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Optimal Designs for Genomic Selection in Hybrid Crops.

Guo T, Yu X, Li X, Zhang H, Zhu C, Flint-Garcia S, McMullen MD, Holland JB, Szalma SJ, Wisser RJ, Yu J.

Mol Plant. 2019 Mar 4;12(3):390-401. doi: 10.1016/j.molp.2018.12.022. Epub 2019 Jan 6.


Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize.

Yang J, Mezmouk S, Baumgarten A, Buckler ES, Guill KE, McMullen MD, Mumm RH, Ross-Ibarra J.

PLoS Genet. 2017 Sep 27;13(9):e1007019. doi: 10.1371/journal.pgen.1007019. eCollection 2017 Sep.


Expanding Maize Genetic Resources with Predomestication Alleles: Maize-Teosinte Introgression Populations.

Liu Z, Cook J, Melia-Hancock S, Guill K, Bottoms C, Garcia A, Ott O, Nelson R, Recker J, Balint-Kurti P, Larsson S, Lepak N, Buckler E, Trimble L, Tracy W, McMullen MD, Flint-Garcia SA.

Plant Genome. 2016 Mar;9(1). doi: 10.3835/plantgenome2015.07.0053.


Genetic Analysis of Kernel Traits in Maize-Teosinte Introgression Populations.

Liu Z, Garcia A, McMullen MD, Flint-Garcia SA.

G3 (Bethesda). 2016 Aug 9;6(8):2523-30. doi: 10.1534/g3.116.030155.


Identification of QTL for resistance to Mediterranean corn borer in a maize tropical line to improve temperate germplasm.

Samayoa LF, Malvar RA, McMullen MD, Butrón A.

BMC Plant Biol. 2015 Nov 4;15:265. doi: 10.1186/s12870-015-0652-9.


The Genomic Impacts of Drift and Selection for Hybrid Performance in Maize.

Gerke JP, Edwards JW, Guill KE, Ross-Ibarra J, McMullen MD.

Genetics. 2015 Nov;201(3):1201-11. doi: 10.1534/genetics.115.182410. Epub 2015 Sep 18.


Prolonged expression of the BX1 signature enzyme is associated with a recombination hotspot in the benzoxazinoid gene cluster in Zea mays.

Zheng L, McMullen MD, Bauer E, Schön CC, Gierl A, Frey M.

J Exp Bot. 2015 Jul;66(13):3917-30. doi: 10.1093/jxb/erv192. Epub 2015 May 11.


Insights into the effects of long-term artificial selection on seed size in maize.

Hirsch CN, Flint-Garcia SA, Beissinger TM, Eichten SR, Deshpande S, Barry K, McMullen MD, Holland JB, Buckler ES, Springer N, Buell CR, de Leon N, Kaeppler SM.

Genetics. 2014 Sep;198(1):409-21. doi: 10.1534/genetics.114.167155. Epub 2014 Jul 17.


The genetic architecture of maize height.

Peiffer JA, Romay MC, Gore MA, Flint-Garcia SA, Zhang Z, Millard MJ, Gardner CA, McMullen MD, Holland JB, Bradbury PJ, Buckler ES.

Genetics. 2014 Apr;196(4):1337-56. doi: 10.1534/genetics.113.159152. Epub 2014 Feb 10.


The genetic architecture of maize stalk strength.

Peiffer JA, Flint-Garcia SA, De Leon N, McMullen MD, Kaeppler SM, Buckler ES.

PLoS One. 2013 Jun 20;8(6):e67066. doi: 10.1371/journal.pone.0067066. Print 2013.


Comprehensive genotyping of the USA national maize inbred seed bank.

Romay MC, Millard MJ, Glaubitz JC, Peiffer JA, Swarts KL, Casstevens TM, Elshire RJ, Acharya CB, Mitchell SE, Flint-Garcia SA, McMullen MD, Holland JB, Buckler ES, Gardner CA.

Genome Biol. 2013 Jun 11;14(6):R55. doi: 10.1186/gb-2013-14-6-r55.


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.


A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome.

Ganal MW, Durstewitz G, Polley A, Bérard A, Buckler ES, Charcosset A, Clarke JD, Graner EM, Hansen M, Joets J, Le Paslier MC, McMullen MD, Montalent P, Rose M, Schön CC, Sun Q, Walter H, Martin OC, Falque M.

PLoS One. 2011;6(12):e28334. doi: 10.1371/journal.pone.0028334. Epub 2011 Dec 8.


Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels.

Cook JP, McMullen MD, Holland JB, Tian F, Bradbury P, Ross-Ibarra J, Buckler ES, Flint-Garcia SA.

Plant Physiol. 2012 Feb;158(2):824-34. doi: 10.1104/pp.111.185033. Epub 2011 Dec 1.


Distinct genetic architectures for male and female inflorescence traits of maize.

Brown PJ, Upadyayula N, Mahone GS, Tian F, Bradbury PJ, Myles S, Holland JB, Flint-Garcia S, McMullen MD, Buckler ES, Rocheford TR.

PLoS Genet. 2011 Nov;7(11):e1002383. doi: 10.1371/journal.pgen.1002383. Epub 2011 Nov 17.


The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population.

Hung HY, Browne C, Guill K, Coles N, Eller M, Garcia A, Lepak N, Melia-Hancock S, Oropeza-Rosas M, Salvo S, Upadyayula N, Buckler ES, Flint-Garcia S, McMullen MD, Rocheford TR, Holland JB.

Heredity (Edinb). 2012 May;108(5):490-9. doi: 10.1038/hdy.2011.103. Epub 2011 Oct 26.


Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population.

Kump KL, Bradbury PJ, Wisser RJ, Buckler ES, Belcher AR, Oropeza-Rosas MA, Zwonitzer JC, Kresovich S, McMullen MD, Ware D, Balint-Kurti PJ, Holland JB.

Nat Genet. 2011 Feb;43(2):163-8. doi: 10.1038/ng.747. Epub 2011 Jan 9.


Genome-wide association study of leaf architecture in the maize nested association mapping population.

Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES.

Nat Genet. 2011 Feb;43(2):159-62. doi: 10.1038/ng.746. Epub 2011 Jan 9.


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.


IView: introgression library visualization and query tool.

Bottoms CA, Flint-Garcia S, McMullen MD.

BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S28. doi: 10.1186/1471-2105-11-S6-S28.


Genetic analysis of central carbon metabolism unveils an amino acid substitution that alters maize NAD-dependent isocitrate dehydrogenase activity.

Zhang N, Gur A, Gibon Y, Sulpice R, Flint-Garcia S, McMullen MD, Stitt M, Buckler ES.

PLoS One. 2010 Apr 1;5(4):e9991. doi: 10.1371/journal.pone.0009991.


Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers.

Yan J, Shah T, Warburton ML, Buckler ES, McMullen MD, Crouch J.

PLoS One. 2009 Dec 24;4(12):e8451. doi: 10.1371/journal.pone.0008451.


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.


Genetic control of photoperiod sensitivity in maize revealed by joint multiple population analysis.

Coles ND, McMullen MD, Balint-Kurti PJ, Pratt RC, Holland JB.

Genetics. 2010 Mar;184(3):799-812. doi: 10.1534/genetics.109.110304. Epub 2009 Dec 14.


Mapping resistance quantitative trait Loci for three foliar diseases in a maize recombinant inbred line population-evidence for multiple disease resistance?

Zwonitzer JC, Coles ND, Krakowsky MD, Arellano C, Holland JB, McMullen MD, Pratt RC, Balint-Kurti PJ.

Phytopathology. 2010 Jan;100(1):72-9. doi: 10.1094/PHYTO-100-1-0072.


A first-generation haplotype map of maize.

Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES.

Science. 2009 Nov 20;326(5956):1115-7. doi: 10.1126/science.1177837.


A genome-wide characterization of microRNA genes in maize.

Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, Narechania A, Maher CA, Guill K, McMullen MD, Ware D.

PLoS Genet. 2009 Nov;5(11):e1000716. doi: 10.1371/journal.pgen.1000716. Epub 2009 Nov 20.


Genetic variation at bx1 controls DIMBOA content in maize.

Butrón A, Chen YC, Rottinghaus GE, McMullen MD.

Theor Appl Genet. 2010 Feb;120(4):721-34. doi: 10.1007/s00122-009-1192-1. Epub 2009 Nov 13.


Genetic properties of the maize nested association mapping population.

McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C, Brown P, Browne C, Eller M, Guill K, Harjes C, Kroon D, Lepak N, Mitchell SE, Peterson B, Pressoir G, Romero S, Oropeza Rosas M, Salvo S, Yates H, Hanson M, Jones E, Smith S, Glaubitz JC, Goodman M, Ware D, Holland JB, Buckler ES.

Science. 2009 Aug 7;325(5941):737-40. doi: 10.1126/science.1174320.


The genetic architecture of maize flowering time.

Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman MM, Harjes C, Guill K, Kroon DE, Larsson S, Lepak NK, Li H, Mitchell SE, Pressoir G, Peiffer JA, Rosas MO, Rocheford TR, Romay MC, Romero S, Salvo S, Sanchez Villeda H, da Silva HS, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu J, Zhang Z, Kresovich S, McMullen MD.

Science. 2009 Aug 7;325(5941):714-8. doi: 10.1126/science.1174276.


DNAAlignEditor: DNA alignment editor tool.

Sanchez-Villeda H, Schroeder S, Flint-Garcia S, Guill KE, Yamasaki M, McMullen MD.

BMC Bioinformatics. 2008 Mar 19;9:154. doi: 10.1186/1471-2105-9-154.


Genetic design and statistical power of nested association mapping in maize.

Yu J, Holland JB, McMullen MD, Buckler ES.

Genetics. 2008 Jan;178(1):539-51. doi: 10.1534/genetics.107.074245.


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.


Genetic basis of resistance to fall armyworm (Lepidoptera: Noctuidae) and southwestern corn borer (Lepidoptera: Crambidae) leaf-feeding damage in maize.

Brooks TD, Bushman BS, Williams WP, McMullen MD, Buckley PM.

J Econ Entomol. 2007 Aug;100(4):1470-5.


Genomic screening for artificial selection during domestication and improvement in maize.

Yamasaki M, Wright SI, McMullen MD.

Ann Bot. 2007 Nov;100(5):967-73. Epub 2007 Aug 18. Review.


Patterns of selection and tissue-specific expression among maize domestication and crop improvement loci.

Hufford KM, Canaran P, Ware DH, McMullen MD, Gaut BS.

Plant Physiol. 2007 Jul;144(3):1642-53. Epub 2007 May 11.


Quantitative trait loci for maysin synthesis in maize (Zea mays L.) lines selected for high silk maysin content.

Meyer JD, Snook ME, Houchins KE, Rector BG, Widstrom NW, McMullen MD.

Theor Appl Genet. 2007 Jun;115(1):119-28. Epub 2007 May 8.


A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps.

Yim YS, Moak P, Sanchez-Villeda H, Musket TA, Close P, Klein PE, Mullet JE, McMullen MD, Fang Z, Schaeffer ML, Gardiner JM, Coe EH Jr, Davis GL.

BMC Genomics. 2007 Feb 9;8:47.


Molecular and functional diversity of maize.

Buckler ES, Gaut BS, McMullen MD.

Curr Opin Plant Biol. 2006 Apr;9(2):172-6. Epub 2006 Feb 3. Review.


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.


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.


Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition.

Morton BR, Bi IV, McMullen MD, Gaut BS.

Genetics. 2006 Jan;172(1):569-77. Epub 2005 Oct 11.


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.


Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks.

Szalma SJ, Buckler ES 4th, Snook ME, McMullen MD.

Theor Appl Genet. 2005 May;110(7):1324-33. Epub 2005 Apr 2.


Salmon silk genes contribute to the elucidation of the flavone pathway in maize (Zea mays L.).

McMullen MD, Kross H, Snook ME, Cortés-Cruz M, Houchins KE, Musket TA, Coe EH Jr.

J Hered. 2004 May-Jun;95(3):225-33.


Quantitative trait locus analysis as a gene discovery tool.

McMullen MD.

Methods Mol Biol. 2003;236:141-54.


Phenotypic versus marker-assisted selection for stalk strength and second-generation European corn borer resistance in maize.

Flint-Garcia SA, Darrah LL, McMullen MD, Hibbard BE.

Theor Appl Genet. 2003 Nov;107(7):1331-6. Epub 2003 Aug 19.


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