Susan McCouch - Publications

Affiliations: 
Cornell University, Ithaca, NY, United States 
Area:
Genetics, Molecular Biology, Biostatistics Biology

128 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Eizenga GC, Jia MH, Jackson AK, Boykin DL, Ali ML, Shakiba E, Tran NT, McCouch SR, Edwards JD. Validation of Yield Component Traits Identified by Genome-Wide Association Mapping in a × Rice Biparental Mapping Population. The Plant Genome. 12. PMID 30951093 DOI: 10.3835/plantgenome2018.04.0021  0.4
2017 Thomson MJ, Singh N, Dwiyanti MS, Wang DR, Wright MH, Perez FA, DeClerck G, Chin JH, Malitic-Layaoen GA, Juanillas VM, Dilla-Ermita CJ, Mauleon R, Kretzschmar T, McCouch SR. Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications. Rice (New York, N.Y.). 10: 40. PMID 28856618 DOI: 10.1186/s12284-017-0181-2  1
2017 Kim J, Lee HJ, Jung YJ, Kang KK, Tyagi W, Kovach M, Sweeney M, McCouch S, Cho YG. Functional properties of an alternative, tissue-specific promoter for rice NADPH-dependent dihydroflavonol reductase. Plos One. 12: e0183722. PMID 28841686 DOI: 10.1371/journal.pone.0183722  0.84
2017 Daygon VD, Calingacion M, Forster LC, Voss JJ, Schwartz BD, Ovenden B, Alonso DE, McCouch SR, Garson MJ, Fitzgerald MA. Metabolomics and genomics combine to unravel the pathway for the presence of fragrance in rice. Scientific Reports. 7: 8767. PMID 28821745 DOI: 10.1038/s41598-017-07693-9  0.4
2017 Shakiba E, Edwards JD, Jodari F, Duke SE, Baldo AM, Korniliev P, McCouch SR, Eizenga GC. Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis. Plos One. 12: e0172133. PMID 28282385 DOI: 10.1371/journal.pone.0172133  0.4
2016 Kim H, Jung J, Singh N, Greenberg A, Doyle JJ, Tyagi W, Chung JW, Kimball J, Hamilton RS, McCouch SR. Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice. Rice (New York, N.Y.). 9: 56. PMID 27730519 DOI: 10.1186/s12284-016-0119-0  1
2016 Bessho-Uehara K, Wang DR, Furuta T, Minami A, Nagai K, Gamuyao R, Asano K, Angeles-Shim RB, Shimizu Y, Ayano M, Komeda N, Doi K, Miura K, Toda Y, Kinoshita T, ... ... McCouch SR, et al. Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice. Proceedings of the National Academy of Sciences of the United States of America. PMID 27466405 DOI: 10.1073/pnas.1604849113  1
2016 McCouch SR, Wright MH, Tung CW, Maron LG, McNally KL, Fitzgerald M, Singh N, DeClerck G, Perez FA, Korniliev P, Greenberg AJ, Naredo ME, Mercado SM, Harrington SE, Shi Y, et al. Corrigendum: Open access resources for genome-wide association mapping in rice. Nature Communications. 7: 11346. PMID 27094317 DOI: 10.1038/ncomms11346  0.4
2016 Wang DR, Bunce JA, Tomecek MB, Gealy D, McClung A, McCouch SR, Ziska LH. Evidence for divergence of response in Indica, Japonica, and wild rice to high CO2 x temperature interaction. Global Change Biology. PMID 26959982 DOI: 10.1111/gcb.13279  1
2016 McCouch SR, Wright MH, Tung CW, Maron LG, McNally KL, Fitzgerald M, Singh N, DeClerck G, Agosto-Perez F, Korniliev P, Greenberg AJ, Naredo ME, Mercado SM, Harrington SE, Shi Y, et al. Open access resources for genome-wide association mapping in rice. Nature Communications. 7: 10532. PMID 26842267 DOI: 10.1038/ncomms10532  1
2016 Crowell S, Korniliev P, Falcão A, Ismail A, Gregorio G, Mezey J, McCouch S. Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters. Nature Communications. 7: 10527. PMID 26841834 DOI: 10.1038/ncomms10527  1
2016 Spindel JE, Begum H, Akdemir D, Collard B, Redoña E, Jannink JL, McCouch S. Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement Heredity. 116: 395-408. DOI: 10.1038/hdy.2015.113  1
2016 Ogawa S, Valencia MO, Lorieux M, Arbelaez JD, McCouch S, Ishitani M, Selvaraj MG. Identification of QTLs associated with agronomic performance under nitrogen-deficient conditions using chromosome segment substitution lines of a wild rice relative, Oryza rufipogon Acta Physiologiae Plantarum. 38. DOI: 10.1007/s11738-016-2119-5  1
2016 Moncada MDP, Tovar E, Montoya JC, González A, Spindel J, McCouch S. A genetic linkage map of coffee (Coffea arabica L.) and QTL for yield, plant height, and bean size Tree Genetics and Genomes. 12: 1-17. DOI: 10.1007/s11295-015-0927-1  1
2015 Piñeros MA, Larson BG, Shaff JE, Schneider DJ, Falcão AX, Yuan L, Clark RT, Craft EJ, Davis TW, Pradier PL, Shaw NM, Assaranurak I, McCouch SR, Sturrock C, Bennett M, et al. Evolving technologies for growing, imaging, and analyzing 3D root system architecture of crop plants. Journal of Integrative Plant Biology. PMID 26683583 DOI: 10.1111/jipb.12456  1
2015 Kang H, Wang Y, Peng S, Zhang Y, Xiao Y, Wang D, Qu S, Li Z, Yan S, Wang Z, Liu W, Ning Y, Korniliev P, Leung H, Mezey J, ... McCouch SR, et al. Dissection of the genetic architecture of rice resistance to the blast fungus Magnaporthe oryzae. Molecular Plant Pathology. PMID 26574735 DOI: 10.1111/mpp.12340  1
2015 Spindel J, Wright M, Chen C, Cobb J, Gage J, Harrington S, Lorieux M, Ahmadi N, McCouch S. Erratum to: Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. PMID 26520113 DOI: 10.1007/s00122-015-2618-6  0.64
2015 Furuta T, Komeda N, Asano K, Uehara K, Gamuyao R, Shim-Angeles RB, Nagai K, Doi K, Wang DR, Yasui H, Yoshimura A, Wu J, McCouch SR, Ashikari M. Convergent Loss of Awn in Two Cultivated Rice Species Oryza sativa and Oryza glaberrima Is Caused by Mutations in Different Loci. G3 (Bethesda, Md.). PMID 26338659 DOI: 10.1534/g3.115.020834  1
2015 Gould B, McCouch S, Geber M. De Novo Transcriptome Assembly and Identification of Gene Candidates for Rapid Evolution of Soil Al Tolerance in Anthoxanthum odoratum at the Long-Term Park Grass Experiment. Plos One. 10: e0124424. PMID 26148203 DOI: 10.1371/journal.pone.0124424  1
2015 Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink JL, McCouch SR. Correction: Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines. Plos Genetics. 11: e1005350. PMID 26125618 DOI: 10.1371/journal.pgen.1005350  1
2015 Hua L, Wang DR, Tan L, Fu Y, Liu F, Xiao L, Zhu Z, Fu Q, Sun X, Gu P, Cai H, McCouch SR, Sun C. LABA1, a Domestication Gene Associated with Long, Barbed Awns in Wild Rice. The Plant Cell. PMID 26082172 DOI: 10.1105/tpc.15.00260  1
2015 Yan J, Aboshi T, Teraishi M, Strickler SR, Spindel JE, Tung CW, Takata R, Matsumoto F, Maesaka Y, McCouch SR, Okumoto Y, Mori N, Jander G. The Tyrosine Aminomutase TAM1 Is Required for β-Tyrosine Biosynthesis in Rice. The Plant Cell. 27: 1265-78. PMID 25901084 DOI: 10.1105/tpc.15.00058  1
2015 Begum H, Spindel JE, Lalusin A, Borromeo T, Gregorio G, Hernandez J, Virk P, Collard B, McCouch SR. Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa). Plos One. 10: e0119873. PMID 25785447 DOI: 10.1371/journal.pone.0119873  1
2015 Arbelaez JD, Moreno LT, Singh N, Tung CW, Maron LG, Ospina Y, Martinez CP, Grenier C, Lorieux M, McCouch S. Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga. Molecular Breeding : New Strategies in Plant Improvement. 35: 81. PMID 25705117 DOI: 10.1007/s11032-015-0276-7  1
2015 Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink JL, McCouch SR. Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines. Plos Genetics. 11: e1004982. PMID 25689273 DOI: 10.1371/journal.pgen.1004982  1
2015 Pariasca-Tanaka J, Lorieux M, He C, McCouch S, Thomson MJ, Wissuwa M. Development of a SNP genotyping panel for detecting polymorphisms in Oryza glaberrima/O. sativa interspecific crosses Euphytica. 201: 67-78. DOI: 10.1007/s10681-014-1183-4  1
2014 Schatz MC, Maron LG, Stein JC, Hernandez Wences A, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban E, Wright MH, Chia JM, Ware D, McCouch SR, McCombie WR. Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biology. 15: 506. PMID 25468217 DOI: 10.1186/PREACCEPT-2784872521277375  1
2014 Gould B, McCouch S, Geber M. Variation in soil aluminium tolerance genes is associated with local adaptation to soils at the Park Grass Experiment. Molecular Ecology. 23: 6058-72. PMID 25145641 DOI: 10.1111/mec.12893  1
2014 Kim H, Jeong EG, Ahn SN, Doyle J, Singh N, Greenberg AJ, Won YJ, McCouch SR. Nuclear and chloroplast diversity and phenotypic distribution of rice (Oryza sativa L.) germplasm from the democratic people's republic of Korea (DPRK; North Korea). Rice (New York, N.Y.). 7: 7. PMID 25006358 DOI: 10.1186/s12284-014-0007-4  1
2014 Varshney RK, Terauchi R, McCouch SR. Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. Plos Biology. 12: e1001883. PMID 24914810 DOI: 10.1371/journal.pbio.1001883  1
2014 Alfred J, Dangl JL, Kamoun S, McCouch SR. New horizons for plant translational research. Plos Biology. 12: e1001880. PMID 24914542 DOI: 10.1371/journal.pbio.1001880  1
2014 Li JY, Liu J, Dong D, Jia X, McCouch SR, Kochian LV. Natural variation underlies alterations in Nramp aluminum transporter (NRAT1) expression and function that play a key role in rice aluminum tolerance. Proceedings of the National Academy of Sciences of the United States of America. 111: 6503-8. PMID 24728832 DOI: 10.1073/pnas.1318975111  1
2014 Crowell S, Falcão AX, Shah A, Wilson Z, Greenberg AJ, McCouch SR. High-Resolution Inflorescence Phenotyping Using a Novel Image-Analysis Pipeline, PANorama. Plant Physiology. 165: 479-495. PMID 24696519 DOI: 10.1104/pp.114.238626  1
2014 Cardoso C, Zhang Y, Jamil M, Hepworth J, Charnikhova T, Dimkpa SO, Meharg C, Wright MH, Liu J, Meng X, Wang Y, Li J, McCouch SR, Leyser O, Price AH, et al. Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 orthologs. Proceedings of the National Academy of Sciences of the United States of America. 111: 2379-84. PMID 24464483 DOI: 10.1073/pnas.1317360111  1
2014 Eizenga GC, Ali ML, Bryant RJ, Yeater KM, McClung AM, McCouch SR. Registration of the Rice Diversity Panel 1 for genomewide association studies Journal of Plant Registrations. 8: 109-116. DOI: 10.3198/jpr2013.03.0013crmp  1
2014 Ogawa S, Selvaraj MG, Fernando AJ, Lorieux M, Ishitani M, McCouch S, Arbelaez JD. N- and P-mediated seminal root elongation response in rice seedlings Plant and Soil. 375: 303-315. DOI: 10.1007/s11104-013-1955-y  1
2014 Gartner GAL, McCouch SR, Botero MDPM. Segregation analysis of molecular markers in a population de-rived from Coffea liberica Hiern x C. eugenioides L Acta Agronomica. 63.  1
2013 Dharmawardhana P, Ren L, Amarasinghe V, Monaco M, Thomason J, Ravenscroft D, McCouch S, Ware D, Jaiswal P. A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. Rice (New York, N.Y.). 6: 15. PMID 24280345 DOI: 10.1186/1939-8433-6-15  1
2013 Spindel J, Wright M, Chen C, Cobb J, Gage J, Harrington S, Lorieux M, Ahmadi N, McCouch S. Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 126: 2699-716. PMID 23918062 DOI: 10.1007/s00122-013-2166-x  1
2013 Jung JK, McCouch S. Getting to the roots of it: Genetic and hormonal control of root architecture. Frontiers in Plant Science. 4: 186. PMID 23785372 DOI: 10.3389/fpls.2013.00186  1
2013 Takano-Kai N, Jiang H, Powell A, McCouch S, Takamure I, Furuya N, Doi K, Yoshimura A. Multiple and independent origins of short seeded alleles of GS3 in rice. Breeding Science. 63: 77-85. PMID 23641184 DOI: 10.1270/jsbbs.63.77  1
2013 Cobb JN, Declerck G, Greenberg A, Clark R, McCouch S. Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 126: 867-87. PMID 23471459 DOI: 10.1007/s00122-013-2066-0  1
2013 Clark RT, Famoso AN, Zhao K, Shaff JE, Craft EJ, Bustamante CD, McCouch SR, Aneshansley DJ, Kochian LV. High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development. Plant, Cell & Environment. 36: 454-66. PMID 22860896 DOI: 10.1111/j.1365-3040.2012.02587.x  1
2013 Bandillo N, Raghavan C, Muyco PA, Sevilla MAL, Lobina IT, Dilla-Ermita CJ, Tung CW, McCouch S, Thomson M, Mauleon R, Singh RK, Gregorio G, Redoña E, Leung H. Multi-parent advanced generation inter-cross (MAGIC) populations in rice: Progress and potential for genetics research and breeding Rice. 6. DOI: 10.1186/1939-8433-6-11  1
2013 Imai I, Kimball JA, Conway B, Yeater KM, McCouch SR, McClung A. Validation of yield-enhancing quantitative trait loci from a low-yielding wild ancestor of rice Molecular Breeding. 32: 101-120. DOI: 10.1007/s11032-013-9855-7  1
2013 Gartner GAL, McCouch SR, Moncada MDP. A genetic map of an interspecific diploid pseudo testcross population of coffee Euphytica. 192: 305-323. DOI: 10.1007/s10681-013-0926-y  1
2012 Chen C, DeClerck G, Tian F, Spooner W, McCouch S, Buckler E. PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants. Plos One. 7: e46596. PMID 23144785 DOI: 10.1371/journal.pone.0046596  1
2012 McCouch SR, McNally KL, Wang W, Sackville Hamilton R. Genomics of gene banks: A case study in rice. American Journal of Botany. 99: 407-23. PMID 22314574 DOI: 10.3732/ajb.1100385  1
2012 Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L, Li J, He W, Zhang G, Zheng X, Zhang F, ... ... McCouch S, et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology. 30: 105-11. PMID 22158310 DOI: 10.1038/nbt.2050  1
2012 Shen QJ, Yu D, Jeon JS, Piffanelli P, Abbruscato P, Guo ZJ, Zhang Y, Itoh T, Lee SS, Buell CR, Nagato Y, McCouch S, Yano M, Wang Gl, Jena KK, et al. Nomenclature report on rice WRKY's - conflict regarding gene names and its solution Rice. 5: 1-3. DOI: 10.1186/1939-8433-5-3  1
2012 McCouch SR, Kovach MJ, Sweeney M, Jiang H, Semon M. The dynamics of rice domestication: A balance between gene flow and genetic isolation Biodiversity in Agriculture: Domestication, Evolution, and Sustainability. 311-329. DOI: 10.1017/CBO9781139019514.018  1
2012 Thomson MJ, Zhao K, Wright M, McNally KL, Rey J, Tung CW, Reynolds A, Scheffler B, Eizenga G, McClung A, Kim H, Ismail AM, de Ocampo M, Mojica C, Reveche MY, ... ... McCouch SR, et al. High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform Molecular Breeding. 29: 875-886. DOI: 10.1007/s11032-011-9663-x  1
2011 Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nature Communications. 2: 467. PMID 21915109 DOI: 10.1038/ncomms1467  1
2011 Famoso AN, Zhao K, Clark RT, Tung CW, Wright MH, Bustamante C, Kochian LV, McCouch SR. Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. Plos Genetics. 7: e1002221. PMID 21829395 DOI: 10.1371/journal.pgen.1002221  1
2011 Clark RT, MacCurdy RB, Jung JK, Shaff JE, McCouch SR, Aneshansley DJ, Kochian LV. Three-dimensional root phenotyping with a novel imaging and software platform. Plant Physiology. 156: 455-65. PMID 21454799 DOI: 10.1104/pp.110.169102  1
2011 Tian Z, Yu Y, Lin F, Yu Y, Sanmiguel PJ, Wing RA, McCouch SR, Ma J, Jackson SA. Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis. Bmc Genomics. 12: 142. PMID 21385395 DOI: 10.1186/1471-2164-12-142  1
2011 Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, et al. Gramene database in 2010: updates and extensions. Nucleic Acids Research. 39: D1085-94. PMID 21076153 DOI: 10.1093/nar/gkq1148  1
2011 Liakat Ali M, McClung AM, Jia MH, Kimball JA, McCouch SR, Eizenga GC. A rice diversity panel evaluated for genetic and agro-morphological diversity between subpopulations and its geographic distribution Crop Science. 51: 2021-2035. DOI: 10.2135/cropsci2010.11.0641  1
2011 Ahmed ZU, Panaullah GM, Gauch H, McCouch SR, Tyagi W, Kabir MS, Duxbury JM. Genotype and environment effects on rice (Oryza sativa L.) grain arsenic concentration in Bangladesh Plant and Soil. 338: 367-382. DOI: 10.1007/s11104-010-0551-7  1
2011 Kaushik A, Jain S, McCouch SR, Jain RK. Phylogenetic relationships among various groups of rice {Oryza sativa L.) as revealed by microsatellite and transposable element-based marker analysis Indian Journal of Genetics and Plant Breeding. 71: 139-150.  1
2010 Wright MH, Tung CW, Zhao K, Reynolds A, McCouch SR, Bustamante CD. ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. Bioinformatics (Oxford, England). 26: 2952-60. PMID 20926420 DOI: 10.1093/bioinformatics/btq533  1
2010 Famoso AN, Clark RT, Shaff JE, Craft E, McCouch SR, Kochian LV. Development of a novel aluminum tolerance phenotyping platform used for comparisons of cereal aluminum tolerance and investigations into rice aluminum tolerance mechanisms. Plant Physiology. 153: 1678-91. PMID 20538888 DOI: 10.1104/pp.110.156794  1
2010 Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A, Bustamante CD, McCouch SR. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. Plos One. 5: e10780. PMID 20520727 DOI: 10.1371/journal.pone.0010780  1
2010 Maas LF, McClung A, McCouch S. Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 120: 895-908. PMID 19949767 DOI: 10.1007/s00122-009-1219-7  1
2010 Orjuela J, Garavito A, Bouniol M, Arbelaez JD, Moreno L, Kimball J, Wilson G, Rami JF, Tohme J, McCouch SR, Lorieux M. A universal core genetic map for rice. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 120: 563-72. PMID 19847389 DOI: 10.1007/s00122-009-1176-1  1
2010 Ji H, Kim SR, Kim YH, Kim H, Eun MY, Jin ID, Cha YS, Yun DW, Ahn BO, Lee MC, Lee GS, Yoon UH, Lee JS, Lee YH, Suh SC, ... ... McCouch SR, et al. Inactivation of the CTD phosphatase-like gene OsCPL1 enhances the development of the abscission layer and seed shattering in rice. The Plant Journal : For Cell and Molecular Biology. 61: 96-106. PMID 19807881 DOI: 10.1111/j.1365-313X.2009.04039.x  1
2010 McCouch SR, Zhao K, Wright M, Tung CW, Ebana K, Thomson M, Reynolds A, Wang D, Declerck G, Ali ML, Mcclung A, Eizenga G, Bustamante C. Development of genome-wide SNP assays for rice Breeding Science. 60: 524-535. DOI: 10.1270/jsbbs.60.524  1
2010 Tung CW, Zhao K, Wright MH, Ali ML, Jung J, Kimball J, Tyagi W, Thomson MJ, McNally K, Leung H, Kim H, Ahn SN, Reynolds A, Scheffler B, Eizenga G, ... ... McCouch SR, et al. Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.) Rice. 3: 205-217. DOI: 10.1007/s12284-010-9056-5  1
2010 This D, Comstock J, Courtois B, Xu Y, Ahmadi N, Vonhof WM, Fleet C, Setter T, McCouch S. Genetic analysis of water use efficiency in rice (Oryza sativa L.) at the leaf level Rice. 3: 72-86. DOI: 10.1007/s12284-010-9036-9  1
2010 Cho YG, Kang HJ, Lee YT, Jong SK, Eun MY, McCouch SR. Identification of quantitative trait loci for physical and chemical properties of rice grain Plant Biotechnology Reports. 4: 61-73. DOI: 10.1007/s11816-009-0120-9  1
2010 Asante MD, Kovach MJ, Huang L, Harrington S, Dartey PK, Akromah R, Semon M, McCouch S. The genetic origin of fragrance in NERICA1 Molecular Breeding. 26: 419-424. DOI: 10.1007/s11032-009-9382-8  1
2010 Thomson MJ, Ismail AM, McCouch SR, Mackill DJ. Marker assisted breeding Abiotic Stress Adaptation in Plants: Physiological, Molecular and Genomic Foundation. 451-469. DOI: 10.1007/978-90-481-3112-9_20  1
2009 Ni J, Pujar A, Youens-Clark K, Yap I, Jaiswal P, Tecle I, Tung CW, Ren L, Spooner W, Wei X, Avraham S, Ware D, Stein L, McCouch S. Gramene QTL database: development, content and applications. Database : the Journal of Biological Databases and Curation. 2009: bap005. PMID 20157478 DOI: 10.1093/database/bap005  1
2009 Kovach MJ, Calingacion MN, Fitzgerald MA, McCouch SR. The origin and evolution of fragrance in rice (Oryza sativa L.). Proceedings of the National Academy of Sciences of the United States of America. 106: 14444-9. PMID 19706531 DOI: 10.1073/pnas.0904077106  1
2009 Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T, Kanamori H, Padhukasahasram B, Bustamante C, Yoshimura A, Doi K, McCouch S. Evolutionary history of GS3, a gene conferring grain length in rice. Genetics. 182: 1323-34. PMID 19506305 DOI: 10.1534/genetics.109.103002  1
2009 Fitzgerald MA, McCouch SR, Hall RD. Not just a grain of rice: the quest for quality. Trends in Plant Science. 14: 133-9. PMID 19230745 DOI: 10.1016/j.tplants.2008.12.004  1
2009 Xu Y, This D, Pausch RC, Vonhof WM, Coburn JR, Comstock JP, McCouch SR. Leaf-level water use efficiency determined by carbon isotope discrimination in rice seedlings: genetic variation associated with population structure and QTL mapping. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 118: 1065-81. PMID 19224195 DOI: 10.1007/s00122-009-0963-z  1
2009 Gray J, Bevan M, Brutnell T, Buell CR, Cone K, Hake S, Jackson D, Kellogg E, Lawrence C, McCouch S, Mockler T, Moose S, Paterson A, Peterson T, Rokshar D, et al. A recommendation for naming transcription factor proteins in the grasses. Plant Physiology. 149: 4-6. PMID 19126689 DOI: 10.1104/pp.108.128504  1
2009 Thomson MJ, Polato NR, Prasetiyono J, Trijatmiko KR, Silitonga TS, McCouch SR. Genetic diversity of isolated populations of Indonesian landraces of rice (Oryza sativa L.) collected in East Kalimantan on the Island of Borneo Rice. 2: 80-92. DOI: 10.1007/s12284-009-9023-1  1
2009 López-Gartner G, Cortina H, McCouch SR, Moncada MDP. Analysis of genetic structure in a sample of coffee (Coffea arabica L.) using fluorescent SSR markers Tree Genetics and Genomes. 5: 435-446. DOI: 10.1007/s11295-008-0197-2  1
2008 Iyer-Pascuzzi AS, Jiang H, Huang L, McCouch SR. Genetic and functional characterization of the rice bacterial blight disease resistance gene xa5 Phytopathology. 98: 289-295. PMID 18944079 DOI: 10.1094/PHYTO-98-3-0289  1
2008 Kovach MJ, McCouch SR. Leveraging natural diversity: back through the bottleneck. Current Opinion in Plant Biology. 11: 193-200. PMID 18313975 DOI: 10.1016/j.pbi.2007.12.006  1
2008 Avraham S, Tung CW, Ilic K, Jaiswal P, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Stevens P, Vincent L, Zapata F, et al. The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Research. 36: D449-54. PMID 18194960 DOI: 10.1093/nar/gkm908  1
2008 Woo MO, Ham TH, Ji HS, Choi MS, Jiang W, Chu SH, Piao R, Chin JH, Kim JA, Park BS, Seo HS, Jwa NS, McCouch S, Koh HJ. Inactivation of the UGPase1 gene causes genic male sterility and endosperm chalkiness in rice (Oryza sativa L.). The Plant Journal : For Cell and Molecular Biology. 54: 190-204. PMID 18182026 DOI: 10.1111/j.1365-313X.2008.03405.x  1
2008 Xie X, Jin F, Song MH, Suh JP, Hwang HG, Kim YG, McCouch SR, Ahn SN. Fine mapping of a yield-enhancing QTL cluster associated with transgressive variation in an Oryza sativa x O. rufipogon cross. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 116: 613-22. PMID 18092146 DOI: 10.1007/s00122-007-0695-x  1
2008 Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni J, Pujar A, Ravenscroft D, Ren L, Spooner W, Tecle I, Thomason J, et al. Gramene: a growing plant comparative genomics resource. Nucleic Acids Research. 36: D947-53. PMID 17984077 DOI: 10.1093/nar/gkm968  1
2008 McCouch SR. Gene nomenclature system for rice Rice. 1: 72-84. DOI: 10.1007/s12284-008-9004-9  1
2008 Phillips RL, Magor NP, Shires D, Leung H, McCouch SR, Macintosh D. Student Opportunity: Short-Term Exposure to International Agriculture Rice. 1: 11-15. DOI: 10.1007/s12284-008-9003-x  1
2007 Kovach MJ, Sweeney MT, McCouch SR. New insights into the history of rice domestication. Trends in Genetics : Tig. 23: 578-87. PMID 17963977 DOI: 10.1016/j.tig.2007.08.012  1
2007 Mather KA, Caicedo AL, Polato NR, Olsen KM, McCouch S, Purugganan MD. The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics. 177: 2223-32. PMID 17947413 DOI: 10.1534/genetics.107.079616  1
2007 Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, Bustamante CD, Purugganan MD. Genome-wide patterns of nucleotide polymorphism in domesticated rice. Plos Genetics. 3: 1745-56. PMID 17907810 DOI: 10.1371/journal.pgen.0030163  1
2007 Sweeney MT, Thomson MJ, Cho YG, Park YJ, Williamson SH, Bustamante CD, McCouch SR. Global dissemination of a single mutation conferring white pericarp in rice. Plos Genetics. 3: e133. PMID 17696613 DOI: 10.1371/journal.pgen.0030133  1
2007 Sweeney M, McCouch S. The complex history of the domestication of rice. Annals of Botany. 100: 951-7. PMID 17617555 DOI: 10.1093/aob/mcm128  1
2007 Iyer-Pascuzzi AS, McCouch SR. Recessive resistance genes and the Oryza sativa-Xanthomonas oryzae pv. oryzae pathosystem. Molecular Plant-Microbe Interactions : Mpmi. 20: 731-9. PMID 17601161 DOI: 10.1094/MPMI-20-7-0731  1
2007 Cho YI, Jiang W, Chin JH, Piao Z, Cho YG, McCouch S, Koh HJ. Identification of QTLs associated with physiological nitrogen use efficiency in rice. Molecules and Cells. 23: 72-9. PMID 17464214  1
2007 Ilic K, Kellogg EA, Jaiswal P, Zapata F, Stevens PF, Vincent LP, Avraham S, Reiser L, Pujar A, Sachs MM, Whitman NT, McCouch SR, Schaeffer ML, Ware DH, Stein LD, et al. The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiology. 143: 587-99. PMID 17142475 DOI: 10.1104/pp.106.092825  1
2007 Thomson MJ, Septiningsih EM, Suwardjo F, Santoso TJ, Silitonga TS, McCouch SR. Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 114: 559-68. PMID 17136372 DOI: 10.1007/s00122-006-0457-1  1
2007 Cho YG, Kang HJ, Lee JS, Lee YT, Lim SJ, Gauch H, Eun MY, McCouch SR. Identification of quantitative trait loci in rice for yield, yield components, and agronomic traits across years and locations Crop Science. 47: 2403-2417. DOI: 10.2135/cropsci2006.08.0509  1
2007 Iyer-Pascuzzi AS, McCouch SR. Functional markers for xa5-mediated resistance in rice (Oryza sativa, L.) Molecular Breeding. 19: 291-296. DOI: 10.1007/s11032-006-9055-9  1
2007 McCouch SR, Sweeney M, Li J, Jiang H, Thomson M, Septiningsih E, Edwards J, Moncada P, Xiao J, Garris A, Tai T, Martinez C, Tohme J, Sugiono M, McClung A, et al. Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa Euphytica. 154: 317-339. DOI: 10.1007/s10681-006-9210-8  1
2007 Coffman WR, Lesser WH, Mccouch SR. Commercialization and the scientific research process: The example of plant breeding Science and the University. 94-109.  1
2007 Semagn K, Ndjiondjop MN, Lorieux M, Cissoko M, Jones M, McCouch S. Molecular profiling of an interspecific rice population derived from a cross between WAB 56-104 (Oryza sativa) and CG 14 (Oryza glaberrima) African Journal of Biotechnology. 6: 2014-2022.  1
2006 Tang T, Lu J, Huang J, He J, McCouch SR, Shen Y, Kai Z, Purugganan MD, Shi S, Wu CI. Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication. Plos Genetics. 2: e199. PMID 17112320 DOI: 10.1371/journal.pgen.0020199  1
2006 Pujar A, Jaiswal P, Kellogg EA, Ilic K, Vincent L, Avraham S, Stevens P, Zapata F, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Ware D, McCouch S. Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiology. 142: 414-28. PMID 16905665 DOI: 10.1104/pp.106.085720  1
2006 Olsen KM, Caicedo AL, Polato N, McClung A, McCouch S, Purugganan MD. Selection under domestication: evidence for a sweep in the rice waxy genomic region. Genetics. 173: 975-83. PMID 16547098 DOI: 10.1534/genetics.106.056473  1
2006 Thomson MJ, Edwards JD, Septiningsih EM, Harrington SE, McCouch SR. Substitution mapping of dth1.1, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL. Genetics. 172: 2501-14. PMID 16452146 DOI: 10.1534/genetics.105.050500  1
2006 Sweeney MT, Thomson MJ, Pfeil BE, McCouch S. Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. The Plant Cell. 18: 283-94. PMID 16399804 DOI: 10.1105/tpc.105.038430  1
2006 Ammiraju JS, 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 S, et al. 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 Research. 16: 140-7. PMID 16344555 DOI: 10.1101/gr.3766306  1
2005 Jaiswal P, Avraham S, Ilic K, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Stevens P, Vincent L, Ware D, Zapata F. Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages. Comparative and Functional Genomics. 6: 388-97. PMID 18629207 DOI: 10.1002/cfg.496  1
2005 Xu Y, McCouch SR, Zhang Q. How can we use genomics to improve cereals with rice as a reference genome? Plant Molecular Biology. 59: 7-26. PMID 16217598 DOI: 10.1007/s11103-004-4681-2  0.32
2005 Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S. Genetic structure and diversity in Oryza sativa L. Genetics. 169: 1631-8. PMID 15654106 DOI: 10.1534/genetics.104.035642  0.72
2005 Semon M, Nielsen R, Jones MP, McCouch SR. The population structure of African cultivated rice oryza glaberrima (Steud.): evidence for elevated levels of linkage disequilibrium caused by admixture with O. sativa and ecological adaptation. Genetics. 169: 1639-47. PMID 15545652 DOI: 10.1534/genetics.104.033175  1
2004 Iyer AS, McCouch SR. The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance. Molecular Plant-Microbe Interactions : Mpmi. 17: 1348-54. PMID 15597740 DOI: 10.1094/MPMI.2004.17.12.1348  1
2003 Yap IV, Schneider D, Kleinberg J, Matthews D, Cartinhour S, McCouch SR. A graph-theoretic approach to comparing and integrating genetic, physical and sequence-based maps. Genetics. 165: 2235-47. PMID 14704199  1
2003 Septiningsih EM, Trijatmiko KR, Moeljopawiro S, McCouch SR. 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. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 107: 1433-41. PMID 14513216 DOI: 10.1007/s00122-003-1376-z  1
2003 Septiningsih EM, Prasetiyono J, Lubis E, Tai TH, Tjubaryat T, Moeljopawiro S, McCouch SR. 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. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 107: 1419-32. PMID 14513215 DOI: 10.1007/s00122-003-1373-2  1
2003 Thomson MJ, Tai TH, McClung AM, Lai XH, Hinga ME, Lobos KB, Xu Y, Martinez CP, McCouch SR. 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. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 107: 479-93. PMID 12736777 DOI: 10.1007/s00122-003-1270-8  1
2003 Blair MW, Garris AJ, Iyer AS, Chapman B, Kresovich S, McCouch SR. High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice ( Oryza sativa L.). Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 107: 62-73. PMID 12677405 DOI: 10.1007/s00122-003-1231-2  1
2003 Jiang N, Bao Z, Zhang X, Hirochika H, Eddy SR, McCouch SR, Wessler SR. An active DNA transposon family in rice. Nature. 421: 163-7. PMID 12520302 DOI: 10.1038/nature01214  1
2002 Jaiswal P, Ware D, Ni J, Chang K, Zhao W, Schmidt S, Pan X, Clark K, Teytelman L, Cartinhour S, Stein L, McCouch S. Gramene: development and integration of trait and gene ontologies for rice. Comparative and Functional Genomics. 3: 132-6. PMID 18628886 DOI: 10.1002/cfg.156  1
2002 McCouch 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, et al. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.) (supplement). Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 9: 257-79. PMID 12597280 DOI: 10.1093/dnares/9.6.257  1
2002 McCouch 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, et al. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 9: 199-207. PMID 12597276 DOI: 10.1093/dnares/9.6.199  1
2002 Blair MW, Hedetale V, McCouch SR. Fluorescent-labeled microsatellite panels useful for detecting allelic diversity in cultivated rice ( Oryza sativa L.). Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 105: 449-457. PMID 12582550 DOI: 10.1007/s00122-002-0921-5  1
2002 Ware DH, Jaiswal P, Ni J, Yap IV, Pan X, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K, Cartinhour S, Stein LD, McCouch SR. Gramene, a tool for grass genomics. Plant Physiology. 130: 1606-13. PMID 12481044 DOI: 10.1104/pp.015248  1
2002 Jiang N, Bao Z, Temnykh S, Cheng Z, Jiang J, Wing RA, McCouch SR, Wessler SR. Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics. 161: 1293-305. PMID 12136031  1
2002 Leach J, McCouch S, Slezak T, Sasaki T, Wessler S. Why finishing the rice genome matters. Science (New York, N.Y.). 296: 45. PMID 11962488  1
2002 Goldberg D, McCouch S, Kleinberg J. Constructing comparative genome maps with unresolved marker order. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 139-50. PMID 11928470  1
2002 Ware D, Jaiswal P, Ni J, Pan X, Chang K, Clark K, Teytelman L, Schmidt S, Zhao W, Cartinhour S, McCouch S, Stein L. Gramene: a resource for comparative grass genomics. Nucleic Acids Research. 30: 103-5. PMID 11752266  1
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