title: Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization.
abstract: Our goal is to construct a robust physical map for maize (Zea mays) comprehensively integrated with the genetic map. We have used a two-dimensional 24 x 24 overgo pooling strategy to anchor maize expressed sequence tagged (EST) unigenes to 165,888 bacterial artificial chromosomes (BACs) on high-density filters. A set of 70,716 public maize ESTs seeded derivation of 10,723 EST unigene assemblies. From these assemblies, 10,642 overgo sequences of 40 bp were applied as hybridization probes. BAC addresses were obtained for 9,371 overgo probes, representing an 88% success rate. More than 96% of the successful overgo probes identified two or more BACs, while 5% identified more than 50 BACs. The majority of BACs identified (79%) were hybridized with one or two overgos. A small number of BACs hybridized with eight or more overgos, suggesting that these BACs must be gene rich. Approximately 5,670 overgos identified BACs assembled within one contig, indicating that these probes are highly locus specific. A total of 1,795 megabases (Mb; 87%) of the total 2,050 Mb in BAC contigs were associated with one or more overgos, which are serving as sequence-tagged sites for single nucleotide polymorphism development. Overgo density ranged from less than one overgo per megabase to greater than 20 overgos per megabase. The majority of contigs (52%) hit by overgos contained three to nine overgos per megabase. Analysis of approximately 1,022 Mb of genetically anchored BAC contigs indicates that 9,003 of the total 13,900 overgo-contig sites are genetically anchored. Our results indicate overgos are a powerful approach for generating gene-specific hybridization probes that are facilitating the assembly of an integrated genetic and physical map for maize.
authors.affiliation: Department of Agronomy, University of Missouri, Columbia, Missouri 65211, USA. gardiner@ag.arizona.edu
authors.forename: Jack
authors.initials: J
authors.lastname: Gardiner
authors.forename: Steven
authors.initials: S
authors.lastname: Schroeder
authors.forename: Mary L
authors.initials: ML
authors.lastname: Polacco
authors.forename: Hector
authors.initials: H
authors.lastname: Sanchez-Villeda
authors.forename: Zhiwei
authors.initials: Z
authors.lastname: Fang
authors.forename: Michele
authors.initials: M
authors.lastname: Morgante
authors.forename: Tim
authors.initials: T
authors.lastname: Landewe
authors.forename: Kevin
authors.initials: K
authors.lastname: Fengler
authors.forename: Francisco
authors.initials: F
authors.lastname: Useche
authors.forename: Michael
authors.initials: M
authors.lastname: Hanafey
authors.forename: Scott
authors.initials: S
authors.lastname: Tingey
authors.forename: Hugh
authors.initials: H
authors.lastname: Chou
authors.forename: Rod
authors.initials: R
authors.lastname: Wing
authors.forename: Carol
authors.initials: C
authors.lastname: Soderlund
authors.forename: Edward H
authors.initials: EH
authors.lastname: Coe
mesh_terms: D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D020451:Contig Mapping / Q000379:methods*; D020224:Expressed Sequence Tags; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D003313:Zea mays / Q000235:genetics*