ArticleBMC genomics2009
A high-throughput strategy for screening of bacterial artificial chromosome libraries and anchoring of clones on a genetic map constructed with single nucleotide polymorphisms.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Effective BAC clone anchoring with genotyping-by-sequencing and Diversity Arrays Technology in a large genome cereal rye.Scientific reports · 2018Article
- High-throughput physical map anchoring via BAC-pool sequencing.BMC plant biology · 2015Article
- Construction and characterization of three wheat bacterial artificial chromosome libraries.International journal of molecular sciences · 2014Article
- Intergenomic single nucleotide polymorphisms as a tool for bacterial artificial chromosome contig building of homoeologous Brassica napus regions.BMC genomics · 2014Article
- Consolidation of the genetic and cytogenetic maps of turbot (Scophthalmus maximus) using FISH with BAC clones.Chromosoma · 2014Article
- Screening of a Brassica napus bacterial artificial chromosome library using highly parallel single nucleotide polymorphism assays.BMC genomics · 2013Article
- A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Development and evaluation of SoySNP50K, a high-density genotyping array for soybean.PloS one · 2013Article
- SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure.BMC genomics · 2012Article
- Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms.BMC genomics · 2012Article
- Advances in BAC-based physical mapping and map integration strategies in plants.Journal of biomedicine & biotechnology · 2012Review
- A new implementation of high-throughput five-dimensional clone pooling strategy for BAC library screening.BMC genomics · 2010Article
- Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species.BMC genomics · 2010Article
- A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat.BMC genomics · 2009Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCurrent techniques of screening bacterial artificial chromosome (BAC) libraries for molecular markers during the construction of physical maps are slow, laborious and often assign multiple BAC contigs to a single locus on a genetic map. These limitations are the principal impediment in the construction of physical maps of large eukaryotic genomes. It is hypothesized that this impediment can be overcome by screening multidimensional pools of BAC clones using the highly parallel Illumina GoldenGate assay.
resultsTo test the efficacy of the Golden Gate assay in BAC library screening, multidimensional pools involving 302976 Aegilops tauschii BAC clones were genotyped for the presence/absence of specific gene sequences with multiplexed Illumina GoldenGate oligonucleotide assays previously used to place single nucleotide polymorphisms on an Ae. tauschii genetic map. Of 1384 allele-informative oligonucleotide assays, 87.6% successfully clustered BAC pools into those positive for a BAC clone harboring a specific gene locus and those negative for it. The location of the positive BAC clones within contigs assembled from 199190 fingerprinted Ae. tauschii BAC clones was used to evaluate the precision of anchoring of BAC clones and contigs on the Ae. tauschii genetic map. For 41 (95%) assays, positive BAC clones were neighbors in single contigs. Those contigs could be unequivocally assigned to loci on the genetic map. For two (5%) assays, positive clones were in two different contigs and the relationships of these contigs to loci on the Ae. tauschii genetic map were equivocal. Screening of BAC libraries with a simple five-dimensional BAC pooling strategy was evaluated and shown to allow direct detection of positive BAC clones without the need for manual deconvolution of BAC clone pools.
conclusionThe highly parallel Illumina oligonucleotide assay is shown here to be an efficient tool for screening BAC libraries and a strategy for high-throughput anchoring of BAC contigs on genetic maps during the construction of physical maps of eukaryotic genomes. In most cases, screening of BAC libraries with Illumina oligonucleotide assays results in the unequivocal relationship of BAC clones with loci on the genetic map.
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