ArticleScience (New York, N.Y.)2021
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.
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Article in Science (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 406 papers.
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406citing papers in PubMed
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406 citing papers in PubMed, 696 citations in OpenAlex.
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- Investigating GERMs: how genotype, environment, and rhizosphere microbiome interactions underlie heat response in maize and sorghum.The New phytologist · 2026Article
346 more citing papers are in PubMed but not listed here.
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Authors and funding
46 authors at 8 institutions in 1 country.
Matthew B HuffordDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0003-3945-1143
Arun S SeetharamDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0002-6789-9298
Margaret R WoodhouseUSDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0003-2164-8300
Kapeel M ChouguleCold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
Shujun OuDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0001-5938-7180
Jianing LiuDepartment of Genetics, University of Georgia, Athens, GA 30602, USA.ORCID 0000-0003-4398-1542
William A RicciDepartment of Plant Biology, University of Georgia, Athens, GA 30602, USA.ORCID 0000-0001-7944-623X
Tingting GuoDepartment of Agronomy, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0002-6647-6998
Andrew OlsonCold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.ORCID 0000-0003-4946-9021
Yinjie QiuDepartment of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA.ORCID 0000-0002-0584-0688
Rafael Della ColettaDepartment of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA.ORCID 0000-0001-6988-9598
Silas TittesCenter for Population Biology, University of California, Davis, CA 95616, USA.ORCID 0000-0003-4697-7434
Asher I HudsonCenter for Population Biology, University of California, Davis, CA 95616, USA.
Alexandre P MarandDepartment of Genetics, University of Georgia, Athens, GA 30602, USA.ORCID 0000-0001-9100-8320
Sharon WeiCold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
Zhenyuan LuCold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.ORCID 0000-0003-1758-2636
Bo WangCold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
Marcela K Tello-RuizCold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.ORCID 0000-0002-7499-5368
Rebecca D PiriInstitute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
Na WangDepartment of Plant Biology, University of Georgia, Athens, GA 30602, USA.ORCID 0000-0001-9296-1412
Dong Won KimDepartment of Plant Biology, University of Georgia, Athens, GA 30602, USA.
Yibing ZengDepartment of Genetics, University of Georgia, Athens, GA 30602, USA.
Christine H O'ConnorDepartment of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA.
Xianran LiDepartment of Agronomy, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0002-4252-6911
Amanda M GilbertDepartment of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA.
Erin BaggsDepartment of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.ORCID 0000-0003-3076-9489
Ksenia V KrasilevaDepartment of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.ORCID 0000-0002-1679-0700
John L PortwoodUSDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0002-6339-0881
Ethalinda K S CannonUSDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0002-0678-8754
Carson M AndorfUSDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0003-2380-6704
Nancy ManchandaDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
Samantha J SnodgrassDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0001-9209-6051
David E HufnagelDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0002-6221-2493
Qiuhan JiangDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0003-4889-6240
Sarah PedersenDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
Michael L SyringDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0002-0193-4062
David A KudrnaArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.ORCID 0000-0002-3092-3629
Victor LlacaCorteva Agriscience, Johnston, IA 50131, USA.ORCID 0000-0003-4822-2924
Kevin FenglerCorteva Agriscience, Johnston, IA 50131, USA.
Robert J SchmitzDepartment of Genetics, University of Georgia, Athens, GA 30602, USA.ORCID 0000-0001-7538-6663
Jeffrey Ross-IbarraCenter for Population Biology, University of California, Davis, CA 95616, USA.ORCID 0000-0003-1656-4954
Jianming YuDepartment of Agronomy, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0001-5326-3099
Jonathan I GentDepartment of Plant Biology, University of Georgia, Athens, GA 30602, USA.ORCID 0000-0002-3584-7717
Candice N HirschDepartment of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA.ORCID 0000-0002-8833-3023
Doreen WareUSDA-ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA.ORCID 0000-0002-8125-3821
R Kelly DaweDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA. kdawe@uga.edu.ORCID 0000-0003-3407-4553
Iowa State University · USUniversity of Georgia · USCold Spring Harbor Laboratory · USUniversity of Minnesota · USUniversity of California, Davis · USCorteva (United States) · USUniversity of California, Berkeley · USUniversity of Arizona · US
Funding
Graphical Processing Units and a Large-Memory Compute Node for Applications in Genomics, Neuroscience, and Structural BiologyS10OD028632 · OD · COLD SPRING HARBOR LABORATORY · PI SIEPEL, ADAM CHARLES · 2020 to 2020
$437kNIH HHS S10 OD028632
Abstract
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.
Indexed as
Genome, PlantMolecular Sequence AnnotationCentromereChromosome MappingChromosomes, PlantDisease ResistanceDNA MethylationGenes, PlantGenetic VariationGenotypeHigh-Throughput Nucleotide SequencingMultifactorial InheritancePhenotypePlant DiseasesPolymorphism, Single NucleotideRegulatory Sequences, Nucleic Acid
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