ArticleBMC genomics2006
A general pipeline for the development of anchor markers for comparative genomics in plants.
Article in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 56 citations in OpenAlex.
- Development and Characterization of Transcription Factor Gene-Derived Microsatellite (TFGM) Markers in Medicago truncatula and Their Transferability in Leguminous and Non-Leguminous Species.Molecules (Basel, Switzerland) · 2015Article
- PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes.Bioinformatics (Oxford, England) · 2015Article
- A multiple-alignment based primer design algorithm for genetically highly variable DNA targets.BMC bioinformatics · 2013Article
- The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome.Annals of botany · 2013Article
- Exploiting EST databases for the development and characterisation of 3425 gene-tagged CISP markers in biofuel crop sugarcane and their transferability in cereals and orphan tropical grasses.BMC research notes · 2013Article
- A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers.Annals of botany · 2013Article
- Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Matita, a new retroelement from peanut: characterization and evolutionary context in the light of the Arachis A-B genome divergence.Molecular genetics and genomics : MGG · 2012Article
- A rearrangement of the Z chromosome topology influences the sex-linked gene display in the European corn borer, Ostrinia nubilalis.Molecular genetics and genomics : MGG · 2011Article
- Cytogenetic map of common bean (Phaseolus vulgaris L.).Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2010Article
- ConservedPrimers 2.0: a high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery.BMC bioinformatics · 2009Article
- Identification of candidate genome regions controlling disease resistance in Arachis.BMC plant biology · 2009Article
- Development of intron-flanking EST markers for the Lolium/Festuca complex using rice genomic information.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
- Article
- A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome.BMC plant biology · 2009Article
- The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
- Localization of anchor loci representing five hundred annotated rice genes to wheat chromosomes using PLUG markers.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
- An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes.BMC genomics · 2009Article
- Legume anchor markers link syntenic regions between Phaseolus vulgaris, Lotus japonicus, Medicago truncatula and Arachis.Genetics · 2008Article
- BAC libraries construction from the ancestral diploid genomes of the allotetraploid cultivated peanut.BMC plant biology · 2008Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundComplete or near-complete genomic sequence information is presently only available for a few plant species representing a large phylogenetic diversity among plants. In order to effectively transfer this information to species lacking sequence information, comparative genomic tools need to be developed. Molecular markers permitting cross-species mapping along co-linear genomic regions are central to comparative genomics. These "anchor" markers, defining unique loci in genetic linkage maps of multiple species, are gene-based and possess a number of features that make them relatively sparse. To identify potential anchor marker sequences more efficiently, we have established an automated bioinformatic pipeline that combines multi-species Expressed Sequence Tags (EST) and genome sequence data.
resultsTaking advantage of sequence data from related species, the pipeline identifies evolutionarily conserved sequences that are likely to define unique orthologous loci in most species of the same phylogenetic clade. The key features are the identification of evolutionarily conserved sequences followed by automated design of intron-flanking Polymerase Chain Reaction (PCR) primer pairs. Polymorphisms can subsequently be identified by size- or sequence variation of PCR products, amplified from mapping parents or populations. We illustrate our procedure in legumes and grasses and exemplify its application in legumes, where model plant studies and the genome- and EST-sequence data available have a potential impact on the breeding of crop species and on our understanding of the evolution of this large and diverse family.
conclusionWe provide a database of 459 candidate anchor loci which have the potential to serve as map anchors in more than 18,000 legume species, a number of which are of agricultural importance. For grasses, the database contains 1335 candidate anchor loci. Based on this database, we have evaluated 76 candidate anchor loci with respect to marker development in legume species with no sequence information available, demonstrating the validity of this approach.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.