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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #321911

Title: High-resolution genetic mapping of maize pan-genome sequence anchors

item LU, FEI - Cornell University
item ROMAY, MARIA - Cornell University
item GLAUBITZ, JEFFREY - Cornell University
item Bradbury, Peter
item ELSHIRE, ROBERT - Cornell University
item WANG, TIANYU - Chinese Academy Of Agricultural Sciences
item LI, YU - Chinese Academy Of Agricultural Sciences
item LI, YONGXIANG - Chinese Academy Of Agricultural Sciences
item SEMAGN, KASSA - International Maize & Wheat Improvement Center (CIMMYT)
item ZHANG, XUECAI - International Maize & Wheat Improvement Center (CIMMYT)
item HERNANDEZ, ALVARO - University Of Illinois
item MIKEL, MARK - University Of Illinois
item SOIFER, ILYA - Nrgene
item BARAD, OMER - Nrgene
item Buckler, Edward - Ed

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/11/2015
Publication Date: 4/16/2015
Publication URL: http://DOI: 10/1038/ncomms7914
Citation: Lu, F., Romay, M.C., Glaubitz, J.C., Bradbury, P., Elshire, R.J., Wang, T., Li, Y., Li, Y., Semagn, K., Zhang, X., Hernandez, A.G., Mikel, M.A., Soifer, I., Barad, O., Buckler IV, E.S. 2015. High-resolution genetic mapping of maize pan-genome sequence anchors. Nature Communications. 6:694.

Interpretive Summary: Genomes can be very large and complex. The maize genome has an average size of 2.3 billion base pairs, and it exhibits a high level of variation from one variety to another. Surprisingly, over 50% of the genome is not even shared between two varieties of maize. Most of this variation is the product of transposons - jumping genes - moving around the genome of maize over the last several million years. This tremendous structural variation in the genome has made it difficult to reconstruct the exact sequence of maize varieties. This study developed techniques to use skim DNA sequencing and genetic mapping approaches to help localize these structurally variable regions of the maize genome. The analytical and computation approaches could be applied to any species. As shown in this paper, these structural variants are likely to be important for adaptation of crops to specific environments.

Technical 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.