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]

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

 
• Sánchez 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. Nat 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: 8060-8064.   [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.   [TOC]

 
• 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]

 
• 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.   [TOC]

 
• 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 Biotechnology Journal 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. Nat 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]

 
• 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]

 
• 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

• 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]

 
• 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]

 
• 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]