ArticleGenome research2000
A high-throughput AFLP-based method for constructing integrated genetic and physical maps: progress toward a sorghum genome map.
Article in Genome research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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71 citing papers in PubMed, 210 citations in OpenAlex.
- Amplified Fragment Length Polymorphism: Applications and Recent Developments.Methods in molecular biology (Clifton, N.J.) · 2021Review
- A colony multiplex quantitative PCR-Based 3S3DBC method and variations of it for screening DNA libraries.PloS one · 2015Article
- Construction and characterization of three wheat bacterial artificial chromosome libraries.International journal of molecular sciences · 2014Article
- Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.).Functional & integrative genomics · 2014Article
- Article
- 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
- Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms.BMC genomics · 2012Article
- Two-phase analysis in consensus genetic mapping.G3 (Bethesda, Md.) · 2012Article
- Advances in BAC-based physical mapping and map integration strategies in plants.Journal of biomedicine & biotechnology · 2012Review
- A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome.BMC genomics · 2011Article
- Genome-wide comparative in silico analysis of calcium transporters of rice and sorghum.Genomics, proteomics & bioinformatics · 2011Article
- Sequence-based physical mapping of complex genomes by whole genome profiling.Genome research · 2011Article
- Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources.BMC genomics · 2010Article
- A new implementation of high-throughput five-dimensional clone pooling strategy for BAC library screening.BMC genomics · 2010Article
- Integration of physical and genetic maps of common bean through BAC-derived microsatellite markers.BMC genomics · 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
- A simple, high throughput method to locate single copy sequences from Bacterial Artificial Chromosome (BAC) libraries using High Resolution Melt analysis.BMC genomics · 2010Article
- Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar.BMC genomics · 2010Article
- Exploiting rice-sorghum synteny for targeted development of EST-SSRs to enrich the sorghum genetic linkage map.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
11 more citing papers are in PubMed but not listed here.
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11 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Sorghum is an important target for plant genomic mapping because of its adaptation to harsh environments, diverse germplasm collection, and value for comparing the genomes of grass species such as corn and rice. The construction of an integrated genetic and physical map of the sorghum genome (750 Mbp) is a primary goal of our sorghum genome project. To help accomplish this task, we have developed a new high-throughput PCR-based method for building BAC contigs and locating BAC clones on the sorghum genetic map. This task involved pooling 24,576 sorghum BAC clones ( approximately 4x genome equivalents) in six different matrices to create 184 pools of BAC DNA. DNA fragments from each pool were amplified using amplified fragment length polymorphism (AFLP) technology, resolved on a LI-COR dual-dye DNA sequencing system, and analyzed using Bionumerics software. On average, each set of AFLP primers amplified 28 single-copy DNA markers that were useful for identifying overlapping BAC clones. Data from 32 different AFLP primer combinations identified approximately 2400 BACs and ordered approximately 700 BAC contigs. Analysis of a sorghum RIL mapping population using the same primer pairs located approximately 200 of the BAC contigs on the sorghum genetic map. Restriction endonuclease fingerprinting of the entire collection of sorghum BAC clones was applied to test and extend the contigs constructed using this PCR-based methodology. Analysis of the fingerprint data allowed for the identification of 3366 contigs each containing an average of 5 BACs. BACs in approximately 65% of the contigs aligned by AFLP analysis had sufficient overlap to be confirmed by DNA fingerprint analysis. In addition, 30% of the overlapping BACs aligned by AFLP analysis provided information for merging contigs and singletons that could not be joined using fingerprint data alone. Thus, the combination of fingerprinting and AFLP-based contig assembly and mapping provides a reliable, high-throughput method for building an integrated genetic and physical map of the sorghum genome.
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