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

Fei Lu; Maria C. Romay; Jeffrey C. Glaubitz; Peter J. Bradbury; Robert J. Elshire; Tianyu Wang; Yu Li; Yongxiang Li; Kassa Semagn; Xuecai Zhang; Alvaro G. Hernandez; Mark A. Mikel; Ilya Soifer; Omer Barad; Edward S. Buckler

doi:10.1038/ncomms7914

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

Fei Lu, Maria C. Romay, Jeffrey C. Glaubitz, Peter J. Bradbury, Robert J. Elshire, Tianyu Wang, Yu Li, Yongxiang Li, Kassa Semagn, Xuecai Zhang, Alvaro G. Hernandez, Mark A. Mikel, Ilya Soifer, Omer Barad, Edward S. Buckler

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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 â € pan-genomeâ €™, which is essential to fully understand the genetic control of phenotypes. However, the pan-genomeâ €™ 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.

Original language	English (US)
Article number	6914
Journal	Nature communications
Volume	6
DOIs	https://doi.org/10.1038/ncomms7914
State	Published - Apr 16 2015

ASJC Scopus subject areas

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
Physics and Astronomy(all)

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10.1038/ncomms7914

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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 {\^a} € pan-genome{\^a} €{\texttrademark}, which is essential to fully understand the genetic control of phenotypes. However, the pan-genome{\^a} €{\texttrademark} 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.",

author = "Fei Lu and Romay, {Maria C.} and Glaubitz, {Jeffrey C.} and Bradbury, {Peter J.} and Elshire, {Robert J.} and Tianyu Wang and Yu Li and Yongxiang Li and Kassa Semagn and Xuecai Zhang and Hernandez, {Alvaro G.} and Mikel, {Mark A.} and Ilya Soifer and Omer Barad and Buckler, {Edward S.}",

note = "Funding Information: This work was supported by the National Science Foundation (DBI-0820619, DBI-0965342), the USDA-ARS, the Bill and Melinda Gates Foundation and the Ministry of Science and Technology of China (2011CB100105 and 2011DFA30450). We thank J. Ross-Ibarra, Z. Zhang, J.G. Wallace, Q. Sun and S. Miller for helpful discussions. Publisher Copyright: {\textcopyright} 2015 Macmillan Publishers Limited. All rights reserved.",

year = "2015",

month = apr,

day = "16",

doi = "10.1038/ncomms7914",

language = "English (US)",

volume = "6",

journal = "Nature Communications",

issn = "2041-1723",

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T1 - High-resolution genetic mapping of maize pan-genome sequence anchors

AU - Lu, Fei

AU - Romay, Maria C.

AU - Glaubitz, Jeffrey C.

AU - Bradbury, Peter J.

AU - Elshire, Robert J.

AU - Wang, Tianyu

AU - Li, Yu

AU - Li, Yongxiang

AU - Semagn, Kassa

AU - Zhang, Xuecai

AU - Hernandez, Alvaro G.

AU - Mikel, Mark A.

AU - Soifer, Ilya

AU - Barad, Omer

AU - Buckler, Edward S.

N1 - Funding Information: This work was supported by the National Science Foundation (DBI-0820619, DBI-0965342), the USDA-ARS, the Bill and Melinda Gates Foundation and the Ministry of Science and Technology of China (2011CB100105 and 2011DFA30450). We thank J. Ross-Ibarra, Z. Zhang, J.G. Wallace, Q. Sun and S. Miller for helpful discussions. Publisher Copyright: © 2015 Macmillan Publishers Limited. All rights reserved.

PY - 2015/4/16

Y1 - 2015/4/16

N2 - 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 â € pan-genomeâ €™, which is essential to fully understand the genetic control of phenotypes. However, the pan-genomeâ €™ 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.

AB - 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 â € pan-genomeâ €™, which is essential to fully understand the genetic control of phenotypes. However, the pan-genomeâ €™ 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.

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

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