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TeoNAM: A Nested Association Mapping Population for Domestication and Agronomic Trait Analysis in Maize.

Chen Q, Yang CJ, York AM, Xue W, Daskalska LL, DeValk CA, Krueger KW, Lawton SB, Spiegelberg BG, Schnell JM, Neumeyer MA, Perry JS, Peterson AC, Kim B, Bergstrom L, Yang L, Barber IC, Tian F, Doebley JF.

Genetics. 2019 Sep 3. pii: genetics.302594.2019. doi: 10.1534/genetics.119.302594. [Epub ahead of print]


The genome-wide dynamics of purging during selfing in maize.

Roessler K, Muyle A, Diez CM, Gaut GRJ, Bousios A, Stitzer MC, Seymour DK, Doebley JF, Liu Q, Gaut BS.

Nat Plants. 2019 Sep;5(9):980-990. doi: 10.1038/s41477-019-0508-7. Epub 2019 Sep 2.


Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize.

Xue W, Anderson SN, Wang X, Yang L, Crisp PA, Li Q, Noshay J, Albert PS, Birchler JA, Bilinski P, Stitzer MC, Ross-Ibarra J, Flint-Garcia S, Chen X, Springer NM, Doebley JF.

Genetics. 2019 Sep;213(1):143-160. doi: 10.1534/genetics.119.302378. Epub 2019 Jul 18.


The genetic architecture of teosinte catalyzed and constrained maize domestication.

Yang CJ, Samayoa LF, Bradbury PJ, Olukolu BA, Xue W, York AM, Tuholski MR, Wang W, Daskalska LL, Neumeyer MA, Sanchez-Gonzalez JJ, Romay MC, Glaubitz JC, Sun Q, Buckler ES, Holland JB, Doebley JF.

Proc Natl Acad Sci U S A. 2019 Mar 19;116(12):5643-5652. doi: 10.1073/pnas.1820997116. Epub 2019 Mar 6.


Stepwise cis-Regulatory Changes in ZCN8 Contribute to Maize Flowering-Time Adaptation.

Guo L, Wang X, Zhao M, Huang C, Li C, Li D, Yang CJ, York AM, Xue W, Xu G, Liang Y, Chen Q, Doebley JF, Tian F.

Curr Biol. 2018 Sep 24;28(18):3005-3015.e4. doi: 10.1016/j.cub.2018.07.029. Epub 2018 Sep 13.


Construction of the third-generation Zea mays haplotype map.

Bukowski R, Guo X, Lu Y, Zou C, He B, Rong Z, Wang B, Xu D, Yang B, Xie C, Fan L, Gao S, Xu X, Zhang G, Li Y, Jiao Y, Doebley JF, Ross-Ibarra J, Lorant A, Buffalo V, Romay MC, Buckler ES, Ware D, Lai J, Sun Q, Xu Y.

Gigascience. 2018 Apr 1;7(4):1-12. doi: 10.1093/gigascience/gix134.


ZmCCT9 enhances maize adaptation to higher latitudes.

Huang C, Sun H, Xu D, Chen Q, Liang Y, Wang X, Xu G, Tian J, Wang C, Li D, Wu L, Yang X, Jin W, Doebley JF, Tian F.

Proc Natl Acad Sci U S A. 2018 Jan 9;115(2):E334-E341. doi: 10.1073/pnas.1718058115. Epub 2017 Dec 26.


Genome-wide Analysis of Transcriptional Variability in a Large Maize-Teosinte Population.

Wang X, Chen Q, Wu Y, Lemmon ZH, Xu G, Huang C, Liang Y, Xu D, Li D, Doebley JF, Tian F.

Mol Plant. 2018 Mar 5;11(3):443-459. doi: 10.1016/j.molp.2017.12.011. Epub 2017 Dec 22.


Defining the Role of the MADS-Box Gene, Zea Agamous-like1, a Target of Selection During Maize Domestication.

Wills DM, Fang Z, York AM, Holland JB, Doebley JF.

J Hered. 2018 Mar 16;109(3):333-338. doi: 10.1093/jhered/esx073.


Selection During Maize Domestication Targeted a Gene Network Controlling Plant and Inflorescence Architecture.

Studer AJ, Wang H, Doebley JF.

Genetics. 2017 Oct;207(2):755-765. doi: 10.1534/genetics.117.300071. Epub 2017 Jul 28.


A Gene for Genetic Background in Zea mays: Fine-Mapping enhancer of teosinte branched1.2 to a YABBY Class Transcription Factor.

Yang CJ, Kursel LE, Studer AJ, Bartlett ME, Whipple CJ, Doebley JF.

Genetics. 2016 Dec;204(4):1573-1585. Epub 2016 Oct 11.


Mapping Prolificacy QTL in Maize and Teosinte.

Yang L, Yang CJ, Cheng Q, Xue W, Doebley JF.

J Hered. 2016;107(7):674-678. Epub 2016 Sep 22.


Fine Mapping of a QTL Associated with Kernel Row Number on Chromosome 1 of Maize.

Calderón CI, Yandell BS, Doebley JF.

PLoS One. 2016 Mar 1;11(3):e0150276. doi: 10.1371/journal.pone.0150276. eCollection 2016.


Evidence That the Origin of Naked Kernels During Maize Domestication Was Caused by a Single Amino Acid Substitution in tga1.

Wang H, Studer AJ, Zhao Q, Meeley R, Doebley JF.

Genetics. 2015 Jul;200(3):965-74. doi: 10.1534/genetics.115.175752. Epub 2015 May 4.


The role of cis regulatory evolution in maize domestication.

Lemmon ZH, Bukowski R, Sun Q, Doebley JF.

PLoS Genet. 2014 Nov 6;10(11):e1004745. doi: 10.1371/journal.pgen.1004745. eCollection 2014 Nov.


Genetic dissection of a genomic region with pleiotropic effects on domestication traits in maize reveals multiple linked QTL.

Lemmon ZH, Doebley JF.

Genetics. 2014 Sep;198(1):345-53. doi: 10.1534/genetics.114.165845. Epub 2014 Jun 20.


Defining the Role of prolamin-box binding factor1 Gene During Maize Domestication.

Lang Z, Wills DM, Lemmon ZH, Shannon LM, Bukowski R, Wu Y, Messing J, Doebley JF.

J Hered. 2014 Jul-Aug;105(4):576-582. Epub 2014 Mar 28.


From many, one: genetic control of prolificacy during maize domestication.

Wills DM, Whipple CJ, Takuno S, Kursel LE, Shannon LM, Ross-Ibarra J, Doebley JF.

PLoS Genet. 2013 Jun;9(6):e1003604. doi: 10.1371/journal.pgen.1003604. Epub 2013 Jun 27.


ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize.

Hung HY, Shannon LM, Tian F, Bradbury PJ, Chen C, Flint-Garcia SA, McMullen MD, Ware D, Buckler ES, Doebley JF, Holland JB.

Proc Natl Acad Sci U S A. 2012 Jul 10;109(28):E1913-21. doi: 10.1073/pnas.1203189109. Epub 2012 Jun 18.


Comparative population genomics of maize domestication and improvement.

Hufford MB, Xu X, van Heerwaarden J, Pyhäjärvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, Swanson-Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross-Ibarra J.

Nat Genet. 2012 Jun 3;44(7):808-11. doi: 10.1038/ng.2309.


Maize HapMap2 identifies extant variation from a genome in flux.

Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, Elshire RJ, Gaut B, Geller L, Glaubitz JC, Gore M, Guill KE, Holland J, Hufford MB, Lai J, Li M, Liu X, Lu Y, McCombie R, Nelson R, Poland J, Prasanna BM, Pyhäjärvi T, Rong T, Sekhon RS, Sun Q, Tenaillon MI, Tian F, Wang J, Xu X, Zhang Z, Kaeppler SM, Ross-Ibarra J, McMullen MD, Buckler ES, Zhang G, Xu Y, Ware D.

Nat Genet. 2012 Jun 3;44(7):803-7. doi: 10.1038/ng.2313.


Parallel domestication of the Shattering1 genes in cereals.

Lin Z, Li X, Shannon LM, Yeh CT, Wang ML, Bai G, Peng Z, Li J, Trick HN, Clemente TE, Doebley J, Schnable PS, Tuinstra MR, Tesso TT, White F, Yu J.

Nat Genet. 2012 May 13;44(6):720-4. doi: 10.1038/ng.2281.


Megabase-scale inversion polymorphism in the wild ancestor of maize.

Fang Z, Pyhäjärvi T, Weber AL, Dawe RK, Glaubitz JC, González Jde J, Ross-Ibarra C, Doebley J, Morrell PL, Ross-Ibarra J.

Genetics. 2012 Jul;191(3):883-94. doi: 10.1534/genetics.112.138578. Epub 2012 Apr 27.


Evidence for a natural allelic series at the maize domestication locus teosinte branched1.

Studer AJ, Doebley JF.

Genetics. 2012 Jul;191(3):951-8. doi: 10.1534/genetics.112.138479. Epub 2012 Apr 13.


The role of teosinte glume architecture (tga1) in coordinated regulation and evolution of grass glumes and inflorescence axes.

Preston JC, Wang H, Kursel L, Doebley J, Kellogg EA.

New Phytol. 2012 Jan;193(1):204-15. doi: 10.1111/j.1469-8137.2011.03908.x. Epub 2011 Sep 29.


Identification of a functional transposon insertion in the maize domestication gene tb1.

Studer A, Zhao Q, Ross-Ibarra J, Doebley J.

Nat Genet. 2011 Sep 25;43(11):1160-3. doi: 10.1038/ng.942.


grassy tillers1 promotes apical dominance in maize and responds to shade signals in the grasses.

Whipple CJ, Kebrom TH, Weber AL, Yang F, Hall D, Meeley R, Schmidt R, Doebley J, Brutnell TP, Jackson DP.

Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):E506-12. doi: 10.1073/pnas.1102819108. Epub 2011 Aug 1.


Do large effect QTL fractionate? A case study at the maize domestication QTL teosinte branched1.

Studer AJ, Doebley JF.

Genetics. 2011 Jul;188(3):673-81. doi: 10.1534/genetics.111.126508. Epub 2011 Apr 21.


Genetic signals of origin, spread, and introgression in a large sample of maize landraces.

van Heerwaarden J, Doebley J, Briggs WH, Glaubitz JC, Goodman MM, de Jesus Sanchez Gonzalez J, Ross-Ibarra J.

Proc Natl Acad Sci U S A. 2011 Jan 18;108(3):1088-92. doi: 10.1073/pnas.1013011108. Epub 2010 Dec 28.


MADS-box genes of maize: frequent targets of selection during domestication.

Zhao Q, Weber AL, McMullen MD, Guill K, Doebley J.

Genet Res (Camb). 2011 Feb;93(1):65-75. doi: 10.1017/S0016672310000509. Epub 2010 Dec 14.


Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis).

Van Heerwaarden J, Ross-Ibarra J, Doebley J, Glaubitz JC, González Jde J, Gaut BS, Eguiarte LE.

Mol Ecol. 2010 Mar;19(6):1162-73. doi: 10.1111/j.1365-294X.2010.04559.x. Epub 2010 Feb 15.


Using association mapping in teosinte to investigate the function of maize selection-candidate genes.

Weber AL, Zhao Q, McMullen MD, Doebley JF.

PLoS One. 2009 Dec 9;4(12):e8227. doi: 10.1371/journal.pone.0008227.


Population structure and genetic diversity of New World maize races assessed by DNA microsatellites.

Vigouroux Y, Glaubitz JC, Matsuoka Y, Goodman MM, Sánchez G J, Doebley J.

Am J Bot. 2008 Oct;95(10):1240-53. doi: 10.3732/ajb.0800097.


The genetic architecture of complex traits in teosinte (Zea mays ssp. parviglumis): new evidence from association mapping.

Weber AL, Briggs WH, Rucker J, Baltazar BM, de Jesús Sánchez-Gonzalez J, Feng P, Buckler ES, Doebley J.

Genetics. 2008 Oct;180(2):1221-32. doi: 10.1534/genetics.108.090134. Epub 2008 Sep 14.


The role of regulatory genes during maize domestication: evidence from nucleotide polymorphism and gene expression.

Zhao Q, Thuillet AC, Uhlmann NK, Weber A, Rafalski JA, Allen SM, Tingey S, Doebley J.

Genetics. 2008 Apr;178(4):2133-43. doi: 10.1534/genetics.107.085506.


A weak effect of background selection on trinucleotide microsatellites in maize.

Thuillet AC, Tenaillon MI, Anderson LK, Mitchell SE, Kresovich S, Stack SM, Gaut B, Doebley J.

J Hered. 2008 Jan-Feb;99(1):45-55. Epub 2007 Oct 24.


Linkage mapping of domestication loci in a large maize teosinte backcross resource.

Briggs WH, McMullen MD, Gaut BS, Doebley J.

Genetics. 2007 Nov;177(3):1915-28. Epub 2007 Oct 18.


Major regulatory genes in maize contribute to standing variation in teosinte (Zea mays ssp. parviglumis).

Weber A, Clark RM, Vaughn L, Sánchez-Gonzalez Jde J, Yu J, Yandell BS, Bradbury P, Doebley J.

Genetics. 2007 Dec;177(4):2349-59. Epub 2007 Oct 18.


The molecular genetics of crop domestication.

Doebley JF, Gaut BS, Smith BD.

Cell. 2006 Dec 29;127(7):1309-21. Review.


Plant science. Unfallen grains: how ancient farmers turned weeds into crops.

Doebley J.

Science. 2006 Jun 2;312(5778):1318-9. No abstract available.


A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture.

Clark RM, Wagler TN, Quijada P, Doebley J.

Nat Genet. 2006 May;38(5):594-7. Epub 2006 Apr 23.


Panzea: a database and resource for molecular and functional diversity in the maize genome.

Zhao W, Canaran P, Jurkuta R, Fulton T, Glaubitz J, Buckler E, Doebley J, Gaut B, Goodman M, Holland J, Kresovich S, McMullen M, Stein L, Ware D.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D752-7.


A unified mixed-model method for association mapping that accounts for multiple levels of relatedness.

Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES.

Nat Genet. 2006 Feb;38(2):203-8. Epub 2005 Dec 25.


Maize association population: a high-resolution platform for quantitative trait locus dissection.

Flint-Garcia SA, Thuillet AC, Yu J, Pressoir G, Romero SM, Mitchell SE, Doebley J, Kresovich S, Goodman MM, Buckler ES.

Plant J. 2005 Dec;44(6):1054-64.


A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement.

Yamasaki M, Tenaillon MI, Bi IV, Schroeder SG, Sanchez-Villeda H, Doebley JF, Gaut BS, McMullen MD.

Plant Cell. 2005 Nov;17(11):2859-72. Epub 2005 Oct 14.


The origin of the naked grains of maize.

Wang H, Nussbaum-Wagler T, Li B, Zhao Q, Vigouroux Y, Faller M, Bomblies K, Lukens L, Doebley JF.

Nature. 2005 Aug 4;436(7051):714-9.


Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus.

Clark RM, Tavaré S, Doebley J.

Mol Biol Evol. 2005 Nov;22(11):2304-12. Epub 2005 Aug 3.


The effects of artificial selection on the maize genome.

Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD, Gaut BS.

Science. 2005 May 27;308(5726):1310-4. Erratum in: Science. 2005 Oct 7;310(5745):54.


Molecular evolution of FLORICAULA/LEAFY orthologs in the Andropogoneae (Poaceae).

Bomblies K, Doebley JF.

Mol Biol Evol. 2005 Apr;22(4):1082-94. Epub 2005 Feb 2.


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