Diversity Arrays Technology (DArT) for whole-genome profiling of barley.

Diversity Arrays Technology (DArT) can detect and type DNA variation at several hundred genomic loci in parallel without relying on sequence information. Here we show that it can be effectively applied to genetic mapping and diversity analyses of barley, a species with a 5,000-Mbp genome. We tested several complexity reduction methods and selected two that generated the most polymorphic genomic representations. Arrays containing individual fragments from these representations generated DArT fingerprints with a genotype call rate of 98.0% and a scoring reproducibility of at least 99.8%. The fingerprints grouped barley lines according to known genetic relationships. To validate the Mendelian behavior of DArT markers, we constructed a genetic map for a cross between cultivars Steptoe and Morex. Nearly all polymorphic array features could be incorporated into one of seven linkage groups (98.8%). The resulting map comprised approximately 385 unique DArT markers and spanned 1,137 centimorgans. A comparison with the restriction fragment length polymorphism-based framework map indicated that the quality of the DArT map was equivalent, if not superior, to that of the framework map. These results highlight the potential of DArT as a generic technique for genome profiling in the context of molecular breeding and genomics.

[1]  P. Langridge,et al.  Mapping and QTL analysis of the barley population Clipper × Sahara , 2003 .

[2]  V. Lefebvre,et al.  Toward a marker-dense meiotic map of the potato genome: lessons from linkage group I. , 2003, Genetics.

[3]  Xiaolei Wu,et al.  Molecular genetic linkage maps for allotetraploid Leymus wildryes (Gramineae: Triticeae). , 2003, Genome.

[4]  Detlef Weigel,et al.  Large-scale identification of single-feature polymorphisms in complex genomes. , 2003, Genome research.

[5]  D. Pental,et al.  A high-density linkage map in Brassica juncea (Indian mustard) using AFLP and RFLP markers , 2003, Theoretical and Applied Genetics.

[6]  M. Cervera,et al.  Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers , 2002, Molecular Genetics and Genomics.

[7]  R. Matyášek,et al.  Distribution of 5-methylcytosine residues in 5S rRNA genes in Arabidopsis thaliana and Secale cereale , 2002, Molecular Genetics and Genomics.

[8]  Thomas Wiehe,et al.  Recombination and gene conversion in a 170-kb genomic region of Arabidopsis thaliana. , 2002, Genetics.

[9]  K. Manly,et al.  Map Manager QTX, cross-platform software for genetic mapping , 2001, Mammalian Genome.

[10]  T. Gingeras,et al.  Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation. , 2001, Genome research.

[11]  H. Hopp,et al.  Quantitative evaluation of genetic diversity in wheat germplasm using molecular markers , 2001 .

[12]  M. Knox,et al.  Stability and inheritance of methylation states at PstI sites in Pisum , 2001, Molecular Genetics and Genomics.

[13]  E. Boerwinkle,et al.  High‐throughput multiplex SNP genotyping with MALDI‐TOF mass spectrometry: Practice, problems and promise , 2001, Human mutation.

[14]  A. Kilian,et al.  Diversity arrays: a solid state technology for sequence information independent genotyping. , 2001, Nucleic acids research.

[15]  R. Mank,et al.  Further characterization of AFLP® data as a tool in genetic diversity assessments among maize (Zea mays L.) inbred lines , 2000, Molecular Breeding.

[16]  A. Melchinger,et al.  Two high-density AFLP® linkage maps of Zea mays L.: analysis of distribution of AFLP markers , 1999, Theoretical and Applied Genetics.

[17]  D. Kudrna,et al.  Genetic and molecular characterization of barley chromosome telomeres , 1999 .

[18]  P. Kwok.  Genotyping by mass spectrometry takes flight , 1998, Nature Biotechnology.

[19]  Daniel R. Richards,et al.  Direct allelic variation scanning of the yeast genome. , 1998, Science.

[20]  James L. Winkler,et al.  Accessing Genetic Information with High-Density DNA Arrays , 1996, Science.

[21]  G. Martin,et al.  Chromosome landing: a paradigm for map-based gene cloning in plants with large genomes. , 1995, Trends in genetics : TIG.

[22]  K. Saigo,et al.  The Drosophila forked gene encodes two major RNAs, which, in gypsy or springer insertion mutants, are partially or completely truncated within the 5′-LTR of the inserted retrotransposon , 1993, Molecular and General Genetics MGG.

[23]  D. Kudrna,et al.  A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome , 1993, Theoretical and Applied Genetics.

[24]  G. Churchill,et al.  Optimizing parental selection for genetic linkage maps. , 1993, Genome.

[25]  R. Messeguer,et al.  Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear DNA , 1991, Plant Molecular Biology.

[26]  J. Weber,et al.  Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. , 1989, American journal of human genetics.

[27]  U Landegren,et al.  A ligase-mediated gene detection technique. , 1988, Science.

[28]  Lloyd M. Smith,et al.  Fluorescence detection in automated DNA sequence analysis , 1986, Nature.

[29]  A. Razin,et al.  Sequence specificity of methylation in higher plant DNA , 1981, Nature.

[30]  James C. Bezdek,et al.  Pattern Recognition with Fuzzy Objective Function Algorithms , 1981, Advanced Applications in Pattern Recognition.

[31]  D. Botstein,et al.  Construction of a genetic linkage map in man using restriction fragment length polymorphisms. , 1980, American journal of human genetics.

[32]  M. Nei,et al.  Mathematical model for studying genetic variation in terms of restriction endonucleases. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[33]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[34]  W. Gilbert,et al.  A new method for sequencing DNA. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[35]  E. Southern.  Detection of specific sequences among DNA fragments separated by gel electrophoresis. , 1975, Journal of molecular biology.

[36]  U. Schibler,et al.  Changes in size and secondary structure of the ribosomal transcription unit during vertebrate evolution. , 1975, Journal of molecular biology.

[37]  A. Cohen,et al.  Estimating the Parameter in a Conditional Poisson Distribution , 1960 .

[38]  I. Ashikawa.  Surveying CpG methylation at 5′-CCGG in the genomes of rice cultivars , 2004, Plant Molecular Biology.

[39]  P. Keim,et al.  DNA methylation and AFLP marker distribution in the soybean genome , 1999, Theoretical and Applied Genetics.

[40]  P. Vos,et al.  AFLP: a new technique for DNA fingerprinting. , 1995, Nucleic acids research.