title: High-resolution genetic mapping of maize pan-genome sequence anchors.
abstract: In addition to single-nucleotide polymorphisms, structural variation is abundant in many plant genomes. The structural variation across a species can be represented by a 'pan-genome', which is essential to fully understand the genetic control of phenotypes. However, the pan-genome's complexity hinders its accurate assembly via sequence alignment. Here we demonstrate an approach to facilitate pan-genome construction in maize. By performing 18 trillion association tests we map 26 million tags generated by reduced representation sequencing of 14,129 maize inbred lines. Using machine-learning models we select 4.4 million accurately mapped tags as sequence anchors, 1.1 million of which are presence/absence variations. Structural variations exhibit enriched association with phenotypic traits, indicating that it is a significant source of adaptive variation in maize. The ability to efficiently map ultrahigh-density pan-genome sequence anchors enables fine characterization of structural variation and will advance both genetic research and breeding in many crops.
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, New York 14850, USA.
authors.forename: Fei
authors.initials: F
authors.lastname: Lu
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, New York 14850, USA.
authors.forename: Maria C
authors.initials: MC
authors.lastname: Romay
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, New York 14850, USA.
authors.forename: Jeffrey C
authors.initials: JC
authors.lastname: Glaubitz
authors.affiliation: United States Department of Agriculture/Agricultural Research Service, Ithaca, New York 14850, USA.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Bradbury
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, New York 14850, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Elshire
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Tianyu
authors.initials: T
authors.lastname: Wang
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Li
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Yongxiang
authors.initials: Y
authors.lastname: Li
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Nairobi 00621, Kenya.
authors.forename: Kassa
authors.initials: K
authors.lastname: Semagn
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Apdo 6-641, 06600 Mexico DF, Mexico.
authors.forename: Xuecai
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
authors.forename: Alvaro G
authors.initials: AG
authors.lastname: Hernandez
authors.affiliation: 1] Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA [2] Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Mikel
authors.affiliation: NRGENE, 3 Golda Meir St. Park HaMada, Ness Ziona 7403648, Israel.
authors.forename: Ilya
authors.initials: I
authors.lastname: Soifer
authors.affiliation: NRGENE, 3 Golda Meir St. Park HaMada, Ness Ziona 7403648, Israel.
authors.forename: Omer
authors.initials: O
authors.lastname: Barad
authors.affiliation: 1] Institute for Genomic Diversity, Cornell University, Ithaca, New York 14850, USA [2] United States Department of Agriculture/Agricultural Research Service, Ithaca, New York 14850, USA.
authors.forename: Edward S
authors.initials: ES
authors.lastname: Buckler
mesh_terms: D002874:Chromosome Mapping; D018745:Genome, Plant / Q000235:genetics*; D000069550:Machine Learning; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D003313:Zea mays / Q000235:genetics*