)

Moncada MP, CP Martínez, J Tohme, E Guimaraes, M Chatel, J Borrero, H Gauch, Jr. and SR McCouch (2001) Quantitative trait loci for yield and yield components in an Oryza sativa x Oryza rufipogon BC2F2 population evaluated in an upland environment. Theor Appl Genet 102:41-52

Basu D, K Dehesh, HJ Schneider-Poetsch, SE Harrington, SR McCouch and PH Quail (2001) Rice PHYC gene: structure, expression, map position and evolution. Pl Mol Biol 44:27-42

McCouch SR (2001) Genomics and Synteny. Plant Physiol 125:152-155

Ishii T, Y Xu, SR McCouch (2001) Nuclear and chloroplast microsatellite variation in A-genome species of rice. Genome 44:648-666

Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S and McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Research 11:1441-1452
Temnykh

Temnykh S, W D Park, N Ayres, S Cartinhour, N Hauck, L Lipovich, YG Cho, T Ishii , SR McCouch (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.) Theor Appl Genet 100:697-712

Cho YG, T Ishii, S Temnykh, X Chen, L Lipovich, SR McCouch (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.) Theor Appl Genet 100:713-722

Maheswaran M, N Huang, SR Sreerangasamy and SR McCouch (2000) Mapping quantitative trait loci associated with days to flowering and photoperiod sensitivity in rice (Oryza sativa L.) Mol Breed 6:145-155

Ishii T and SR McCouch (2000) Microsatellites and microsynteny in the chloroplast genomes of Oryza and eight other Gramineae species. Theor Appl Genet 100:1257-1266