panzea

Publications

202 publications from 2009 onwards. Earlier work is listed under 2008 and earlier.

2019

  1. Transposable elements contribute to dynamic genome content in maize.

    Anderson SN, Stitzer MC, Brohammer AB, Zhou P, Noshay JM, Hirsch CD, Ross-Ibarra J, Hirsch CD, and Springer NM

    bioRxiv

    doi:10.1101/547398Link

  2. Dynamic patterns of transcript abundance of transposable element families in maize.

    Anderson SN, Stitzer MC, Zhou P, Ross-Ibarra J, Hirsch CD, and Springer NM

    bioRxiv

    doi:10.1101/668558Link

  3. Detecting adaptive differentiation in structured populations with genomic data and common gardens.

    Josephs EB, Berg JJ, Ross-Ibarra J and Coop G

    Genetics 212 (3): 5643-5652.

    doi:10.1534/genetics.118.301786Link

  4. The temporal dynamics of background selection in non-equilibrium populations.

    Torres R, Stetter MG, Hernandez RD, and Ross-Ibarra J

    bioRxiv

    doi:10.1101/618389Link

  5. 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, and Doebley JF

    Genetics 212(3)

    doi:10.1534/genetics.119.302378Link

  6. 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 JDJ, Romay MC, Glaubitz JC, Sun Q, Buckler ES, Holland JB, Doebley JF

    PNAS 116 (12): 5643-5652. doi: doi.org/10.1073/pnas.1820997116.

    doi:10.1073/pnas.1820997116Link

  7. Metabolome-scale genome-wide association studies reveal chemical diversity and genetic control of maize specialized metabolites.

    Zhou S, Kremling K, Bandillo N, Richter A, Zhang YK, Ahern KR, Artyukhin AB, Hui JX, Younkin GC, Schroeder FC, Buckler ES, Jander G

    The Plant Cell 31(5): 937-955 doi: doi.org/10.1105/tpc.18.00772

    doi:10.1105/tpc.18.00772Link

2018

  1. Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets.

    AlKhalifah N, Campbell DA, Falcon CM, Gardiner JM, Miller ND, Romay MC, Walls R,Walton R,Yeh C, Bohn M, Bubert J, Buckler ES, Ciampitti I, Flint-Garcia S, Gore M , Graham C , Hirsch C, Holland JB, Hooker D, Kaeppler S, Knoll J, Lauter N, Lee EC, Lorenz A, Lynch JP, Moose SP, Murray SC, Nelson R, Rocheford T, Rodriguez O, Schnable JC, Scully B, Smith M, Springer N, Thomison P, Tuinstra M, Wisser RJ, Xu W, Ertl D, Schnable PS, De Leon N, Spalding EP, Edwards J, Lawrence-Dill CJ

    BMC Research Notes 11:452

    doi:10.1186/s13104-018-3508-1Link

  2. Genome-wide association and genomic prediction models of tocochromanols in fresh sweet corn kernels.

    Baseggio M, Murray M, Magallanes-Lundback M, Kaczmar N, Chamness J, Buckler ES, Smith ME, DellaPenna D, Tracy, WF, Gore MA

    The Plant Genome 12:180038.

    doi:10.3835/plantgenome2018.06.0038Link

  3. Quantitative trait loci mapping of western corn rootworm (Coleoptera: Chrysomelidae) host plant resistance in two populations of doubled haploid lines in maize (Zea mays l.)

    Bohn MO, Marroquin JJ, Flint-Garcia S, Dashiell K, Willmot DB, Hibbard BE

    Journal of Economic Entomology 111(1):435

    doi:10.1093/jee/tox310Link

  4. Ecogeography of teosinte

    de Jesus Sanchez Gonzalez J, Corral JAR, Garcia GM, Ojeda GR, De la Cruz Larios L, Holland JB, Medrano RM, Romero GEG

    PLoS One

    doi:10.1371/journal.pone.0192676Link

  5. Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy

    Gault C, Kremling K, Buckler ES

    bioRxiv

    doi:10.1101/267682Link

  6. 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

    PNAS 115(2):E334

    doi:10.1073/pnas.1718058115Link

  7. Diverse chromosomal locations of quantitative trait loci for tolerance to maize chlorotic mottle virus in five maize populations.

    Jones MW, Penning BW, Jamann TM, Glaubitz JC, Romay MC, Buckler ES, Redinbaugh MG

    Phytopathology 108 (6): 748 - 758 doi: doi.org/10.1094/PHYTO-09-17-0321-R.

    doi:10.1094/PHYTO-09-17-0321-RLink

  8. Dysregulation of expression correlates with rare-allele burden and fitness loss in maize

    Kremling KAG, Chen S, Su M, Lepak NK, Romay MC, Swarts KL, Lu F, Lorant A, Bradbury PJ, Buckler ES

    Nature 555:520

    doi:10.1038/nature25966Link

  9. Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation.

    Li B, Kremling, KAG, Wu P, Bukowski R, Romay MC, Xie E, Buckler ES, and Chen M

    Genome Research 28:1555-1565

    doi:10.1101/gr.229716.117Link

  10. Increased experimental conditions and marker densities identified more genetic loci associated with southern and northern leaf blight resistance in maize.

    Li Y, Chen L, Li C, Bradbury PJ, Shi Y, Song Y, Zhang D, Zhang Z, Buckler ES, Li Y, Wang T

    Scientific Reports 8:68-48.

    doi:10.1038/s41598-018-25304-zLink

  11. Breaking the curse of dimensionality to identify causal variants in Breeding 4.

    Ramstein GB, Jensen SE, Buckler ES

    Theoretical and Applied Genetics 132(3):559-567

    doi:10.1007/s00122-018-3267-3Link

  12. The maize W22 genome provides a foundation for functional genomics and transposon biology.

    Springer NM, Anderson SN, Andorf CM, Ahern KR, Bai F, Barad O, Barbazuk WB, Bass HW, Baruch K, Ben-Zvi G, Buckler ES, Bukowski R, Campbell MS, Cannon EKS, Chomet P, Dawe RK, Davenport R, Dooner HK, Du LH, Du C, Easterling KA, Gault C, Guan JC, Hunter CT, Jander G, Jiao Y, Koch KE, Kol G, Köllner TG, Kudo T, Li Q, Lu F, Mayfield-Jones D, Mei W, McCarty DR, Noshay JM, Portwood JL, Ronen G, Settles AM, Shem-Tov D, Shi J, Soifer I, Stein JC, Stitzer MC, Suzuki M, Vera DL, Vollbrecht E, Vrebalov JT, Ware D, Wei S, Wimalanathan K, Woodhouse MR, Xiong W, Brutnell TP

    Nature Genetics 50:1282-1288 doi: doi.org/10.1038/s41588-018-0158-0.

    doi:10.1038/s41588-018-0158-0Link

  13. Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima

    Stetter MG , Thornton K, Ross-Ibarra J

    PLoS Genetics 14(11)

    doi:10.1371/journal.pgen.1007794Link

  14. The genomic ecosystem of transposable elements in maize

    Stitzer MC, Anderson SN, Springer NM, Ross‐Ibarra J

    bioRxiv

    doi:10.1101/559922Link

  15. Maize domestication and gene interaction.

    Stitzer MC, Ross‐Ibarra J

    New Phytologist (2)220:395-408

    doi:10.1111/nph.15350Link

  16. Exceptional intraspecific gene order and gene structural variations between Mo17 and other maize genomes.

    Sun S, Zhou Y, Chen J, Shi J, Zhao H, Zhao H, Song W, Zhang M, Cui Y, Dong X, Liu H, Ma X, Jiao Y, Wang B, Wei X, Stein JC, Glaubitz JC, Lu F, Yu G, Liang C, Fengler K, Li B, Rafalski A, Schnable PS, Ware DH, Buckler ES, Lai J

    Nature Genetics 50: 1289-1295

    doi:10.1038/s41588-018-0182-0Link

  17. Quantitative Genetic Analysis of the Maize Leaf Microbiome

    Wallace JG, Kremling KA, Buckler ES

    Phytobiomes Journal 2(4):2471-2906

    doi:10.1094/PBIOMES-02-18-0008-RLink

  18. On the road to breeding 4.0: unraveling the good, the bad, and the boring of crop quantitative genomics.

    Wallace JG, Rodgers-Melnick E, Buckler ES

    Annual Review of Genetics 52:421-444.

    doi:10.1146/annurev-genet-120116-024846Link

  19. Large-scale replicated field study of maize rhizosphere identifies heritable microbes.

    Walters WA, Jin ZJ, Youngblut N, Wallace JG, Sutter J, Zhang W, Gonzalez-Pena A, Peiffer J, Koren O, Shi Q, Knight R, Glavina del Rion T, Tringe SG, Buckler ES, Dangl JL, Ley RE

    PNAS 115 (28): 7368-7373. doi: doi.org/10.1073/pnas.1800918115.

    doi:10.1073/pnas.1800918115Link

  20. Comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing.

    Wang B, Regulski M, Tseng E, Olson A, Goodwin S, McCombie RW, Ware D

    Genome Research 28: 921-932

    doi:10.1101/gr.227462.117Link

  21. 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, Hi D, Doebly JF, Tian F

    Molecular Plant 11(3):443

    doi:10.1016/j.molp.2017.12.011Link

  22. Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence.

    Washburn JD, Mejia-Guerra MK, Ramstein G, Kremling KAG, Valluru R, Buckler ES, and Wang H

    PNAS 116(12):5542-5549.

    doi:10.1073/pnas.1814551116Link

  23. 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, Doebly JF

    Journal of Heredity 109(3):333

    doi:10.1093/jhered/esx073Link

  24. Ethylene signaling regulates natural variation in the abundance of antifungal acetylated diferuloylsucroses and Fusarium graminearum resistance in maize seedling roots.

    Zhou S, Zhang YK, Kremling KA, Ding Y, Bennett JS, Bae JS, Kim DK, Kolomiets MV, Schmelz EA, Schroeder FC, Buckler ES, Jander G

    New Phytologist 221(4): 2096-2111

    doi:10.1111/nph.15520Link

2017

  1. Enhancing genomic prediction with genome-wide association studies in multiparental maize populations.

    Bian Y, Holland JB

    Heredity

    doi:10.1038/hdy.2017.4Link

  2. Construction of the third generation Zea mays haplotype map

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

    GigaScience

    doi:10.1093/gigascience/gix134Link

  3. Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain

    Diepenbrock CH, Kandianus CB, Lipka AE, Magallanes-Lundback M, Vaillancourt B, Gongora-Castillo E, Wallace JG, Cepela J, Mesberg A, Bradbury P, Ilut DC, Mateos-Hernandez M, Hamilton J, Owens BF, Tiede T, Buckler ES, Rocheford T, Buell CR, Gore MA, DellPenna D

    The Plant Cell

    doi:10.1105/tpc.17.00475Link

  4. The effect of artificial selection on phenotypic plasticity in maize

    Gage JL, Jarquin D, Romay C, Lorenz A, Buckler ES, Kaeppler S, Alkhalifah N, Bohn M, Campbell DA, Edwards J, Ertl D, Flint-Garcia S, Gardiner J, Good B, Hirsch CH, Holland J, Hooker DC, Knoll J, Kolkman J, Kruger G, Lauter N, Lawrence-Dill CJ, Lee E, Lynch J, Murray SC, Nelson R, Petzoldt J, Rocheford T, Schnable J, Schnable PS, Scully B, Smith M, Springer NM, Srinivasan S, Walton R, Weldekidan T, Wisser RJ, Xu W, Yu J, de Leon N

    Nature Communications doi: 10.1038

    Link

  5. Assessment of natural variability of maize lipid transfer protein using a validated sandwich ELISA.

    Gu X, Lee T, Geng T, Liu K, Thoma R, Crowley K, Edrington T, Ward JM, Wang Y, Flint-Garcia S, Bell E, Glenn K

    J. Agric. Food Chem. 65:1740–1749.

    Link

  6. k-mer grammar uncovers maize regulatory architecture

    Guerra MKM, Buckler ES

    bioRxiv doi: 10.1101

    Link

  7. Improved maize reference genome with single molecules technologies

    Jaio Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin C, Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR, Springer NM, Antoniou E, McCombie WR, Ware GG

    Nature

    doi:10.1038/nature22971Link

  8. Evaluation of highly multiplexed PCR combined with semi-conductor-based sequencing for targeted resequencing in maize

    Jamann TS, Sood S, Wisser RJ, Holland JB

    PLoS One

    doi:10.1371/journal.pone.0168910Link

  9. High-Throughput Resequencing of Maize Landraces at Genomic Regions Associated with Flowering Time

    Jamann TS, Sood S, Wisser RJ, Holland JB

    PLoS ONE 12(1):e0168910.

    Link

  10. The complex sequence landscape of maize revealed by single molecule technologies.

    Jiao Y, Peluso P, Shi J, Liang L, Stitzer M, Wang B, Campbell M, Stein J, Wei X, Chin C, Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider K, Wolfgruber T, May M, Springer N, Antoniou E, McCombie R, Presting G, McMullen M, Ross-Ibarra J, Dawe K, Hastie A, Rank D, Ware D

    bioRxiv doi:/10.1101/079004

    doi:10.1101/079004Link

  11. Diverse chromosomal loctions of quantitative trait loci for tolerance to maize chlorotic mottle virus in five maize populations

    Jones MW, Penning BW, Jamann TM, Glaubitz JC, Romay C, Buckler ES, Redinbaugh MG

    Phytopathology

    doi:10.1094/PHYTO-09-17-0321-RLink

  12. Genetic analysis of teosinte alleles for kernel composition traits in maize.

    Karn A, Gillman J, Flint-Garcia S

    G3 7(4):1157

    Link

  13. Development of rigorous fatty acid near-infrared spectroscopy quantitation methods in support of soybean oil improvement.

    Karn A, Heim C, Flint-Garcia S, Bilyeu K, Gillman J

    J Am Oil Chem Soc 94: 69.

    Link

  14. Genetic Analysis of Lodging in Diverse Maize Hybrids

    Larsson SJ, Peiffer JA, Edwards JW, Ersoz ES, Flint Garcia SA, Holland JB, McMullen MD, Tuinstra MR, Romay C, Buckler ES

    bioRxiv

    doi:10.1101/185769Link

  15. Identification of teosinte alleles for resistance to douther blight near isogenic maize lines

    Lennon JR, Krakowsky M, Goodman M, Flint-Garcia S, Balint-Kurti PJ

    Crop Science 57:1973

    doi:10.2135/cropsci2016.12.0979Link

  16. The potential role of genetic assimilation during maize domestication

    Lorant A, Pederson S, Holst I, Hufford MB, Winter K, Piperno D, Ross-Ibarra J

    PLoS One

    doi:10.1371/journal.pone.0184202Link

  17. A study of allelic diversity underlying flowering-time adaptation in maize landraces

    Navarro JAR, Willcox M, Burgueno J, Romay C, Swarts K, Trachsel S, Preciado E, Terron A, Delgado HV, Vidal V, Ortega A, Banda AE, Montiel NOG, Ortiz-Monasterio I, San Vincente F, Espinoza AG, Atlin G, Wenzi P, Hearne S, Buckler ES

    Nature Genetics 49:476

    doi:10.1038/ng.3784Link

  18. Selection for water-soluble carbohydrate accumulation and investigation of genetic x environment interactions in an elite wheat breeding population

    Ovenden B, Milgate A, Lissle C, Wade LJ, Rebetzke GJ, Holland JB

    Theoretical and Applied Genetics

    doi:10.1007/s00122-017-2969-2Link

  19. Genome-Wide Assocation for Water-Soluble Carbohydrate and Relative Maturity in Wheat Using SNP and DArT Marker Arrays

    Ovenden B, Milgate A, Wade LJ, Rebetzke GJ, Holland JB

    G3 7(8):2821

    Link

  20. Population extremes for assessing trait value and correlated response of genetically complex traits.

    Rebetzke GJ, Richards RA, Holland JB

    Field Crops Research 201:122-132.

    Link

  21. Gene fractionation and function in the ancient subgenome of maize

    Renny-Byfiekd S, Rodgers-Melnick E, Ross-Ibarra J

    Molecular Biology and Evolution 34(8)

    Link

  22. How to make a domesticate

    Stetter MG, Gates DJ, Me W,Ross-Ibarra J

    Current Biology 27(17)

    doi:10.1016/j.cub.2017.06.048Link

  23. Maize YABBY Genes drooping leaf1 and drooping leaft2 Regulate Plant Architechture

    Strable J, Wallace JG, Unger-Wallace E, Briggs S, Bradbury P, Buckler ES, Vollbrecht E

    The Plant Cell

    doi:10.1871/tpc.16.00477Link

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

    Studer AJ, Want H, Doebly JF

    Genetics 2017(2), 755

    Link

  25. Genomic estimation of complex traits reveals ancient maize adaptationto temperate North America

    Swarts K, Gutaker RM, Benz B, Blake M, Bukowski R, Holland J, Kruse-Peeples M,Lepak N, Prim L,Romay MC, Ross-Ibarra J, de Jesus Sanchez Gonzales J, Schuenemann VJ, Krause J, Matson RG, Weigel D, Buckler ES, Burbano HA

    Science 357(6350):512

    doi:10.1126/science.aam942Link

  26. The interplay of demography and selection during maze domestication and diffusion

    Wang L, Beissinger TM, Lorant A, Ross-Ibarra C, Hufford MB

    Genome Biology 18:215

    Link

  27. 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 Genetics

    doi:10.1371/journal.pgen.1007019Link

  28. Rapid Cycling Genomic Selection in a Multi-parental Tropical Maize Population

    Zhang X, Perez-Rodriguez P, Burgeno J, Olsen M, Buckler E, Atlin G, Prasanna BM, Vargas M, San Vincente F, Crossa J

    G3 7:2315

    Link

2016

  1. Modifications to a LATE MERISTEM IDENTITY-1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.).

    Andres RJ, Coneva V, Frank MH, Tuttle JR, Samayoa LF, Han SW, Kaur B, Zhu L, Fang H, Bowman DT, Rojas-Pierce M, Haigler CH, Jones DC, Holland JB, Chitwood DH, Kuraparthy V

    Proceedings of the National Academy of Sciences 114(1):E57-E66.

    Link

  2. Recent demography drives changes in linked selection across the maize genome.

    Beissinger TM, Wang L, Crosby K, Durvasula A, Hufford MB, Ross-Ibarra J

    Nature Plants 2:16084

    Link

  3. A proposal regarding best practices for validating the identity of genetic stocks and the effects of genetic variants.

    Bergelson J, Buckler ES, Ecker JR, Nordborg M, Weigel D

    The Plant Cell 28(3):606-609

    Link

  4. Fine mapping of a QTL associated with kernel row number on chromosome 1 of maize.

    Calderón C L, Yandell BS, Doebley JF

    PLoS ONE [doi:/10.1371/journal.pone.0150276](https://doi.org/10.1371/journal.pone.0150276)

    doi:10.1371/journal.pone.0150276doi:/10.1371/journal.pone.0150276Link

  5. ANGSD-wrapper: utilities for analysing next generation sequencing data.

    Durvasula A, Hoffman PJ, Kent TV, Liu C, Kono TJY, Morrell PL, Ross-Ibarra J

    Molecular Ecology Resources 16(6):1449-1454.

    LinkLink

  6. Biosynthesis of 8-O-methylated benzoxazinoid defense compounds in maize.

    Handrick V, Robert CA, Ahern KR, Zhou S, Machado RA, Maag D, Glauser G, Fernandez-Penny FE, Chandran JN, Rodgers-Melnik E, Schneider B, Buckler ES, Boland W, Gershenzon J, Jander G, Erb M, Köllner TG

    The Plant Cell 28(7):1682.

    Link

  7. Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize.

    Hirsch C, Hirsch CD, Brohammer AB, Bowman MJ, Soifer I, Barad O, Shem-Tov D, Baruch K, Lu F, Hernandez AG, Fields CJ, Wright CL, Koehler K, Springer NM, Buckler ES, Buell CR, de Leon N, Kaeppler SM, Childs K, Mikel MM

    The Plant Cell 28(11):2700-2714

    Link

  8. Responses to recurrent index selection for reduced Fusarium ear rot and lodging and for increased yield in maize.

    Horne DW, Eller MS, Holland JB

    Crop Science 56:85-94.

    PDF

  9. Identification of alleles conferring resistance to gray leaf spot in maize derived from its wild progenitor species teosinte (Zea mays spp. parviglumis).

    Lennon JR, Krakowsky M, Goodman M, Flint-Garcia S, Balint-Kurti

    Crop Science 56:209-218.

    Link

  10. Analysis of recombination QTLs, segregation distortion, and epistasis for fitness in maize multiple populations using ultra-high-density markers.

    Li C, Li Y, Shi Y, Song Y, Zhang D, Buckler ES, Zhang Z, Wang T

    Theoretical and Applied Genetics 123(9):1775.

    Link

  11. Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations.

    Li C, Sun B, Li Y, Liu C, Wu X, Zhang D, Shi Y, Song Y, Buckler ES, Zhang Z, Wang T, Li Y

    BCM Genomics 17:894.

    Link

  12. Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population.

    Li Y, Li C, Bradbury PJ, Liu X, Lu F, Romay MC, Glaubitz JC, Wu X, Peng B, Shi Y, Song Y, Zhang D, Li1 Y, Zhang Z, Buckler ES, Wang T

    The Plant Journal 86(5):391-402

    Link

  13. Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies.

    Liu X, Huang M, Fan B, Buckler ES, Zhang Z

    PLoS Genetics 12:e1005767.

    Link

  14. Expanding maize genetic resources with pre-domestication alleles: maize-teosinte introgression populations.

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

    Plant Genome

    doi:10.3835/plantgenome2015.07.0053Link

  15. Genetic analysis of kernel traits in maize-teosinte introgression populations.

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

    G3 6:2523-2530.

    Link

  16. Fast-flowering mini-maize: seed to seed in 60 days.

    McCaw ME, Wallace JG, Albert PS, Buckler ES, Birchler JA

    Genetics 204:35-42

    PDF

  17. Genetic characterization of the North Carolina State University maize lines.

    Nelson PT, Krakowsky MD, Coles ND, Holland JB, Bubeck DM, Smith JSC, Goodman MM

    Crop Science 56:259-275.

    Link

  18. The genetics of leaf flecking in maize and its relationship to plant defense and disease resistance.

    Olukolu B, Bian Y, De Vries B, Tracy W, Wisser R, Holland J, Balint-Kurti P

    Plant Physiology 172:1787-1803

    Link

  19. Maize diversity associated with social origin and environmental variation in southern Mexico.

    Orozco-Ramirez Q, Santacruz-Varela A, Ross-Ibarra J, Brush S

    Heredity 116:477-484.

    Link

  20. Development of a high density linkage map and tagging leaf spot resistance in pearl millet using GBS markers.

    Punnuri SM, Wallace JG, Knoll JE, Hyma KE, Mitchell SE, Buckler ES, Varshey RK, Singh BP

    Plant Genome

    doi:10.3835/plantgenome2015.10.0106Link

  21. Genome sequence of a 5,310-year-old maize cob provides insights into the early stages of maize domestication.

    Ramos-Madrigal J, Smith BD, Moreno-Mayar JV, Gopalakrishnan S, Ross-Ibarra J, Gilbert MTP, Wales N

    Current Biology 26:3195-3201

    Link

  22. Characterization of biosynthetic pathways for the production of the volatile homoterpenes DMNT and TMTT in Zea mays.

    Richter A, Schaff C, Zhang Z, Lipka AE, Tian F, Kollner TG, Schnee C, Preiss S, Irmisch S, Jander G, Boland W, Gershenzon J, Buckler ES, Degenhardt J

    The Plant Cell 28(10):2651

    Link

  23. Open chromatin reveals the functional maize genome.

    Rodgers-Melnick E, Vera DL, Bass HW, Buckler ES

    PNAS 113(22):E3177-E3184

    LinkData

  24. GAPIT Version 2: Enhanced integrated tool for genomic association and prediction.

    Tang Y, Liu X, Wang J, Li M, Wang Q, Tian F, Su Z, Pan Y, Liu D, Lipka AE, Buckler ES, Zhang Z

    Plant Genome

    doi:10.3835/plantgenome2015.11.0120Link

  25. Correlation-based network analysis of metabolite and enzyme profiles reveals a role of citrate biosynthesis in modulating N and C metabolism in Zea mays

    Toubiana D, Xue W, Zhang N, Karemling K, Gur A, Pilosof S, Gibon Y, Sitt M, Buckler ES, Fernie A, Fait A

    Frontiers in Plant Science

    doi:10.3389/fpls.2016.01022Link

  26. Metabolomic assessment of key maize resources: GC-MS and NMR profiling of grain from B73 hybrids of the nested association mapping (NAM) founders and of geographically diverse landraces.

    Venkatesh, TV, AW Chassy, O Fiehn, S Flint-Garcia, Q Zeng, K Skogerson, GG Harrigan

    Journal of Agricultural and Food Chemistry 64:2162–2172.

    Link

  27. Genome-wide association for plant height and flowering time across 15 tropical maize populations under managed drought stress and well-watered conditions in Sub-Saharan Africa.

    Wallace JG, Beyene Y, Semagn K, Zhang X, Buckler ES

    Crop Science 56:2365.

    Link

  28. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.

    Wang B, Tseng E, Regulski M, Clark TA, Hon T, Jiao Y, Lu Z, Olson A, Stein JC, Ware D

    Nature Communications 7:11708.

    Link

  29. Joint-linkage mapping and GWAS reveal extensive genetic loci that regulate male inflorescence size in maize.

    Wu X, Li Y, Shi Y, Song Y, Zhang D, Li C, Buckler ES, Li Y, Zhang Z, Wang T

    Plant Biotechnology Journal

    doi:10.1111/pbi.12519Link

  30. Genetic architecture of domestication-related traits in maize.

    Xue S, Bradbury PJ, Casstevens TM, Holland JB

    Genetics 204(1):99.

    Link

  31. A gene for genetic background in Zea mays: fine-mapping enhancer of teosinte branched1.2 (etb1.2) to a YABBY class transcription factor.

    Yang CJ, Kursel LE, Studer A, Bartlett ME, Whipple CJ, Doebley JF

    Genetics 204(4):1573.

    PDF

  32. Mapping prolificacy QTL in maize and teosinte

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

    Journal of Heredity 107(7):674.

    Link

2015

  1. New insight into a complex plant–fungal pathogen interaction.

    Balint-Kurti PJ, Holland JB

    Nature Genetics 47:101-103.

    PDF

  2. 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 J, Ross-Ibarra J, Buffalo V, Lorant A, Romay MC, Buckler ES, Xu Y, Lai J, Ware D, Sun Q

    BioRxiv ([doi:http://dx.doi.org/10.1101/026963](http://dx.doi.org/10.1101/026963)).

    doi:10.1101/026963LinkData

  3. The origin and evolution of maize in the American Southwest.

    Fonseca RR, Smith BD, Wales N, Cappellini E, Skoglund P, Fumagalli M, Samaniego JA, Carøe C, Ávila-Arcos MC, Hufnagel DE, Korneliussen TS, Vieira FG, Jakobsson M, Arriaza B, Willerslev E, Nielsen R, Hufford MB, Albrechtsen A, Ross-Ibarra J & Gilbert MTP

    Nature Plants 1:14003.

    PDF

  4. The genomic impacts of drift and selection for hybrid performance in maize.

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

    Genetics 3:1201-1211.

    LinkLink

  5. Plant biology: genetic, evolutionary and plant breeding insights from the domestication of maize.

    Hake S, Ross-Ibarra J

    eLife 4:e05861.

    Link

  6. Construction of high-quality recombination maps with low-coverage genomic sequencing for joint linkage analysis in maize.

    Li C, Li Y, Bradbury PJ, Wu X, Shi Y, Song Y, Zhang D, Rodgers-Melnick E, Buckler ES, Zhang Z, Li Y, Wang T

    BMC Biology 13:78.

    Link

  7. Genetic control of the leaf angle and leaf orientation value as revealed by ultra-high density maps in three connected maize populations.

    Li C, Li Y, Shi Y, Song Y, Zhang D, Buckler ES, Zhang Z, Wang T, Li Y

    PLoS ONE 10: e0121624.

    Link

  8. High-resolution genetic mapping of maize pan-genome sequence anchors.

    Lu F, Romay MC, Glaubitz JC, Bradbury PJ, Elshire RJ, Wang T, Li Y, Li Y, Semagn K, Zhang X, Hernandez AG, Mikel MA, Soifer I, Barad O, Buckler ES

    Nature Communications 6:6914.

    LinkData

  9. Transposable elements contribute to activation of maize genes in response to abiotic stress.

    Makarevitch I, Waters M, West P, Stitzer M, Ross-Ibarra J, Springer NM

    PLoS Genetics 11: e1004915.

    Link

  10. Joint-multiple family linkage analysis predicts within-family variation better than single-family analysis of the maize nested association mapping population.

    Ogut F, Bian Y, Bradbury PJ, Holland JB

    Heredity 114: 552-563.

    LinkData

  11. Recombination in diverse maize is stable, predictable, and associated with genetic load.

    Rodgers-Melnick E, Bradbury PJ, RJ Elshire, Glaubitz JC, Acharya CB, Mitchell SE, Li C, Li Y, Buckler ES

    PNAS 112: 3823-3828.

    LinkLinkData

  12. Genome-wide association study reveals a set of genes associated with resistance to the Mediterranean corn borer (Sesamia nonagrioides L.) in a maize diversity panel.

    Samayoa LF, Malvar RA, Olukolu BA, Holland JB, Butron A

    BMC Plant Biology 15:35.

    LinkLink

  13. Seed filling in domesticated maize and rice depends on SWEET-mediated hexose transport.

    Sosso D, Luo D, Li, Q, Sasse J et al

    Nature Genetics 47:1489-1493.

    PDF

  14. Independent molecular basis of convergent highland adaptation in maize.

    Takuno S, Ralph P, Swarts K, Elshire RJ, Glaubitz JC, Buckler ES, Hufford MB, Ross-Ibarra J

    Genetics 200:1297-1312.

    Link

  15. Hallauer’s Tusón: a decade of selection for tropical-to-temperate phenological adaptation in maize.

    Teixeira, J.E.C., T. Weldekidan, N. de Leon, S. Flint-Garcia, J.B. Holland, N. Lauter, S.C. Murray, W. Xu, D.A. Hessel, A.E. Kleintop, J.A. Hawk, A. Hallauer, R.J. Wisser

    Heredity 114: 229-240.

    PDF

  16. Compositional assessments of key maize populations: B73 hybrids of the Nested Association Mapping founder lines and diverse landrace inbred lines.

    Venkatesh TV, Harrigan GG, Perez T, Flint-Garcia S

    Journal of Agricultural and Food Chemistry 63: 5282–5295.

    PDF

  17. 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, and Doebley JF

    Genetics 200: 965–974.

    PDF

2014

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

    [Lemmon, Z. H. and J. Doebley. 2014.](http://www.genetics.org/content/198/1/345.long)

    Genetics 198: 345–353.

    Lemmon, Z. H. and J. Doebley. 2014.LinkData

  2. Limits on the reproducibility of marker associations with southern leaf blight resistance in the maize nested association mapping population.

    Bian Y, Yang Q, Balint-Kurti PJ, Wisser RJ, Holland JB

    BMC Genomics 15:1056.

    Link

  3. TASSEL-GBS: A high capacity genotyping by sequencing analysis pipeline.

    Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES

    PLoS ONE 9: e90346.

    LinkLink

  4. 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 198: 409-421.

    LinkLink

  5. 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

    Journal of Heredity 105: 576-582.

    LinkLink

  6. The role of cis regulatory evolution in maize domestication.

    Lemmon ZH, Bukowski R, Sun Q, Doebley JF

    PLoS Genetics 10: e1004745.

    Link

  7. Enrichment of statistical power for genome-wide association studies.

    Li M, Liu X, Bradbury P, Yu J, Zhang Y-M, Todhunter RJ, Buckler ES, Zhang Z

    BMC Biology 12: 73.

    LinkLink

  8. The pattern and distribution of deleterious mutations in maize.

    Mezmouk S, Ross-Ibarra J

    G3 4: 163-171.

    Link

  9. A genome-wide association study of the maize hypersensitive defense response identifies genes that cluster in related pathways.

    Olukolu BA, Wang G-F, Vontimitta V, Venkata BP, Marla S, Ji J, Gachomo E, Chu K, Negeri A, Benson J, Nelson R, Bradbury P, Nielsen D, Holland JB, Balint-Kurti PJ, Johal G

    PLoS Genetics 10: e1004562.

    LinkLink

  10. A foundation for provitamin A biofortification of maize: genome-wide association and genomic prediction models of carotenoid levels.

    Owens BF, Lipka AE, Magallanes-Lundback M, Tiede T, Diepenbrock CH, Kandianis CB, Kim E, Cepela J, Mateos-Hernandez M, Buell CR, Buckler ES, DellaPenna D, Gore MA, Rocheford T

    Genetics 198: 1699-1716.

    Link

  11. The genetic architecture of maize height.

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

    Genetics 196: 1337-1356.

    LinkLink

  12. Yield effects of two Southern leaf blight resistance QTL in near-isogenic maize hybrids.

    Santa-Cruz, J.H., K.L. Kump, C. Arellano, M.M. Goodman, M.D. Krakowsky, J.B. Holland, and P.J. Balint-Kurti

    Crop Science 54:882-894.

    LinkLink

  13. Mining natural variation for maize improvement: Selection on phenotypes and genes.

    Sood S, Flint-Garcia SA, Willcox MC, Holland JB

    pg. 615-649 in Genomics of Plant Genetic Resources. Volume 1. Managing, sequencing and mining genetic resources, edited by R. Tuberosa, A. Graner, and E. Frison. Springer, New York.

  14. Novel methods to optimize genotypic imputation for low-coverage, next-generation sequence data in crop plants.

    Swarts K, Li H, Romero Navarro JA, An D, Romay MC, Hearne S, Acharya C, Glaubitz JC, Mitchell S, Elshire RJ, Buckler ES, Bradbury PJ

    Plant Genome 7(3).

    LinkLink

  15. Advances and limits of using population genetics to understand local adaptation.

    Tiffin P, Ross-Ibarra J

    Trends in Ecology and Evolution 29:673-680.

    Link

  16. Association mapping across numerous traits reveals patterns of functional variation in maize.

    Wallace JG, Bradbury PJ, Zhang N, Gibon Y, Stitt M, Buckler ES

    PLoS Genetics 10: e1004845.

    LinkData

  17. Entering the second century of maize quantitative genetics.

    Wallace JG, Larsson SJ, Buckler ES

    Heredity 112: 30-38.

    PDF

  18. A SUPER powerful method for genome wide association study.

    Wang Q, Tian F, Pan Y, Buckler ES, Zhang Z

    PLoS ONE 9: e107684.

    LinkLink

  19. Genome-wide association study of Fusarium ear rot disease in the USA maize inbred line collection.

    Zila CT, Ogut F, Romay MC, Gardner CA, Buckler ES, Holland JB

    BMC Biology 14: 372.

    PDFLinkData

2013

  1. Genetic analysis of visually scored orange kernel color in maize.

    Chandler K, Lipka AE, Owens BF, Li HH, Buckler ES, Rocheford T, Gore MA

    Crop Science 53: 189-200.

    PDFLink

  2. Genetics and consequences of crop domestication.

    Flint-Garcia SA

    Journal of Agricultural and Food Chemistry 61: 8267-8276.

    PDF

  3. Lessons from Dwarf8 on the strengths and weaknesses of structured association mapping.

    Larsson SJ, Lipka AE, Buckler ES

    PLoS Genetics 9: e1003246.

    LinkLink

  4. Genome-wide association study and pathway-level analysis of tocochromanol levels in maize grain.

    Lipka AE, Gore MA, Magallanes-Lundback M, Mesberg A, Lin H, Tiede T, Chen C, Buell CR, Buckler ES, Rocheford T, DellaPenna D

    G3 3: 1287-1299.

    LinkLink

  5. Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol.

    Lu F, Lipka AE, Glaubitz J, Elshire R, Cherney JH, Casler MD, Buckler ES, Costich DE

    PLoS Genetics 9: e1003215.

    LinkLink

  6. Natural variation in maize aphid resistance is associated with 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one glucoside methyltransferase activity.

    Meihls LN, Handrick V, Glauser G, Barbier H, Kuar H, Haribal MM, Lipka AE, Gershenzon J, Buckler ES, Erb M, Kollner TG, Jander G

    Plant Cell 25: 2341-2355.

    PDFLink

  7. Population genomic and genome-wide association studies of agroclimatic traits in sorghum.

    Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE, Harriman J, Glaubitz JC, Buckler ES, Kresovich S

    PNAS 110: 453-458.

    PDF

  8. Genetic architecture of maize stalk strength.

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

    PLoS ONE 8: e67066.

    LinkLink

  9. Diversity and heritability of the maize rhizosphere microbiome under field conditions.

    Peiffer JA, Spor A, Koren O, Jin Z, Tringe SG, Dangl JL, Buckler ES, Ley RE

    PNAS 110: 6548-6553.

    PDF

  10. 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 Biology 14: R55.

    LinkLinkData

  11. 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 Genetics 9: e1003604.

    LinkLink

  12. A genome-wide association study reveals genes associated with fusarium ear rot resistance in a maize core diversity panel.

    Zila CT, Samayoa LF, Santiago R, Butron A, Holland JB

    G3 3: 2095-2104.

    LinkLink

2012

  1. PICARA, an analytical pipeline providing probabilistic inference about a priori candidate genes underlying genome-wide association QTL in plants.

    Chen C, DeClerk G, Tian F, Spooner W, McCouch S, Buckler E

    PLoS ONE 7: e46596.

    LinkLink

  2. Maize HapMap2 identifies extant variation from a genome in flux.

    Chia J-M, 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

    Nature Genetics 44: 803-807.

    PDFData

  3. 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 Physiology 158: 824-834.

    PDFLinkData

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

    Fang Z, Pyhäjärvi T, Weber AL, Dawe RK, Glaubitz JC, Sanchez Gonzalez JJ, Ross-Ibarra C, Doebley J, Morrell PL, Ross-Ibarra J

    Genetics 191: 883-894.

    PDF

  5. Comparative population genomics of maize domestication and improvement.

    Hufford MB, Xu X, van Heerwaarden J, Pyhäjärvi T, Chia J-M, 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

    Nature Genetics 44: 808-811.

    PDFData

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

    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

    Heredity 108: 490-499.

    PDFLinkData

  7. ZmCCT and the genetic basis of daylength adaptation underlying the post-domestication spread of maize.

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

    PNAS 109: E1913-E1921.

    PDFLinkData

  8. Genic and nongenic contributions to natural variation of quantitative traits in maize.

    Li X, Zhu C, Yeh C-T, Wu W, Takacs EM, Petsch KA, Tian F, Bai G, Buckler ES, Muehlbauer GJ, Timmermans MCP, Scanlon MJ, Schnable PS, Yu J

    Genome Research 22: 2436-2444.

    PDFLink

  9. Parallel domestication of the Shattering1 genes in cereals.

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

    Nature Genetics 44: 720-724.

    PDF

  10. GAPIT: genome association and prediction integrated tool.

    Lipka AE, Tian F, Wang Q, Peiffer J, Li M, Bradbury PJ, Gore MA, Buckler ES, Zhang Z

    Bioinformatics 28: 2397-2399.

    PDF

  11. Crop genomics: advances and applications.

    Morrell PL, Buckler ES, Ross-Ibarra J

    Nature Reviews Genetics 13: 85-96.

    PDF

  12. 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 Phytologist 193: 204-215.

    PDF

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

    Studer AJ, Doebley JF

    Genetics 191: 951-958.

    PDFData

  14. Can genomics boost productivity of orphan crops?

    Varshney RK, Ribaut J-M, Buckler ES, Tuberosa R, Rafalski JA, Langridge P

    Nature Biotechnology 30: 1172-1176.

    PDF

2011

  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 Genetics 7: e1002383.

    LinkLinkData

  2. Allelic effect variation at key photoperiod response quantitative trait loci in maize.

    Coles ND, Zila CT, Holland JB

    Crop Science 51: 1036-1049.

    PDF

  3. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.

    Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE

    PLoS ONE 6: e19379

    PDFLink

  4. 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 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

    PLoS ONE 6: e28334.

    LinkLink

  5. 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

    Nature Genetics 43: 163-168.

    PDFData

  6. Joint QTL linkage mapping for multiple-cross mating design sharing one commmon parent.

    Li H, Bradbury P, Ersoz E, Buckler ES, Wang J

    PLoS ONE 6: e17573.

    PDFLink

  7. Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize.

    Poland JA, Bradbury PJ, Buckler ES, Nelson RJ

    PNAS 108: 6893-6898.

    PDFData

  8. Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought.

    Setter TL, Yan J, Warburton M, Ribaut J-M, Xu Y, Sawkins M, Buckler ES, Zhang Z, Gore MA

    Journal of Experimental Botany 62: 701-716.

    PDF

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

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

    Nature Genetics 43: 1160-1163.

    PDFData

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

    Studer AJ, Doebley JF

    Genetics 188: 673-681.

    PDFData

  11. 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

    Nature Genetics 43: 159-162.

    PDFData

  12. 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, Sanchez Gonzalez JJ, Ross-Ibarra J

    PNAS 108: 1088-1092.

    PDFData

  13. 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

    PNAS 108: E506-E512.

    PDF

  14. Multivariate analysis of maize disease resistances suggests a pleiotropic genetic basis and implicates a GST gene.

    Wisser RJ, Kolkman JM, Patzoldt ME, Holland JB, Yu J, Krakowsky M, Nelson RJ, Balint-Kurti PJ

    PNAS 108: 7339-7344.

    PDF

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

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

    Genetics Research 93: 65-75.

    PDF

2010

  1. IView: Introgression library visualization and query tool.

    Bottoms C, Flint-Garcia S, McMullen MD

    BMC Bioinformatics 11(Suppl 6): S28.

    PDF

  2. Genetic variation at bx1 controls DIMBOA content in maize.

    Butron A, Chen YC, Rottinghaus GE, McMullen MD

    Theor Appl Genet 120: 721-734.

    PDF

  3. 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 184: 799-812.

    PDFData

  4. Physiological and genetic characterization of end-of-day far-red light response in maize seedlings.

    Dubois PG, Olsefski GT, Flint-Garcia S, Setter TL, Hoekenga OA, Brutnell TP

    Plant Physiol 154: 173-186.

    PDF

  5. Increased food and ecosystem security via perennial grains.

    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

    Science 328: 1638-1639.

    PDF

  6. Dedication: Major M. Goodman, maize geneticist and breeder.

    Holland JB, Nelson PT

    Plant Breeding Reviews 33: 1-29.

    PDF

  7. Genome-wide association studies of 14 agronomic traits in rice landraces.

    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

    Nature Genetics 42: 961-967.

    PDF

  8. Association and linkage analysis of aluminum tolerance genes in maize.

    Krill AM, Kirst M, Kochian LV, Buckler ES, Hoekenga OA

    PLoS ONE 5: e9958.

    PDFLink

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

    van Heerwaarden J, Ross-Ibarra J, Doebley J, Glaubitz JC, Sanchez Gonzalez JJ, Gaut BS, Eguiarte L

    Molecular Ecology 19: 1162-1173.

    PDFData

  10. Genetic diversity in a crop metapopulation.

    van Heerwaarden J, van Eeuwijk FA, Ross-Ibarra J

    Heredity 104: 28-39.

    PDF

  11. Rare genetic variation at Zea mays crtRB1 increases β-carotene in maize grain.

    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

    Nature Genetics 42: 322-327.

    PDF

  12. Fine quantitative trait loci mapping of carbon and nitrogen metabolism enzyme activities and seedling biomass in the maize IBM mapping population.

    Zhang N, Gibon Y, Gur A, Chen C, Lepak N, Höhne M, Zhang Z, Kroon D, Tschoep H, Stitt M, Buckler E

    Plant Physiology 154: 1753-1765.

    PDFLink

  13. Genetic analyis 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 5: e9991.

    PDFLink

  14. Mixed linear model approach adapted for genome-wide association studies.

    Zhang Z, Ersoz E, Lai C-Q, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM, Buckler ES

    Nature Genetics 42: 355-360.

    PDF

  15. 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 100: 72-79.

    PDF

2009

  1. 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, 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

    Science 325: 714-718.

    PDFData

  2. Wide variability in kernel composition, seed characteristics, and zein profiles among diverse maize inbreds, landraces, and teosinte.

    Flint-Garcia SA, Bodnar AL, Scott MP

    Theor Appl Genet 119: 1129-1142.

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  3. Heterosis is prevalent for multiple traits in diverse maize germplasm.

    Flint-Garcia SA, Buckler ES, Tiffin P, Ersoz E, Springer NM

    PLoS ONE 4: e7433.

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  4. Maize amino acid pathways maintain high levels of genetic diversity.

    Flint-Garcia SA, Guill KE, Sanchez-Villeda H, Schroeder SG, McMullen MD

    Maydica 54: 375-386.

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  5. A first-generation haplotype map of maize.

    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

    Science 326: 1115-1117.

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  6. Large-scale discovery of gene-enriched SNPs.

    Gore MA, Wright MH, Ersoz ES, Bouffard P, Skekeres ES, Jarvie TP, Hurwitz BL, Narachania A, Harkins TT, Grills GS, Ware DH, Buckler ES

    Plant Genome 2: 121-133.

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  7. Development of single nucleotide polymorphism (SNP) markers for use in commmercial maize (Zea mays L.) germplasm.

    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

    Mol. Breeding 24: 165-176.

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  8. A-maize-ing diversity.

    Mackay TFC

    Science 325: 688-689.

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  9. Genetics and biochemistry of insect resistance in maize.

    McMullen MD, Frey M, Degenhardt J

    pp. 271-289 in Handbook of Maize: Its Biology, edited by J. Bennetzen and S. Hake. Springer, New York, NY.

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  10. Genetic properties of the maize Nested Association Mapping population.

    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

    Science 325: 737-740.

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  11. Association mapping: critical considerations shift from genotyping to experimental design.

    Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE, Buckler ES

    Plant Cell 21: 2194-2202.

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  12. Natural variation in maize architecture is mediated by allelic differences at the PINOID co-ortholog barren inflorescence2.

    Pressoir G, Brown PJ, Zhu WY, Upadyayula N, Rocheford T, Buckler ES, Kresovich S

    Plant J 58: 618-628.

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  13. Characterization of a major maize domestication QTL on the short arm of chromosome one.

    Quijada P, Shannon LM, Glaubitz JC, Studer AJ, Doebley J

    Maydica 54: 401-408.

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  14. Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10.

    Tian F, Stevens NM, Buckler ES

    PNAS 106: 9979-9986.

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

    Weber AL, Zhao Q, McMullen MD, Doebley J

    PLoS ONE 4: e8227.

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  16. 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 4: e8451.

    PDFLink

  17. Simulation appraisal of the adequacy of number of background markers for relationship estimation in association mapping.

    Yu J, Zhang Z, Zhu C, Tabanoa DA, Pressoir G, Tuinstra MR, Kresovich S, Todhunter RJ, Buckler ES

    Plant Genome 2: 63-77.

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  18. A genome-wide characterization of microRNA genes in maize.

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

    PLoS Genetics 5: e1000716.

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  19. Software engineering the mixed model for genome-wide association studies on large samples.

    Zhang Z, Buckler ES, Casstevens TM, Bradbury PJ

    Briefings in Bioinformatics 10: 664-675.

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