ArticleBMC genomics2007
A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- BAC-FISH Based Physical Map of Endangered CatfishInternational journal of molecular sciences · 2022Article
- Up-regulation of GhTT2-3A in cotton fibres during secondary wall thickening results in brown fibres with improved quality.Plant biotechnology journal · 2018Article
- Effective BAC clone anchoring with genotyping-by-sequencing and Diversity Arrays Technology in a large genome cereal rye.Scientific reports · 2018Article
- Construction and characterization of three wheat bacterial artificial chromosome libraries.International journal of molecular sciences · 2014Article
- Consolidation of the genetic and cytogenetic maps of turbot (Scophthalmus maximus) using FISH with BAC clones.Chromosoma · 2014Article
- The barley Frost resistance-H2 locus.Functional & integrative genomics · 2014Article
- Global transcriptome analysis and identification of a CONSTANS-like gene family in the orchid Erycina pusilla.Planta · 2013Article
- Construction and characterization of a BAC library from the Coffea arabica genotype Timor Hybrid CIFC 832/2.Genetica · 2013Article
- Second-generation genetic linkage map of catfish and its integration with the BAC-based physical map.G3 (Bethesda, Md.) · 2012Article
- Advances in BAC-based physical mapping and map integration strategies in plants.Journal of biomedicine & biotechnology · 2012Review
- Utilization of super BAC pools and Fluidigm access array platform for high-throughput BAC clone identification: proof of concept.Journal of biomedicine & biotechnology · 2012Article
- Distribution of genes and repetitive elements in the Diabrotica virgifera virgifera genome estimated using BAC sequencing.Journal of biomedicine & biotechnology · 2012Article
- Integration of molecular biology tools for identifying promoters and genes abundantly expressed in flowers of Oncidium Gower Ramsey.BMC plant biology · 2011Article
- Sex chromosome evolution in amniotes: applications for bacterial artificial chromosome libraries.Journal of biomedicine & biotechnology · 2011Review
- A Comparative BAC map for the gilthead sea bream (Sparus aurata L.).Journal of biomedicine & biotechnology · 2011Article
- A new implementation of high-throughput five-dimensional clone pooling strategy for BAC library screening.BMC genomics · 2010Article
- A computer simulator for assessing different challenges and strategies of de novo sequence assembly.Genes · 2010Article
- Construction of a BAC library and a physical map of a major QTL for CBB resistance of common bean (Phaseolus vulgaris L.).Genetica · 2010Article
- Generation of a BAC-based physical map of the melon genome.BMC genomics · 2010Article
- A simple, high throughput method to locate single copy sequences from Bacterial Artificial Chromosome (BAC) libraries using High Resolution Melt analysis.BMC genomics · 2010Article
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13 authors.
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Abstract
backgroundMolecular markers serve three important functions in physical map assembly. First, they provide anchor points to genetic maps facilitating functional genomic studies. Second, they reduce the overlap required for BAC contig assembly from 80 to 50 percent. Finally, they validate assemblies based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy in combination with a high-throughput PCR-based screening method to anchor the maize genetic and physical maps.
resultsA total of 110,592 maize BAC clones (approximately 6x haploid genome equivalents) were pooled into six different matrices, each containing 48 pools of BAC DNA. The quality of the BAC DNA pools and their utility for identifying BACs containing target genomic sequences was tested using 254 PCR-based STS markers. Five types of PCR-based STS markers were screened to assess potential uses for the BAC pools. An average of 4.68 BAC clones were identified per marker analyzed. These results were integrated with BAC fingerprint data generated by the Arizona Genomics Institute (AGI) and the Arizona Genomics Computational Laboratory (AGCoL) to assemble the BAC contigs using the FingerPrinted Contigs (FPC) software and contribute to the construction and anchoring of the physical map. A total of 234 markers (92.5%) anchored BAC contigs to their genetic map positions. The results can be viewed on the integrated map of maize 12.
conclusionThis BAC pooling strategy is a rapid, cost effective method for genome assembly and anchoring. The requirement for six replicate positive amplifications makes this a robust method for use in large genomes with high amounts of repetitive DNA such as maize. This strategy can be used to physically map duplicate loci, provide order information for loci in a small genetic interval or with no genetic recombination, and loci with conflicting hybridization-based information.
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