Project Publications

1999

• White S, Doebley J, 1999. The molecular evolution of terminal ear1, a regulatory gene in the genus Zea. Genetics 153: 1455-1462.   [pdf]

 

2000

• Gaut BS, Le Thierry d'Ennequin M, Peek AS, Sawkins MC, 2000. Maize as a model for the evolution of plant nuclear genomes. PNAS 97: 7008-7015.   [pdf]

 
• Sanchez G. JJ, Goodman MM, Stuber CW, 2000. Isozymatic and morphological diversity in the races of maize of Mexico. Econ Bot 54: 43-59.   [TOC]

 
• Sanchez G. JJ, Goodman MM, Stuber CW, 2000. Isozymatic diversity in the races of maize of the Americas. Maydica 45: 185-203.   [TOC]

 

2001

• Buckler ES, 2001. TASSEL: Trait Association, Evolution, and Linkage Analysis software package. Available at http://www.maizegenetics.net

 
• Buckler ES, Thornsberry JM, Kresovich S, 2001. Molecular diversity, structure and domestication of grasses. Genet Res 77: 213-218.   [pdf]

 
• Doebley J, 2001. George Beadle's other hypothesis: one-gene, one-trait. Genetics 158: 487-493.   [pdf]

 
• Gaut BS, 2001. Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses. Genome Res 11: 55-66.   [pdf]

 
• Goodman MM, Carson ML, 2001. Reality vs. myth: Corn breeding, exotics, and genetic engineering. Annual Corn Sorghum Research Conference Proceedings 55: 149-172.

 
• Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES, 2001. Structure of linkage disequilibrium and phenotypic associations in the maize genome. PNAS 98: 11479-11484.   [pdf]

 
• Tallury SP, Goodman MM, 2001. The state of the use of maize genetic diversity in the USA and sub-Saharan Africa, pp. 159-180 in Broadening the Genetic Base of Crop Production, edited by H.D. Cooper, C. Spillane and T. Hodgkin. CAB Publishing, Wallingford, UK.

 
• Tenaillon M, Sawkins M, Long A, Gaut R, Doebley J, Gaut B, 2001. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays). PNAS 98: 9161-9166.   [pdf]

 
• Thornsberry J, Goodman M, Doebley J, Kresovich S, Nielsen D, Buckler E, 2001. Dwarf8 polymorphisms associate with variation in flowering time. Nature Genet 28: 286-289.   [pdf]

 
• Tiffin P, Gaut BS, 2001. Sequence diversity in the tetraploid Zea perennis and the closely related diploid Z. diploperennis: Insights from four nuclear loci. Genetics 158: 401-412.   [pdf]

 

2002

• Buckler ES, Thornsberry J, 2002. Plant molecular diversity and applications to genomics. Curr Opin Plant Biol 5: 107-111.   [pdf]

 
• Casa AM, Mitchell SE, Smith OS, Register JC, Wessler SR, Kresovich S, 2002. Evaluation of Hbr (MITE) markers for assessment of genetic relationships among maize (Zea mays L.) inbred lines. Theor Appl Genet 104: 104-110.   [pdf]

 
• Gaut BS, 2002. Evolutionary dynamics of grass genomes. New Phytol 154: 15-28.   [pdf]

 
• Gethi JG, Labate JA, Kresovich S, Smith ME, Lamkey KR, 2002. SSR variation in important U.S. maize inbred lines. Crop Sci 42: 951-957.   [pdf]

 
• Matsuoka Y, Mitchell SE, Kresovich S, Goodman M, Doebley J, 2002. Microsatellites in Zea - variability, patterns of mutations, and use for evolutionary studies. Theor Appl Genet 104: 436-450.   [pdf]

 
• Matsuoka Y, Vigouroux Y, Goodman MM, Sanchez G. J, Buckler E, Doebley J, 2002. A single domestication for maize shown by multilocus microsatellite genotyping. PNAS 99: 6080-6084.   [pdf]

 
• Tenaillon MI, Sawkins MC, Anderson LK, Doebley JF, Stack SM, Gaut BS, 2002. Patterns of diversity and recombination along chromosome 1 of maize (Zea mays ssp. mays L.). Genetics 162: 1401-1413.   [pdf]

 
• Tiffin P, Gaut BS, 2002. Molecular evolution of the wound induced serine protease inhibitor wip1 in Zea and related genera. Mol Biol Evol 18: 2092-2101.   [pdf]

 
• Vigouroux Y, Jaqueth JS, Matsuoka Y, Smith OS, Beavis WD, Smith JSC, Doebley J, 2002. Rate and pattern of mutation at microsatellite loci in maize. Mol Biol Evol 19: 1251-1260.   [pdf]

 
• Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J, 2002. Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. PNAS 99: 9650-9655.   [pdf]

 
• Whitt SR, Wilson LM, Tenaillon MI, Gaut BS, Buckler ES, 2002. Genetic diversity and selection in the maize starch pathway. PNAS 99: 12959-12962.   [pdf]

 
• Zhang L, Peek AS, Dunams D, Gaut BS, 2002. Population genetics of duplicated disease-defense genes, hm1 and hm2, in maize (Z. mays ssp. mays L.) and its wild ancestor (Z. mays ssp. parviglumis). Genetics 162: 851-860.   [pdf]

 

2003

• Du C, Buckler E, Muse S, 2003. Development of a maize molecular evolutionary genomic database. Comparative and Functional Genomics 4: 246-249.   [Abstract]

 
• Flint-Garcia SA, Thornsberry JM, Buckler ES, 2003. Structure of linkage disequilibrium in plants. Annual Review of Plant Biology 54: 357-74.   [pdf]

 
• Garcia A, Buckler ES, 2003. MaizeMeister: Integrated phenotypic and germplasm tracking software. Available at http://www.maizegenetics.net

 
• Jaenicke-Deprés V, Buckler ES, Smith BD, Gilbert MTP, Cooper A, Doebley J, Pääbo S, 2003. Early allelic selection in maize as revealed by ancient DNA. Science 302: 1206-1208.   [pdf]

 
• Labate JA, Lamkey KR, Mitchell SE, Kresovich S, Sullivan H, Smith JSC, 2003. Molecular, agronomic, and historical aspects of Corn Belt Dent varietal diversity. Crop Sci 43: 80-91.   [pdf]

 
• Liu K, Goodman MM, Muse S, Smith JSC, Buckler ES, Doebley J, 2003. Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165: 2117-2128.   [pdf]

 
• Vigouroux Y, Matsuoka Y, Doebley J, 2003. Directional evolution for microsatellite size in maize. Mol Biol Evol 20: 1480-3.   [pdf]

 
• Whitt SR, Buckler ES, 2003. Using natural allelic diversity to evaluate gene function, pp. 123-140 in Plant Functional Genomics: Methods and Protocols, edited by E. Grotewald. Methods in Molecular Biology, vol 236. Humana Press, Totowa, N.J.

 

2004

• Clark RM, Linton E, Messing J, Doebley JF, 2004. Pattern of diversity in the genomic region near the maize domestication gene tb1. PNAS 101: 700-707.   [pdf]

 
• Doebley JF, 2004. The genetics of maize evolution. Ann Rev Genet 38: 37-59.   [pdf]

 
• Gallavotti A, Zhao Q, Kyozuka J, Meeley RB, Ritter MK, Doebley JF, Pe ME, Schmidt RJ, 2004. The role of barren stalk1 in the architecture of maize. Nature 432: 630-635.   [pdf]

 
• Goodman MM, 2004. Developing temperate inbreds using tropical maize germplasm: Rationale, results, conclusions. Maydica 49: 209-220.   [pdf]

 
• Goodman MM, 2004. Plant breeding requirements for applied molecular biology. Crop Sci 44: 1913-1914.   [pdf]

 
• Tarter JA, Goodman MM, Holland JB, 2004. Recovery of exotic alleles in semiexotic maize inbreds derived from crosses between Latin American accessions and a temperate line. Theor Appl Genet 109: 609-617.   [pdf]

 
• Tenaillon MI, U'Ren J, Tenaillon O, Gaut BS, 2004. Selection versus demography: A multilocus investigation of the domestication process in maize. Mol Biol Evol 21: 1214-1225.   [pdf]

 
• Tiffin P, Hacker R, Gaut BS, 2004. Population genetic evidence for rapid changes in intra-specific diversity and allelic cycling of defense genes in Zea. Genetics 168: 425-434.   [pdf]

 
• Wilson LM, Whitt SR, Ibanez-Carranza AM, Rocheford TR, Goodman MM, Buckler ES, 2004. Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16: 2719-2733.   [pdf]

 

2005

• Clark RM, Tavare S, Doebley J, 2005. Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus. Mol Biol Evol 22: 2304-2312.   [pdf]

 
• Flint-Garcia SA, Thuillet AC, Yu JM, Pressoir G, Romero SM, Mitchell SE, Doebley J, Kresovich S, Goodman MM, Buckler ES, 2005. Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J 44: 1054-1064.   [pdf]    Supporting information: [Fig S1]   [Table S2]

 
• Fukunaga K, Hill J, Vigouroux Y, Matsuoka Y, Sanchez J, Liu KJ, Buckler ES, Doebley J, 2005. Genetic diversity and population structure of teosinte. Genetics 169: 2241-2254.   [pdf]

 
• Liu K, Muse SV, 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128-2129.   [pdf]

 
• Lockton S, Gaut BS, 2005. Plant conserved non-coding sequences and paralogue evolution. Trends Genet 21: 60-65.   [pdf]

 
• Matsuoka Y, 2005. Origin matters: Lessons from the search for the wild ancestor of maize. Breeding Sci 55: 383-390.   [pdf]

 
• Szalma SJ, Buckler ES, Snook ME, McMullen MD, 2005. Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks. Theor Appl Genet 110: 1324-1333.   [pdf]

 
• Vigouroux Y, Mitchell S, Matsuoka Y, Hamblin M, Kresovich S, Smith JSC, Jaqueth J, Smith OS, Doebley J, 2005. An analysis of genetic diversity across the maize genome using microsatellites. Genetics 169: 1617-1630.   [pdf]

 
• Vollbrecht E, Springer PS, Goh L, Buckler ES, Martienssen R, 2005. Architecture of floral branch systems in maize and related grasses. Nature 436: 1119-1126.   [pdf]

 
• Wright SI, Gaut BS, 2005. Molecular population genetics and the search for adaptive evolution in plants. Mol Biol Evol 22: 506-519.   [pdf]

 
• Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, 2005. The effects of artificial selection of the maize genome. Science 308: 1310-1314.   [pdf]

 
• Yamasaki M, Tenaillon MI, Bi IV, Schroeder SG, Sanchez-Villeda H, Doebley JF, Gaut BS, McMullen MD, 2005. A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell 17: 2859-2872.   [pdf]

 

2006

• Anderson LK, Lai A, Stack SM, Rizzon C, Gaut BS, 2006. Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes. Genome Res 16: 115-122.   [pdf]

 
• Buckler ES, Stevens NM, 2006. Maize domestication. In Darwin's Harvest: New Approaces to the Origins, Evolution, and Conservation of Crops, edited by T. Motley, N. Zerega and H. Cross. Columbia University Press, New York, NY.

 
• Buckler ES, Gaut BS, McMullen MD, 2006. Molecular and functional diversity of maize. Curr Opin Plant Biol 9: 172-176.   [pdf]

 
• Buckler ES, Goodman MM, Holtsford TP, Doebley JF, Sanchez J, 2006. Phylogeography of the wild subspecies of Zea mays. Maydica 51: 123-134.   [pdf]

 
• Canaran P, Stein L, Ware D, 2006. Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support. Bioinformatics 22: 885-886.   [pdf]

 
• Doebley J, 2006. Unfallen grains: How ancient farmers turned weeds into crops. Science 312: 1318-1319.   [pdf]

 
• Doebley JF, Gaut BS, Smith BD, 2006. The molecular genetics of crop domestication. Cell 127: 1309-1321.   [pdf]

 
• Holland JB, 2006. Estimating genotypic correlations and their standard errors using multivariate restricted maximum likelihood estimation with SAS Proc MIXED. Crop Sci 46: 642-654.   [pdf]

 
• Kirst M, Caldo R, Casati P, Tanimoto G, Walbot V, Wise RP, Buckler ES, 2006. Genetic diversity contribution to errors in short oligonucleotide microarray analysis. Plant Biotechnol J 4: 489-498.   [Abstract]

 
• Morton BR, Bi IV, McMullen MD, Gaut BS, 2006. Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition. Genetics 172: 569-577.   [pdf]

 
• Robertson LA, Kleinschmidt CE, White DG, Payne GA, Maragos CM, Holland JB, 2006. Heritabilities and correlations of fusarium ear rot resistance and fumonisin contamination resistance in two maize populations. Crop Sci 46: 353-361.   [pdf]

 
• Robertson-Hoyt LA, Jines MP, Balint-Kurti PJ, Kleinschmidt CE, White DG, Payne GA, Maragos CM, Molnar TL, Holland JB, 2006. QTL mapping for fusarium ear rot and fumonisin contamination resistance in two maize populations. Crop Sci 46: 1734-1743.   [pdf]

 
• Tracy WF, Whitt SR, Buckler ES, 2006. Recurrent mutation and genome evolution: Example of Sugary 1 and the origin of sweet maize. Crop Sci 46: S49-S54.   [pdf]

 
• Yu JM, Buckler ES, 2006. Genetic association mapping and genome organization of maize. Curr Opin Biotech 17: 155-160.   [pdf]

 
• Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES, 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genet 38: 203-208.   [pdf]

 
• 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, 2006. Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic Acids Res 34: D752-D757.   [pdf]

 

2007

• Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES, 2007. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635.   [pdf]

 
• Briggs WH, McMullen MD, Gaut BS, Doebley J, 2007. Linkage mapping of domestication loci in a large maize-teosinte backcross resource. Genetics 177: 1915-1928.   [pdf]

 
• Esch E, Szymaniak JM, Yates H, Pawlowski WP, Buckler ES, 2007. Using crossover breakpoints in recombinant inbred lines to identify quantitative trait loci controlling the global recombination frequency. Genetics 177: 1851-1858.   [pdf]

 
• Gaut BS, Wright SI, Rizzon C, Dvorak J, Anderson LK, 2007. Opinion - Recombination: an underappreciated factor in the evolution of plant genomes. Nat Rev Genet 8: 77-84.   [pdf]

 
• Gore M, Bradbury P, Hogers R, Kirst M, Verstege E, van Oeveren J, Peleman J, Buckler E, van Eijk M, 2007. Evaluation of target preparation methods for single-feature polymorphism detection in large complex plant genomes. Plant Genome 47: S135-S148.   [pdf]

 
• Hamblin MT, Warburton ML, Buckler ES, 2007. Empirical comparison of simple sequence repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness. PLoS ONE 2: e1367.   [pdf]   [download data]

 
• Holland JB, 2007. Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10: 156-161.   [pdf]

 
• Hufford KM, Canaran P, Ware DH, McMullen MD, Gaut BS, 2007. Patterns of selection and tissue-specific expression among maize domestication and crop improvement loci. Plant Physiol 144: 1642-1653.   [pdf]

 
• Ross-Ibarra J, Morrell PL, Gaut BS, 2007. Plant domestication, a unique opportunity to identify the genetic basis of adaptation. PNAS 104: 8641-8648.   [pdf]

 
• Stich B, Yu JM, Melchinger AE, Piepho HP, Utz HF, Maurer HP, Buckler ES, 2007. Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy. Genetics 176: 563-570.   [pdf]

 
• Weber A, Clark RM, Vaughn L, Sanchez-Gonzalez JD, Yu JM, Yandell BS, Bradbury P, Doebley J, 2007. Major regulatory genes in maize contribute to standing variation in teosinte (Zea mays ssp parviglumis). Genetics 177: 2349-2359.   [pdf]   [download data]

 
• Yamasaki M, Wright SI, Mcmullen MD, 2007. Genomic screening for artificial selection during domestication and improvement in maize. Ann Bot 100: 967-973.   [pdf]

 
• Zhang Z, Todhunter RJ, Buckler ES, Van Vleck LD, 2007. Technical note: Use of marker-based relationships with multiple-trait derivative-free restricted maximal likelihood. J Anim Sci 85: 881-885.   [pdf]

 

2008

• Adetimirin VO, Vroh-Bi I, The C, Menkir A, Mitchell SE, Kresovich S. 2008. Diversity analyses of elite maize inbred lines adapted to West and Central Africa using SSR markers. Maydica 53: 143-149.   [pdf]

 
• Canaran P, Buckler ES, Glaubitz JC, Stein L, Sun Q, Zhao W, Ware D. 2008. Panzea: an update on new content and features. Nucleic Acids Res 36: D1041-D1043.   [pdf]

 
• Ersoz ES, Yu J, Buckler ES. 2008. Applications of linkage disequilibrium and association mapping in crop plants, pp. 97-120 in Genomics-Assisted Crop Improvement. Vol 1: Genomics Approaches and Platforms, edited by R.K. Varshney and R. Tuberosa. Springer, New York, NY.

 
• Gaut BS, Ross-Ibarra J. 2008. Perspective - Selection on major components of angiosperm genomes. Science 320: 484-486.   [pdf]

 
• Harjes CE, Rocheford TR, Bai L, Brutnell TP, Kandianis CB, Sowinski SG, Stapleton AE, Vallabhaneni R, Williams M, Wurtzel ET, Yan JB, Buckler ES. 2008. Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science 319: 330-333.   [pdf]

 
• Nelson PT, Coles ND, Holland JB, Bubeck DM, Smith S, Goodman MM. 2008. Molecular characterization of maize inbreds with expired US plant variety protection. Crop Sci 48: 1673-1685.   [pdf]   [download data]

 
• Pennisi E. 2008. Profile: Edward Buckler - Romping through maize diversity. Science 322: 40-41.   [pdf]

 
• Ross-Ibarra J, Gaut BS. 2008. Multiple domestications do not appear monophyletic. PNAS 105: E105.   [pdf]

 
• Sanchez-Villeda H, Schroeder S, Flint-Garcia S, Guill KE, Yamasaki M, McMullen MD. 2008. DNAAlignEditor: DNA alignment editor tool. BMC Bioinformatics 9: 154.   [pdf]

 
• Stich B, Mohring J, Piepho HP, Heckenberger M, Buckler ES, Melchinger AE. 2008. Comparison of mixed-model approaches for association mapping. Genetics 178: 1745-1754.   [pdf]

 
• Thuillet AC, Tenaillon MI, Anderson LK, Mitchell SE, Kresovich S, Stack SM, Gaut B, Doebley J. 2008. A weak effect of background selection on trinucleotide microsatellites in maize. J Hered 99: 45-55.   [pdf]

 
• Vigouroux Y, Glaubitz JC, Matsuoka Y, Goodman MM, Sanchez-Gonzalez J, Doebley J. 2008. Population structure and genetic diversity of new world maize races assessed by DNA microsatellites. Am J Bot 95: 1240-1253.   [pdf]   [download data]

 
• Weber AL, Briggs WH, Rucker J, Baltazar BM, Sanchez-Gonzalez JD, Feng P, Buckler ES, Doebley J. 2008. The genetic architecture of complex traits in teosinte (Zea mays ssp parviglumis): new evidence from association mapping. Genetics 180: 1221-1232.   [pdf]   [download data]

 
• Yu JM, Holland JB, McMullen MD, Buckler ES. 2008. Genetic design and statistical power of nested association mapping in maize. Genetics 178: 539-551.   [pdf]

 
• Zhao Q, Thuillet AC, Uhlmann NK, Weber A, Rafalski JA, Allen SM, Tingey S, Doebley J. 2008. The role of regulatory genes during maize domestication: Evidence from nucleotide polymorphism and gene expression. Genetics 178: 2133-2143.   [pdf]

 
• Zhu C, Gore M, Buckler ES, Yu J. 2008. Status and prospects of association mapping in plants. Plant Genome 1: 5-20.   [pdf]

 

2009

• 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, Oropeza Rosas M, 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. 2009. The genetic architecture of maize flowering time. Science 325: 714-718.   [pdf]   [download data]

 
• Flint-Garcia SA, Bodnar AL, Scott MP. 2009. Wide variability in kernel composition, seed characteristics, and zein profiles among diverse maize inbreds, landraces, and teosinte. Theor Appl Genet 119: 1129-1142.   [pdf]

 
• Flint-Garcia SA, Buckler ES, Tiffin P, Ersoz E, Springer NM. 2009. Heterosis is prevalent for multiple traits in diverse maize germplasm. PLoS ONE 4: e7433.   [pdf]

 
• Flint-Garcia SA, Dashiell KE, Prischmann DA, Bohn MO, Hibbard BE. 2009. Conventional screening overlooks resistance sources: rootworm damage of diverse inbred lines and their B73 hybrids is unrelated. J Econ Entomol 102: 1317-1324.   [pdf]

 
• Flint-Garcia SA, Guill KE, Sanchez-Villeda H, Schroeder SG, McMullen MD. 2009. Maize amino acid pathways maintain high levels of genetic diversity. Maydica 54: 375-386.   [pdf]

 
• Gore MA, Wright MH, Ersoz ES, Bouffard P, Skekeres ES, Jarvie TP, Hurwitz BL, Narachania A, Harkins TT, Grills GS, Ware DH, Buckler ES. 2009. Large-scale discovery of gene-enriched SNPs. Plant Genome 2: 121-133.   [pdf]

 
• Gore MA, Chia J-M, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES. 2009. A first-generation haplotype map of maize. Science 326: 1115-1117.   [pdf]   [download data]

 
• Jones E, Chu W-C, Ayele M, Ho J, Bruggeman E, Yourstone K, Rafalski A, Smith OS, McMullen MD, Bezawada C, Warren J, Babayev J, Basu S, Smith S. 2009. Development of single nucleotide polymorphism (SNP) markers for use in commmercial maize (Zea mays L.) germplasm. Mol. Breeding 24: 165-176.   [pdf]

 
• Mackay TFC. 2009. A-maize-ing diversity. Science 325: 688-689.   [Abstract]

 
• McMullen MD, Kresovich S, Sanchez Villeda H, 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. 2009. Genetic properties of the maize Nested Association Mapping population. Science 325: 737-740.   [pdf]   [download data]

 
• McMullen MD, Frey M, Degenhardt J. 2009. Genetics and biochemistry of insect resistance in maize, pp. 271-289 in Handbook of Maize: Its Biology, edited by J. Bennetzen and S. Hake. Springer, New York, NY.   [pdf]

 
• Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE, Buckler ES. 2009. Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21: 2194-2202.   [pdf]

 
• Pressoir G, Brown PJ, Zhu WY, Upadyayula N, Rocheford T, Buckler ES, Kresovich S. 2009. Natural variation in maize architecture is mediated by allelic differences at the PINOID co-ortholog barren inflorescence2. Plant J 58: 618-628.   [pdf]

 
• Quijada P, Shannon LM, Glaubitz JC, Studer AJ, Doebley J. 2009. Characterization of a major maize domestication QTL on the short arm of chromosome one. Maydica 54: 401-408.   [pdf]

 
• Tian F, Stevens NM, Buckler ES. 2009. Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10. PNAS 106: 9979-9986.   [pdf]

 
• Weber AL, Zhao Q, McMullen MD, Doebley J. 2009. Using association mapping in teosinte to investigate the function of maize selection-candidate genes. PLoS ONE4: e8227.   [pdf]

 
• Yan J, Shah T, Warburton ML, Buckler ES, McMullen MD, Crouch J. 2009. Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers. PLoS ONE 4: e8451.   [pdf]

 
• Yu J, Zhang Z, Zhu C, Tabanoa DA, Pressoir G, Tuinstra MR, Kresovich S, Todhunter RJ, Buckler ES. 2009. Simulation appraisal of the adequacy of number of background markers for relationship estimation in association mapping. Plant Genome 2: 63-77.   [pdf]

 
• Zhang L, Chia J-M, Kumari S, Stein JC, Liu Z, Narechania A, Maher CA, Guill K, McMullen MD, Ware D. 2009. A genome-wide characterization of microRNA genes in maize. PLoS Genet 5: e1000716.   [pdf]

 
• Zhang Z, Buckler ES, Casstevens TM, Bradbury PJ. 2009. Software engineering the mixed model for genome-wide association studies on large samples. Briefings in Bioinformatics 10: 664-675.   [pdf]

 

2010

• Bottoms C, Flint-Garcia S, McMullen MD. 2010. IView: Introgression library visualization and query tool. BMC Bioinformatics 11(Suppl 6): S28.   [pdf]

 
• Butron A, Chen YC, Rottinghaus GE, McMullen MD. 2010. Genetic variation at bx1 controls DIMBOA contect in maize. Theor Appl Genet 120: 721-734.   [pdf]

 
• Coles ND, McMullen MD, Balint-Kurti PJ, Pratt RC, Holland JB. 2010. Genetic control of photoperiod sensitivity in maize revealed by joint multiple population analysis. Genetics 184: 799-812.   [pdf]   [download data]

 
• Dubois PG, Olsefski GT, Flint-Garcia S, Setter TL, Hoekenga OA, Brutnell TP. 2010. Physiological and genetic characterization of end-of-day far-red light response in maize seedlings. Plant Physiol 154: 173-186.   [pdf]

 
• Holland JB, Nelson PT. 2010 Dedication: Major M. Goodman, maize geneticist and breeder. Plant Breeding Reviews 33: 1-29.   [pdf]

 
• Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang Q-F, Li J, Han B. 2010. Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics 42: 961-967.   [pdf]

 
• Glover JD, Reganold JP, Bell LW, Borevitz J, Brummer EC, Buckler ES, Cox CM, Cox TS, Crews TE, Culman SW, DeHaan LR, Eriksson D, Gill BS, Holland J, Hu F, Hulke BS, Ibrahim AMH, Jackson W, Jones SS, Murray SC, Paterson AH, Ploschuk E, Sacks EJ, Snapp S, Tao D, Van Tassel DL, Wade LJ, Wyse DL, Xu Y. 2010. Increased food and ecosystem security via perennial grains. Science 328: 1638-1639.   [pdf]

 
• Krill AM, Kirst M, Kochian LV, Buckler ES, Hoekenga OA. 2010. Association and linkage analysis of aluminum tolerance genes in maize. PLoS ONE 5: e9958.   [pdf]

 
• van Heerwaarden J, Ross-Ibarra J, Doebley J, Glaubitz JC, Sanchez Gonzalez JJ, Gaut BS, Eguiarte L. 2010. Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis). Molecular Ecology 19: 1162-1173.   [pdf]   [download data]

 
• van Heerwaarden J, van Eeuwijk FA, Ross-Ibarra J. 2010. Genetic diversity in a crop metapopulation. Heredity 104: 28-39.   [pdf]

 
• Yan J, Bermudez Kandianis C, Harjes CE, Bai L, Kim E-H, Yang X, Skinner DJ, Fu Z, Mitchell S, Li Q, Salas Fernandez MG, Zaharieva M, Babu R, Fu Y, Palacios N, Li J, DellaPenna D, Brutnell T, Buckler ES, Warburton ML, Rocheford T 2010. Rare genetic variation at Zea mays crtRB1 increases β-carotene in maize grain. Nature Genetics 42: 322-327.   [pdf]

 
• Zhang N, Gibon Y, Gur A, Chen C, Lepak N, Höhne M, Zhang Z, Kroon D, Tschoep H, Stitt M, Buckler E. 2010. Fine quantitative trait loci mapping of carbon and nitrogen metabolism enzyme activities and seedling biomass in the maize IBM mapping population. Plant Physiology 154: 1753-1765.   [pdf]

 
• Zhang N, Gur A, Gibon Y, Sulpice R, Flint-Garcia S, McMullen MD, Stitt M, Buckler ES. 2010. Genetic analyis of central carbon metabolism unveils an amino acid substitution that alters maize NAD-dependent isocitrate dehydrogenase activity. PLoS ONE 5: e9991.   [pdf]

 
• Zhang Z, Ersoz E, Lai C-Q, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM, Buckler ES. 2010. Mixed linear model approach adapted for genome-wide association studies. Nature Genetics 42: 355-360.   [pdf]

 
• Zhao Q, Weber A, McMullen MD, Guill K, Doebley J. 2010. MADS-box genes of maize: Frequent targets of selection during domestication. Genetics Research Dec 14: 1-11.   [Abstract]

 
• Zwonitzer JC, Coles ND, Krakowsky MD, Arellano C, Holland JB, McMullen MD, Pratt RC, Balint-Kurti PJ. 2010. Mapping resistance quantitative trait loci for three foliar diseases in a maize recombinant inbred line population — evidence for multiple disease resistance? Phytopathology 100: 72-79.   [pdf]

 

2011

• Brown PJ, Upadyayula N, Mahone GS, Tian F, Bradbury PJ, Myles S, Holland JB, Flint-Garcia S, McMullen MD, Buckler ES, Rocheford TR. 2011. Distinct genetic architectures for male and female inflorescence traits of maize. PLoS Genetics 7: e1002383.   [pdf]

 
• Coles ND, Zila CT, Holland JB. 2011. Allelic effect variation at key photoperiod response quantitative trait loci in maize. Crop Science 51: 1036-1049.   [pdf]

 
• Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6: e19379.   [pdf]

 
• Ganal MW, Durstewitz G, Polley A, Bérard A, Buckler ES, Charcosset A, Clarke JD, Graner E-M, Hansen M, Joets J, Le Paslier M-C, McMullen MD, Montalent P, Rose M, Schon C-C, Sun Q, Walter H, Martin OC, Falque M. 2011. A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS ONE 6: e28334.   [pdf]

 
• 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. 2011. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nature Genetics 43: 163-168.   [pdf]   [download data]

 
• Li H, Bradbury P, Ersoz E, Buckler ES, Wang J. 2011. Joint QTL linkage mapping for multiple-cross mating design sharing one commmon parent. PLoS ONE 6: e17573.   [pdf]

 
• Poland JA, Bradbury PJ, Buckler ES, Nelson RJ. 2011. Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. PNAS 108: 6893-6898.   [pdf]   [download data]

 
• Setter TL, Yan J, Warburton M, Ribaut J-M, Xu Y, Sawkins M, Buckler ES, Zhang Z, Gore MA. 2011. Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought. Journal of Experimental Botany 62: 701-716.   [pdf]

 
• Studer AJ, Doebley JF. 2011. Do large effect QTLs fractionate? A case study at the maize domestication QTL teosinte branched1. Genetics 188: 673-681.   [pdf]   [download data]

 
• Studer A, Zhao Q, Ross-Ibarra J, Doebley J. 2011. Identification of a functional transposon insertion in the maize domestication gene tb1. Nature Genetics 43: 1160-1163.   [pdf]   [download data]

 
• Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES. 2011. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nature Genetics 43: 159-162.   [pdf]   [download data]

 
• van Heerwaarden J, Doebley J, Briggs WH, Glaubitz JC, Goodman MM, Sanchez Gonzalez JJ, Ross-Ibarra J. 2011. Genetic signals of origin, spread, and introgression in a large sample of maize landraces. PNAS 108: 1088-1092.   [pdf]   [download data]

 
• Wisser RJ, Kolkman JM, Patzoldt ME, Holland JB, Yu J, Krakowsky M, Nelson RJ, Balint-Kurti PJ. 2011. Multivariate analysis of maize disease resistances suggests a pleiotropic genetic basis and implicates a GST gene. PNAS 18: 7339-7344.   [pdf]

 
• Zhao Q, Weber AL, McMullen MD, Guill K, Doebley J. 2011. MADS-box genes of maize: frequent targets of selection during maize domestication. Genetics Research 93: 65-75.   [pdf]

 

2012

• Cook JP, McMullen MD, Holland JB, Tian F, Bradbury P, Ross-Ibarra J, Buckler ES, Flint-Garcia SA. 2012 (in press). Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. Plant Physiology (online ahead of print).   [download MaizeSNP50 genotypic data]   [download phenotypic data]

 
• Hung H-Y, 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. 2012 (in press). The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population. Heredity (advance online publication).   [download data]

 
• Morrell PL, Buckler ES, Ross-Ibarra J. 2012. Crop genomics: advances and applications. Nature Reviews Genetics 13: 85-96.   [pdf]