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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.


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.


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.


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.


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.


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.


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.


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.


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.


High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development.

Clark RT, Famoso AN, Zhao K, Shaff JE, Craft EJ, Bustamante CD, McCouch SR, Aneshansley DJ, Kochian LV.

Plant Cell Environ. 2013 Feb;36(2):454-66. doi: 10.1111/j.1365-3040.2012.02587.x. Epub 2012 Sep 3.


Genomics of gene banks: A case study in rice.

McCouch SR, McNally KL, Wang W, Sackville Hamilton R.

Am J Bot. 2012 Feb;99(2):407-23. doi: 10.3732/ajb.1100385. Epub 2012 Feb 6.


Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa.

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.

Nat Commun. 2011 Sep 13;2:467. doi: 10.1038/ncomms1467.


Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping.

Famoso AN, Zhao K, Clark RT, Tung CW, Wright MH, Bustamante C, Kochian LV, McCouch SR.

PLoS Genet. 2011 Aug;7(8):e1002221. doi: 10.1371/journal.pgen.1002221. Epub 2011 Aug 4.


Three-dimensional root phenotyping with a novel imaging and software platform.

Clark RT, MacCurdy RB, Jung JK, Shaff JE, McCouch SR, Aneshansley DJ, Kochian LV.

Plant Physiol. 2011 Jun;156(2):455-65. doi: 10.1104/pp.110.169102. Epub 2011 Mar 31.


Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis.

Tian Z, Yu Y, Lin F, Yu Y, Sanmiguel PJ, Wing RA, McCouch SR, Ma J, Jackson SA.

BMC Genomics. 2011 Mar 8;12:142. doi: 10.1186/1471-2164-12-142.


Gramene database in 2010: updates and extensions.

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, Thomason J, Wei S, Ware D.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1085-94. doi: 10.1093/nar/gkq1148. Epub 2010 Nov 13.


ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations.

Wright MH, Tung CW, Zhao K, Reynolds A, McCouch SR, Bustamante CD.

Bioinformatics. 2010 Dec 1;26(23):2952-60. doi: 10.1093/bioinformatics/btq533. Epub 2010 Oct 5.


Development of a novel aluminum tolerance phenotyping platform used for comparisons of cereal aluminum tolerance and investigations into rice aluminum tolerance mechanisms.

Famoso AN, Clark RT, Shaff JE, Craft E, McCouch SR, Kochian LV.

Plant Physiol. 2010 Aug;153(4):1678-91. doi: 10.1104/pp.110.156794. Epub 2010 Jun 10.


Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome.

Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A, Bustamante CD, McCouch SR.

PLoS One. 2010 May 24;5(5):e10780. doi: 10.1371/journal.pone.0010780.


A universal core genetic map for rice.

Orjuela J, Garavito A, Bouniol M, Arbelaez JD, Moreno L, Kimball J, Wilson G, Rami JF, Tohme J, McCouch SR, Lorieux M.

Theor Appl Genet. 2010 Feb;120(3):563-72. doi: 10.1007/s00122-009-1176-1. Epub 2009 Oct 22.


Inactivation of the CTD phosphatase-like gene OsCPL1 enhances the development of the abscission layer and seed shattering in rice.

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, Jiang W, Yang JI, Jin P, McCouch SR, An G, Koh HJ.

Plant J. 2010 Jan;61(1):96-106. doi: 10.1111/j.1365-313X.2009.04039.x. Epub 2009 Oct 6.


The origin and evolution of fragrance in rice (Oryza sativa L.).

Kovach MJ, Calingacion MN, Fitzgerald MA, McCouch SR.

Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14444-9. doi: 10.1073/pnas.0904077106. Epub 2009 Aug 17.


Not just a grain of rice: the quest for quality.

Fitzgerald MA, McCouch SR, Hall RD.

Trends Plant Sci. 2009 Mar;14(3):133-9. doi: 10.1016/j.tplants.2008.12.004. Epub 2009 Feb 18. Review.


Leaf-level water use efficiency determined by carbon isotope discrimination in rice seedlings: genetic variation associated with population structure and QTL mapping.

Xu Y, This D, Pausch RC, Vonhof WM, Coburn JR, Comstock JP, McCouch SR.

Theor Appl Genet. 2009 Apr;118(6):1065-81. doi: 10.1007/s00122-009-0963-z. Epub 2009 Feb 18.


A major quantitative trait locus for rice yellow mottle virus resistance maps to a cluster of blast resistance genes on chromosome 12.

Ghesquière A, Albar L, Lorieux M, Ahmadi N, Fargette D, Huang N, McCouch SR, Notteghem JL.

Phytopathology. 1997 Dec;87(12):1243-9. doi: 10.1094/PHYTO.1997.87.12.1243.


Genetic and functional characterization of the rice bacterial blight disease resistance gene xa5.

Iyer-Pascuzzi AS, Jiang H, Huang L, McCouch SR.

Phytopathology. 2008 Mar;98(3):289-95. doi: 10.1094/PHYTO-98-3-0289.

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