title: Efficient molecular marker design using the MaizeGDB Mo17 SNPs and Indels track.
abstract: Positional cloning in maize (Zea mays) requires development of markers in the region of interest. We found that primers designed to amplify annotated insertion-deletion polymorphisms of seven base pairs or greater between B73 and Mo17 produce polymorphic markers at a 97% frequency with 49% of the products showing co-dominant fragment length polymorphisms. When the same polymorphisms are used to develop markers for B73 and W22 or Mo17 and W22 mapping populations, 22% and 31% of markers are co-dominant, respectively. There are 38,223 Indel polymorphisms that can be converted to markers providing high-density coverage throughout the maize genome. This strategy significantly increases the efficiency of marker development for fine-mapping in maize.
authors.affiliation: Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611 settles@ufl.edu.
authors.forename: A Mark
authors.initials: AM
authors.lastname: Settles
authors.affiliation: Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611.
authors.forename: Alyssa M
authors.initials: AM
authors.lastname: Bagadion
authors.affiliation: Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611.
authors.forename: Fang
authors.initials: F
authors.lastname: Bai
authors.affiliation: Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611.
authors.forename: Junya
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Division of Biological Sciences, Interdisciplinary Plant Group and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211.
authors.forename: Brady
authors.initials: B
authors.lastname: Barron
authors.affiliation: Division of Biological Sciences, Interdisciplinary Plant Group and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211.
authors.forename: Kristen
authors.initials: K
authors.lastname: Leach
authors.affiliation: Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611.
authors.forename: Janaki S
authors.initials: JS
authors.lastname: Mudunkothge
authors.affiliation: Division of Biological Sciences, Interdisciplinary Plant Group and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211.
authors.forename: Cassandra
authors.initials: C
authors.lastname: Hoffner
authors.affiliation: Division of Biological Sciences, Interdisciplinary Plant Group and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211.
authors.forename: Saadia
authors.initials: S
authors.lastname: Bihmidine
authors.affiliation: Division of Biological Sciences, Interdisciplinary Plant Group and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211.
authors.forename: Erin
authors.initials: E
authors.lastname: Finefield
authors.affiliation: Division of Biological Sciences, Interdisciplinary Plant Group and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211.
authors.forename: Jaime
authors.initials: J
authors.lastname: Hibbard
authors.affiliation: Division of Biological Sciences, Interdisciplinary Plant Group and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211 Biology Department, Saint Michael's College, Colchester, Vermont 05439.
authors.forename: Emily
authors.initials: E
authors.lastname: Dieter
authors.affiliation: Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611.
authors.forename: I Alex
authors.initials: IA
authors.lastname: Malidelis
authors.affiliation: Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611.
authors.forename: Jeffery L
authors.initials: JL
authors.lastname: Gustin
authors.affiliation: Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611.
authors.forename: Vita
authors.initials: V
authors.lastname: Karoblyte
authors.affiliation: Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611.
authors.forename: Chi-Wah
authors.initials: CW
authors.lastname: Tseung
authors.affiliation: Division of Biological Sciences, Interdisciplinary Plant Group and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211.
authors.forename: David M
authors.initials: DM
authors.lastname: Braun
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D030561:Databases, Nucleic Acid; D056426:Genetic Loci; D005819:Genetic Markers; D054643:INDEL Mutation; D020641:Polymorphism, Single Nucleotide; D003313:Zea mays / Q000235:genetics*
chemical_list: D005819:Genetic Markers
keywords: Zea mays; genetic mapping; insertion–deletion polymorphism; molecular marker; positional cloning
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