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Wenzl P, Li H, Carling J, Zhou M, Raman H, Paul E, Hearnden P, Maier C, Xia L, Caig V, Ovesná J, Cakir M, Poulsen D, Wang J, Raman R, Smith KP, Muehlbauer GJ, Chalmers KJ, Kleinhofs A, Huttner E, Kilian A. A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics 2006. [PMID: 16904008 DOI: 10.1186/1471‐2164‐7‐206] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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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Affiliation(s)
- Peter Wenzl
- Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia.
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Wenzl P, Li H, Carling J, Zhou M, Raman H, Paul E, Hearnden P, Maier C, Xia L, Caig V, Ovesná J, Cakir M, Poulsen D, Wang J, Raman R, Smith KP, Muehlbauer GJ, Chalmers KJ, Kleinhofs A, Huttner E, Kilian A. A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics 2006; 7:206. [PMID: 16904008 PMCID: PMC1564146 DOI: 10.1186/1471-2164-7-206] [Citation(s) in RCA: 196] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Accepted: 08/12/2006] [Indexed: 02/02/2023] Open
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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Affiliation(s)
- Peter Wenzl
- Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
- DArT P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
| | - Haobing Li
- School of Agricultural Science, University of Tasmania, PO Box 252-54, Hobart TAS 7001, Australia
| | - Jason Carling
- Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
- DArT P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agricultural Research, PO Box 46, Kings Meadows TAS 7249, Australia
| | - Harsh Raman
- NSW Agricultural Genomics Centre and NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, PMB, Wagga Wagga NSW 2650, Australia
| | - Edie Paul
- GeneFlow Inc., 14582 Olde Kent Rd., Centreville VA 20120, USA
| | - Phillippa Hearnden
- School of Agriculture, Food and Wine, Plant Genomics Centre, The University of Adelaide, PMB1, Glen Osmond SA 5064, Australia
| | - Christina Maier
- Dept. Crop and Soil Sciences and School of Molecular Biosciences, Washington State University, Pullman WA 99164-6420, USA
| | - Ling Xia
- Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
- DArT P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
| | - Vanessa Caig
- Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
- DArT P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
| | - Jaroslava Ovesná
- Research Institute of Crop Production, Drnovská 507, 161 06 Prague 6, Czech Republic
| | - Mehmet Cakir
- Molecular Plant Breeding CRC, WA State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150, Australia
| | - David Poulsen
- Department of Primary Industries & Fisheries, Plant Science, MS 508 Warwick, QLD 4370, Australia
| | - Junping Wang
- NSW Agricultural Genomics Centre and NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, PMB, Wagga Wagga NSW 2650, Australia
| | - Rosy Raman
- NSW Agricultural Genomics Centre and NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, PMB, Wagga Wagga NSW 2650, Australia
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Ken J Chalmers
- School of Agriculture, Food and Wine, Plant Genomics Centre, The University of Adelaide, PMB1, Glen Osmond SA 5064, Australia
| | - Andris Kleinhofs
- Dept. Crop and Soil Sciences and School of Molecular Biosciences, Washington State University, Pullman WA 99164-6420, USA
| | - Eric Huttner
- Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
- DArT P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
| | - Andrzej Kilian
- Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
- DArT P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
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King J, Roberts LA, Kearsey MJ, Thomas HM, Jones RN, Huang L, Armstead IP, Morgan WG, King IP. A demonstration of a 1:1 correspondence between chiasma frequency and recombination using a Lolium perenne/Festuca pratensis substitution. Genetics 2002; 161:307-14. [PMID: 12019244 PMCID: PMC1462085 DOI: 10.1093/genetics/161.1.307] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A single chromosome of the grass species Festuca pratensis has been introgressed into Lolium perenne to produce a diploid monosomic substitution line 2n = 2x = 14. The chromatin of F. pratensis and L. perenne can be distinguished by genomic in situ hybridization (GISH), and it is therefore possible to visualize the substituted F. pratensis chromosome in the L. perenne background and to study chiasma formation in a single marked bivalent. Recombination occurs freely in the F. pratensis/L. perenne bivalent, and chiasma frequency counts give a predicted map length for this bivalent of 76 cM. The substituted F. pratensis chromosome was also mapped with 104 EcoRI/Tru91 and HindIII/Tru91 amplified fragment length polymorphisms (AFLPs), generating a marker map of 81 cM. This map length is almost identical to the map length of 76 cM predicted from the chiasma frequency data. The work demonstrates a 1:1 correspondence between chiasma frequency and recombination and, in addition, the absence of chromatid interference across the Festuca and Lolium centromeres.
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Affiliation(s)
- J King
- Institute of Biological Sciences, University of Wales, Aberystwyth, SY23 3DA, Wales, United Kingdom
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Castiglioni P, Pozzi C, Heun M, Terzi V, Müller KJ, Rohde W, Salamini F. An AFLP-based procedure for the efficient mapping of mutations and DNA probes in barley. Genetics 1998; 149:2039-56. [PMID: 9691056 PMCID: PMC1460261 DOI: 10.1093/genetics/149.4.2039] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A strategy based upon AFLP markers for high-efficiency mapping of morphological mutations and DNA probes to linkage groups in barley is presented. First, 511 AFLP markers were placed on the linkage map derived from the cross Proctor x Nudinka. Second, loci controlling phenotypic traits were assigned to linkage groups by AFLP analysis, using F2 populations consisting of 30-50 mutant plants derived from crosses of the type "mutant x Proctor" and "mutant x Nudinka." To map DNA probes, 67 different wild-type barley lines were selected to generate F2 populations by crossing with Proctor and Nudinka. F2 plants that were polymorphic for a given RFLP fragment were classified into genotypic classes. Linkage of the RFLP polymorphism to 1 of the 511 AFLP loci was indicated by cosegregation. The use of the strategy is exemplified by the mapping of the mutation branched-5 to chromosome 2 and of the DNA probes Bkn2 and BM-7 to chromosomes 5 and 1, respectively. Map expansion and marker order in map regions with dense clustering of markers represented a particular problem. A discussion considering the effect of noncanonical recombinant products on these two parameters is provided.
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Affiliation(s)
- P Castiglioni
- Max-Planck-Institut für Züchtungsforschung, 50829 Cologne, Germany
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Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T. A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 1998; 148:479-94. [PMID: 9475757 PMCID: PMC1459786 DOI: 10.1093/genetics/148.1.479] [Citation(s) in RCA: 549] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A 2275-marker genetic map of rice (Oryza sativa L.) covering 1521.6 cM in the Kosambi function has been constructed using 186 F2 plants from a single cross between the japonica variety Nipponbare and the indica variety Kasalath. The map provides the most detailed and informative genetic map of any plant. Centromere locations on 12 linkage groups were determined by dosage analysis of secondary and telotrisomics using > 130 DNA markers located on respective chromosome arms. A limited influence on meiotic recombination inhibition by the centromere in the genetic map was discussed. The main sources of the markers in this map were expressed sequence tag (EST) clones from Nipponbare callus, root, and shoot libraries. We mapped 1455 loci using ESTs; 615 of these loci showed significant similarities to known genes, including single-copy genes, family genes, and isozyme genes. The high-resolution genetic map permitted us to characterize meiotic recombinations in the whole genome. Positive interference of meiotic recombination was detected both by the distribution of recombination number per each chromosome and by the distribution of double crossover interval lengths.
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Affiliation(s)
- Y Harushima
- Rice Genome Research Program, National Institute of Agrobiological Resources/Institute of Society for Techno-Innovation of Agriculture, Forestry, and Fisheries, Tsukuba, Ibaraki, Japan
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Becker J, Vos P, Kuiper M, Salamini F, Heun M. Combined mapping of AFLP and RFLP markers in barley. MOLECULAR & GENERAL GENETICS : MGG 1995; 249:65-73. [PMID: 8552035 DOI: 10.1007/bf00290237] [Citation(s) in RCA: 209] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
AFLP marker technology allows efficient DNA fingerprinting and the analysis of large numbers of polymorphic restriction fragments on polyacrylamide gels. Using the doubled haploids from the F1 of the cross Proctor x Nudinka, 118 AFLP markers were mapped onto a barley (Hordeum vulgare L.) RFLP map, also including five microsatellite and four protein marker loci. The AFLP markers mapped to all parts of the barley chromosomes and filled in the gaps on barley chromosomes 2L, 4L and 6 in which no RFLP loci had been mapped. Interestingly, the AFLP markers seldom interrupted RFLP clusters, but grouped next to them. The combined map covers 1873 cM, with a total of 282 markers. The merging of AFLP and RFLP markers increased the total map length; 402 cM were added to the map at the tips of chromosomes or in regions corresponding to earlier gaps. Another 375 cM resulted from mapping AFLP markers near to RFLP clusters or in between non-clustered RFLP markers.
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Affiliation(s)
- J Becker
- Max-Planck-Institut für Züchtungsforschung, Köln, Germany
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