A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

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Abstract

Background

Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers.

Results

The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits.

Conclusion

Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.

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Most cited references 58

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Diversity arrays: a solid state technology for sequence information independent genotyping.

D Jaccoud, K. Peng, D Feinstein … (2001)

Here we present the successful application of the microarray technology platform to the analysis of DNA polymorphisms. Using the rice genome as a model, we demonstrate the potential of a high-throughput genome analysis method called Diversity Array Technology, DArT'. In the format presented here the technology is assaying for the presence (or amount) of a specific DNA fragment in a representation derived from the total genomic DNA of an organism or a population of organisms. Two different approaches are presented: the first involves contrasting two representations on a single array while the second involves contrasting a representation with a reference DNA fragment common to all elements of the array. The Diversity Panels created using this method allow genetic fingerprinting of any organism or group of organisms belonging to the gene pool from which the panel was developed. Diversity Arrays enable rapid and economical application of a highly parallel, solid-state genotyping technology to any genome or complex genomic mixtures.

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

Peter Wenzl, Jason Carling, David Kudrna … (2004)

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.

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High density molecular linkage maps of the tomato and potato genomes.

P Broun, Silvas Prince, James G Bittner … (1992)

High density molecular linkage maps, comprised of more than 1000 markers with an average spacing between markers of approximately 1.2 cM (ca. 900 kb), have been constructed for the tomato and potato genomes. As the two maps are based on a common set of probes, it was possible to determine, with a high degree of precision, the breakpoints corresponding to 5 chromosomal inversions that differentiate the tomato and potato genomes. All of the inversions appear to have resulted from single breakpoints at or near the centromeres of the affected chromosomes, the result being the inversion of entire chromosome arms. While the crossing over rate among chromosomes appears to be uniformly distributed with respect to chromosome size, there is tremendous heterogeneity of crossing over within chromosomes. Regions of the map corresponding to centromeres and centromeric heterochromatin, and in some instances telomeres, experience up to 10-fold less recombination than other areas of the genome. Overall, 28% of the mapped loci reside in areas of putatively suppressed recombination. This includes loci corresponding to both random, single copy genomic clones and transcribed genes (detected with cDNA probes). The extreme heterogeneity of crossing over within chromosomes has both practical and evolutionary implications. Currently tomato and potato are among the most thoroughly mapped eukaryotic species and the availability of high density molecular linkage maps should facilitate chromosome walking, quantitative trait mapping, marker-assisted breeding and evolutionary studies in these two important and well studied crop species.

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Author and article information

Journal

Journal ID (nlm-ta): BMC Genomics

Title: BMC Genomics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2164

Publication date Collection: 2006

Publication date (Electronic): 12 August 2006

Volume: 7

Page: 206

Affiliations

[1 ]Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia

[2 ]DArT P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia

[3 ]School of Agricultural Science, University of Tasmania, PO Box 252-54, Hobart TAS 7001, Australia

[4 ]Tasmanian Institute of Agricultural Research, PO Box 46, Kings Meadows TAS 7249, Australia

[5 ]NSW Agricultural Genomics Centre and NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, PMB, Wagga Wagga NSW 2650, Australia

[6 ]GeneFlow Inc., 14582 Olde Kent Rd., Centreville VA 20120, USA

[7 ]School of Agriculture, Food and Wine, Plant Genomics Centre, The University of Adelaide, PMB1, Glen Osmond SA 5064, Australia

[8 ]Dept. Crop and Soil Sciences and School of Molecular Biosciences, Washington State University, Pullman WA 99164-6420, USA

[9 ]Research Institute of Crop Production, Drnovská 507, 161 06 Prague 6, Czech Republic

[10 ]Molecular Plant Breeding CRC, WA State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150, Australia

[11 ]Department of Primary Industries & Fisheries, Plant Science, MS 508 Warwick, QLD 4370, Australia

[12 ]Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA

Article

Publisher ID: 1471-2164-7-206

DOI: 10.1186/1471-2164-7-206

PMC ID: 1564146

PubMed ID: 16904008

SO-VID: d158dce5-5813-43a6-b230-7caaa31c5a84

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

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Abstract

Background

Results

Conclusion

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Genomic Prediction

Most cited references 58

Diversity arrays: a solid state technology for sequence information independent genotyping.

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

High density molecular linkage maps of the tomato and potato genomes.

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