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Validation of Yield Component Traits Identified by Genome-Wide Association Mapping in a tropical japonica × tropical japonica Rice Biparental Mapping Population.

Eizenga GC, Jia MH, Jackson AK, Boykin DL, Ali ML, Shakiba E, Tran NT, McCouch SR, Edwards JD.

Plant Genome. 2019 Mar;12(1). doi: 10.3835/plantgenome2018.04.0021.


Integrating Molecular Markers and Environmental Covariates To Interpret Genotype by Environment Interaction in Rice (Oryza sativa L.) Grown in Subtropical Areas.

Monteverde E, Gutierrez L, Blanco P, Pérez de Vida F, Rosas JE, Bonnecarrère V, Quero G, McCouch S.

G3 (Bethesda). 2019 May 7;9(5):1519-1531. doi: 10.1534/g3.119.400064.


Genome-Wide Association Study Using Historical Breeding Populations Discovers Genomic Regions Involved in High-Quality Rice.

Quero G, Gutiérrez L, Monteverde E, Blanco P, Pérez de Vida F, Rosas J, Fernández S, Garaycochea S, McCouch S, Berberian N, Simondi S, Bonnecarrère V.

Plant Genome. 2018 Nov;11(3). doi: 10.3835/plantgenome2017.08.0076.


An imputation platform to enhance integration of rice genetic resources.

Wang DR, Agosto-Pérez FJ, Chebotarov D, Shi Y, Marchini J, Fitzgerald M, McNally KL, Alexandrov N, McCouch SR.

Nat Commun. 2018 Aug 29;9(1):3519. doi: 10.1038/s41467-018-05538-1.


Ethylene-gibberellin signaling underlies adaptation of rice to periodic flooding.

Kuroha T, Nagai K, Gamuyao R, Wang DR, Furuta T, Nakamori M, Kitaoka T, Adachi K, Minami A, Mori Y, Mashiguchi K, Seto Y, Yamaguchi S, Kojima M, Sakakibara H, Wu J, Ebana K, Mitsuda N, Ohme-Takagi M, Yanagisawa S, Yamasaki M, Yokoyama R, Nishitani K, Mochizuki T, Tamiya G, McCouch SR, Ashikari M.

Science. 2018 Jul 13;361(6398):181-186. doi: 10.1126/science.aat1577.


Genomic regions responsible for seminal and crown root lengths identified by 2D & 3D root system image analysis.

Uga Y, Assaranurak I, Kitomi Y, Larson BG, Craft EJ, Shaff JE, McCouch SR, Kochian LV.

BMC Genomics. 2018 Apr 20;19(1):273. doi: 10.1186/s12864-018-4639-4.


Resistance to Multiple Temperate and Tropical Stem and Sheath Diseases of Rice.

Rosas JE, Martínez S, Blanco P, Pérez de Vida F, Bonnecarrère V, Mosquera G, Cruz M, Garaycochea S, Monteverde E, McCouch S, Germán S, Jannink JL, Gutiérrez L.

Plant Genome. 2018 Mar;11(1). doi: 10.3835/plantgenome2017.03.0029.


Plant genetic resources for food and agriculture: opportunities and challenges emerging from the science and information technology revolution.

Halewood M, Chiurugwi T, Sackville Hamilton R, Kurtz B, Marden E, Welch E, Michiels F, Mozafari J, Sabran M, Patron N, Kersey P, Bastow R, Dorius S, Dias S, McCouch S, Powell W.

New Phytol. 2018 Mar;217(4):1407-1419. doi: 10.1111/nph.14993. Epub 2018 Jan 23. Review.


ALUMINUM RESISTANCE TRANSCRIPTION FACTOR 1 (ART1) contributes to natural variation in aluminum resistance in diverse genetic backgrounds of rice (O. sativa).

Arbelaez JD, Maron LG, Jobe TO, Piñeros MA, Famoso AN, Rebelo AR, Singh N, Ma Q, Fei Z, Kochian LV, McCouch SR.

Plant Direct. 2017 Oct 16;1(4):e00014. doi: 10.1002/pld3.14. eCollection 2017 Oct.


Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications.

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.

Rice (N Y). 2017 Aug 30;10(1):40. doi: 10.1186/s12284-017-0181-2.


Functional properties of an alternative, tissue-specific promoter for rice NADPH-dependent dihydroflavonol reductase.

Kim J, Lee HJ, Jung YJ, Kang KK, Tyagi W, Kovach M, Sweeney M, McCouch S, Cho YG.

PLoS One. 2017 Aug 25;12(8):e0183722. doi: 10.1371/journal.pone.0183722. eCollection 2017.


Metabolomics and genomics combine to unravel the pathway for the presence of fragrance in rice.

Daygon VD, Calingacion M, Forster LC, Voss JJ, Schwartz BD, Ovenden B, Alonso DE, McCouch SR, Garson MJ, Fitzgerald MA.

Sci Rep. 2017 Aug 18;7(1):8767. doi: 10.1038/s41598-017-07693-9.


Hybrid assembly with long and short reads improves discovery of gene family expansions.

Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT.

BMC Genomics. 2017 Jul 19;18(1):541. doi: 10.1186/s12864-017-3927-8.


The buffering capacity of stems: genetic architecture of nonstructural carbohydrates in cultivated Asian rice, Oryza sativa.

Wang DR, Han R, Wolfrum EJ, McCouch SR.

New Phytol. 2017 Jul;215(2):658-671. doi: 10.1111/nph.14614. Epub 2017 May 30.


Erratum to: Population dynamics among six major groups of the Oryza rufipogon species complex, wild relative of cultivated Asian rice.

Kim H, Jung J, Singh N, Greenberg A, Doyle JJ, Tyagi W, Chung JW, Kimball J, Hamilton RS, McCouch SR.

Rice (N Y). 2017 Dec;10(1):17. doi: 10.1186/s12284-017-0156-3. Epub 2017 Apr 26. No abstract available.


Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis.

Shakiba E, Edwards JD, Jodari F, Duke SE, Baldo AM, Korniliev P, McCouch SR, Eizenga GC.

PLoS One. 2017 Mar 10;12(3):e0172133. doi: 10.1371/journal.pone.0172133. eCollection 2017.


Robust phenotyping strategies for evaluation of stem non-structural carbohydrates (NSC) in rice.

Wang DR, Wolfrum EJ, Virk P, Ismail A, Greenberg AJ, McCouch SR.

J Exp Bot. 2016 Nov;67(21):6125-6138. Epub 2016 Oct 5.


Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice.

Kim H, Jung J, Singh N, Greenberg A, Doyle JJ, Tyagi W, Chung JW, Kimball J, Hamilton RS, McCouch SR.

Rice (N Y). 2016 Dec;9(1):56. doi: 10.1186/s12284-016-0119-0. Epub 2016 Oct 12. Erratum in: Rice (N Y). 2017 Dec;10 (1):17.


When more is better: how data sharing would accelerate genomic selection of crop plants.

Spindel JE, McCouch SR.

New Phytol. 2016 Dec;212(4):814-826. doi: 10.1111/nph.14174. Epub 2016 Sep 26.


Redefining 'stress resistance genes', and why it matters.

Maron LG, Piñeros MA, Kochian LV, McCouch SR.

J Exp Bot. 2016 Oct;67(19):5588-5591. Epub 2016 Oct 4. No abstract available.


Whole-genome characterization in pedigreed non-human primates using genotyping-by-sequencing (GBS) and imputation.

Bimber BN, Raboin MJ, Letaw J, Nevonen KA, Spindel JE, McCouch SR, Cervera-Juanes R, Spindel E, Carbone L, Ferguson B, Vinson A.

BMC Genomics. 2016 Aug 24;17:676. doi: 10.1186/s12864-016-2966-x.


Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice.

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, Okuda S, Higashiyama T, Nomoto M, Tada Y, Shinohara H, Matsubayashi Y, Greenberg A, Wu J, Yasui H, Yoshimura A, Mori H, McCouch SR, Ashikari M.

Proc Natl Acad Sci U S A. 2016 Aug 9;113(32):8969-74. doi: 10.1073/pnas.1604849113. Epub 2016 Jul 27.


Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions.

Biscarini F, Cozzi P, Casella L, Riccardi P, Vattari A, Orasen G, Perrini R, Tacconi G, Tondelli A, Biselli C, Cattivelli L, Spindel J, McCouch S, Abbruscato P, Valé G, Piffanelli P, Greco R.

PLoS One. 2016 May 26;11(5):e0155425. doi: 10.1371/journal.pone.0155425. eCollection 2016.


Corrigendum: Open access resources for genome-wide association mapping in rice.

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, Branchini DA, Kuser-Falcão PR, Leung H, Ebana K, Yano M, Eizenga G, McClung A, Mezey J.

Nat Commun. 2016 Apr 20;7:11346. doi: 10.1038/ncomms11346. No abstract available.


Evidence for divergence of response in Indica, Japonica, and wild rice to high CO2 × temperature interaction.

Wang DR, Bunce JA, Tomecek MB, Gealy D, McClung A, McCouch SR, Ziska LH.

Glob Chang Biol. 2016 Jul;22(7):2620-32. doi: 10.1111/gcb.13279. Epub 2016 Apr 19.


Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement.

Spindel JE, Begum H, Akdemir D, Collard B, Redoña E, Jannink JL, McCouch S.

Heredity (Edinb). 2016 Apr;116(4):395-408. doi: 10.1038/hdy.2015.113. Epub 2016 Feb 10.


Open access resources for genome-wide association mapping in rice.

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, Branchini DA, Kuser-Falcão PR, Leung H, Ebana K, Yano M, Eizenga G, McClung A, Mezey J.

Nat Commun. 2016 Feb 4;7:10532. doi: 10.1038/ncomms10532. Erratum in: Nat Commun. 2016;7:11346.


Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters.

Crowell S, Korniliev P, Falcão A, Ismail A, Gregorio G, Mezey J, McCouch S.

Nat Commun. 2016 Feb 4;7:10527. doi: 10.1038/ncomms10527.


Evolving technologies for growing, imaging and analyzing 3D root system architecture of crop plants.

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, Kochian LV.

J Integr Plant Biol. 2016 Mar;58(3):230-41. doi: 10.1111/jipb.12456.


Dissection of the genetic architecture of rice resistance to the blast fungus Magnaporthe oryzae.

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, Wang GL.

Mol Plant Pathol. 2016 Aug;17(6):959-72. doi: 10.1111/mpp.12340. Epub 2016 Feb 20.


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.

Spindel J, Wright M, Chen C, Cobb J, Gage J, Harrington S, Lorieux M, Ahmadi N, McCouch S.

Theor Appl Genet. 2016 Jan;129(1):201-2. doi: 10.1007/s00122-015-2618-6. No abstract available.


Convergent Loss of Awn in Two Cultivated Rice Species Oryza sativa and Oryza glaberrima Is Caused by Mutations in Different Loci.

Furuta T, Komeda N, Asano K, Uehara K, Gamuyao R, Angeles-Shim RB, Nagai K, Doi K, Wang DR, Yasui H, Yoshimura A, Wu J, McCouch SR, Ashikari M.

G3 (Bethesda). 2015 Sep 2;5(11):2267-74. doi: 10.1534/g3.115.020834.


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.

Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink JL, McCouch SR.

PLoS Genet. 2015 Jun 30;11(6):e1005350. doi: 10.1371/journal.pgen.1005350. eCollection 2015 Jun. No abstract available.


LABA1, a Domestication Gene Associated with Long, Barbed Awns in Wild Rice.

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.

Plant Cell. 2015 Jul;27(7):1875-88. doi: 10.1105/tpc.15.00260. Epub 2015 Jun 16.


The Tyrosine Aminomutase TAM1 Is Required for β-Tyrosine Biosynthesis in Rice.

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.

Plant Cell. 2015 Apr;27(4):1265-78. doi: 10.1105/tpc.15.00058. Epub 2015 Apr 21.


Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa).

Begum H, Spindel JE, Lalusin A, Borromeo T, Gregorio G, Hernandez J, Virk P, Collard B, McCouch SR.

PLoS One. 2015 Mar 18;10(3):e0119873. doi: 10.1371/journal.pone.0119873. eCollection 2015.


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.

Arbelaez JD, Moreno LT, Singh N, Tung CW, Maron LG, Ospina Y, Martinez CP, Grenier C, Lorieux M, McCouch S.

Mol Breed. 2015;35(2):81. Epub 2015 Feb 14.


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.

Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink JL, McCouch SR.

PLoS Genet. 2015 Feb 17;11(2):e1004982. doi: 10.1371/journal.pgen.1004982. eCollection 2015 Feb. Erratum in: PLoS Genet. 2015 Jun;11(6):e1005350.


Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica.

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.

Genome Biol. 2014;15(11):506.


Variation in soil aluminium tolerance genes is associated with local adaptation to soils at the Park Grass Experiment.

Gould B, McCouch S, Geber M.

Mol Ecol. 2014 Dec;23(24):6058-72. doi: 10.1111/mec.12893. Epub 2014 Oct 21.


Nuclear and chloroplast diversity and phenotypic distribution of rice (Oryza sativa L.) germplasm from the democratic people's republic of Korea (DPRK; North Korea).

Kim H, Jeong EG, Ahn SN, Doyle J, Singh N, Greenberg AJ, Won YJ, McCouch SR.

Rice (N Y). 2014 Jul 2;7(1):7. doi: 10.1186/s12284-014-0007-4. eCollection 2014.


Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding.

Varshney RK, Terauchi R, McCouch SR.

PLoS Biol. 2014 Jun 10;12(6):e1001883. doi: 10.1371/journal.pbio.1001883. eCollection 2014 Jun.


New horizons for plant translational research.

Alfred J, Dangl JL, Kamoun S, McCouch SR.

PLoS Biol. 2014 Jun 10;12(6):e1001880. doi: 10.1371/journal.pbio.1001880. eCollection 2014 Jun. No abstract available.


Natural variation underlies alterations in Nramp aluminum transporter (NRAT1) expression and function that play a key role in rice aluminum tolerance.

Li JY, Liu J, Dong D, Jia X, McCouch SR, Kochian LV.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6503-8. doi: 10.1073/pnas.1318975111. Epub 2014 Apr 11.


High-Resolution Inflorescence Phenotyping Using a Novel Image-Analysis Pipeline, PANorama.

Crowell S, Falcão AX, Shah A, Wilson Z, Greenberg AJ, McCouch SR.

Plant Physiol. 2014 Jun;165(2):479-495. Epub 2014 Apr 2.


Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 orthologs.

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, Bouwmeester HJ, Ruyter-Spira C.

Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2379-84. doi: 10.1073/pnas.1317360111. Epub 2014 Jan 24. Erratum in: Proc Natl Acad Sci U S A. 2014 April 29;111(17):6528.


A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress.

Dharmawardhana P, Ren L, Amarasinghe V, Monaco M, Thomason J, Ravenscroft D, McCouch S, Ware D, Jaiswal P.

Rice (N Y). 2013 May 29;6(1):15. doi: 10.1186/1939-8433-6-15.


Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding.

Bandillo N, Raghavan C, Muyco PA, Sevilla MA, Lobina IT, Dilla-Ermita CJ, Tung CW, McCouch S, Thomson M, Mauleon R, Singh RK, Gregorio G, Redoña E, Leung H.

Rice (N Y). 2013 May 6;6(1):11. doi: 10.1186/1939-8433-6-11.


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.

Spindel J, Wright M, Chen C, Cobb J, Gage J, Harrington S, Lorieux M, Ahmadi N, McCouch S.

Theor Appl Genet. 2013 Nov;126(11):2699-716. doi: 10.1007/s00122-013-2166-x. Epub 2013 Aug 6. Erratum in: Theor Appl Genet. 2016 Jan;129(1):201-2.


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