An informative set of SNP markers for molecular characterisation of Australian barley germplasm

Crop and Pasture Science

Volumn 61, Issue 1, 2010, Pages 70-83

  Hayden, M J ^a,b   Tabone, T L ^a,c   Nguyen, T M ^a   Coventry, S ^a   Keiper, F J ^d   Fox, R L ^a   Chalmers, K J ^a   Mather, D E ^a   Eglinton, J K ^a  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b LA TROBE UNIVERSITY   (Australia)

^c ROYAL MELBOURNE HOSPITAL   (Australia)

^d SOUTH AUSTRALIAN RESEARCH AND DEVELOPMENT INSTITUTE   (Australia)

Author keywords

Genetic diversity; Genotyping; SNPs

Indexed keywords

BARLEY; GENETIC MARKER; GENETIC RESOURCE; GENETIC VARIATION; GENOTYPE; GERMPLASM; IDENTIFICATION METHOD; MOLECULAR ANALYSIS; PLANT BREEDING; POLYMERASE CHAIN REACTION; POLYMORPHISM;

HORDEUM;

EID: 73249145809     PISSN: 18360947     EISSN: None     Source Type: Journal    
DOI: 10.1071/CP09140     Document Type: Article

References (40)

1. Abbott DC, Brown AHD, Burdon JJ (1992) Genes for scald resistance from wild barley (Hordeum vulgare ssp. spontaneum) and their linkage to isozyme markers. Euphytica 61, 225-231. doi: 10.1007/BF00039662
2. Akkaya MS, Buyukunal-Bal EB (2004) Assessment of genetic variation of bread wheat varieties using microsatellite markers. Euphytica 135, 179-185. doi: 10.1023/B:EUPH.0000014908.02499.41 (Pubitemid 38184793)
3. Anderson JA, Churchill GA, Autrique EJ, Tanksley SD, Sorrells ME (1993) Optimising parental selection for genetic linkage maps. Genome 36, 181-186. doi: 10.1139/g93-024
4. Baek HJ, Beharav A, Nevo E (2003) Ecological-genomic diversity of microsatellites in wild barley, Hordeum spontaneum, populations in Jordan. Theoretical and Applied Genetics 106, 397-410. doi: 10.1007/ s00122-002-1029-1037 (Pubitemid 36599852)
5. Bansal UK, Hayden MJ, Gill MB, Bariana HS (2009) Chromosomal location of an uncharacterised strip rust resistance gene in wheat. Euphytica (in press). doi: 10.1007/s10681-009-0007-4
6. Bovo D, Rugge M, Shiao YH (1999) Origin of spurious multiple bands in the amplification of microsatellite sequences. Molecular Pathology 52, 50-51. doi: 10.1136/mp.52.1.50
7. Chen J, Iannone MA, Li M-S, Taylor D, Rivers P, Nelsen AJ, Slentz- Kesler KA, Roses A, Weiner MP (2000) A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Research 10, 549-557. doi: 10.1101/ gr.10.4.549
8. Cooke RJ, Bredemeijer GMM, Ganal MW, Peeters R, Isaac P, Rendell S, Jackson J, Röder MS, Korzun V, Wendehake K, Areshchenkova T, Dijcks M, Laborie D, Bertrand L, Vosman B (2003) Assessment of the uniformity of wheat and tomato varieties at DNA microsatellite loci. Euphytica 132, 331-341. doi: 10.1023/A:1025046919570 (Pubitemid 37084093)
9. Dunbar SA (2006) Applications of Luminex® xMAP-technology for rapid, high-throughput multiplexed nucleic acid detection. Clinica Chimica Acta 363, 71-82. doi: 10.1016/j.cccn.2005.06.023 (Pubitemid 41745226)
10. Fernando P, Evans BJ, Morales JC, Melnick DJ (2001) Electrophoresis artifacts - a previously unrecognized cause of error in microsatellite analysis. Molecular Ecology Notes 1, 325-328. doi: 10.1046/j.1471- 8278.2001.00083.x
11. Gonzalez-Martinez SC, Ersoz E, Brown GR, Wheeler NC, Neale DB (2005) DNA sequence variation and selection of tag single-nucleotide polymorphisms at candidate genes for drought-stress response in Pinus taeda L. Genetics 172, 1915-1926. doi: 10.1534/genetics. 105.047126
12. Hayden MJ, Kuchel H, Chalmers KJ (2004) Sequence tagged microsatellites for the Xgwm533 locus provide new diagnostic markers to select for the presence of stem rust resistance gene Sr2 in bread wheat (Triticum aestivum L.). Theoretical and Applied Genetics 109, 1641-1647. doi: 10.1007/s00122-004-1787-5 (Pubitemid 40024929)
13. Hayden MJ, Nguyen TM, Waterman A, Chalmers KJ (2008a) Multiplex- Ready PCR: A new method for multiplexed SSR and SNP genotyping. BMC Genomics 9, 80. doi: 10.1186/1471-2164-9-80
14. Hayden MJ, Nguyen TM, Waterman A, McMichael GL, Chalmers KJ (2008b) Application of multiplex-ready PCR for fluorescence-based SSR genotyping in barley and wheat. Molecular Breeding 21, 271-281. doi: 10.1007/s11032-007-9127-5 (Pubitemid 351311446)
15. Hayden MJ, Tabone T, Mather DE (2009) Development and assessment of simple PCR markers for SNP genotyping in barley. Theoretical and Applied Genetics 119, 939-951. doi: 10.1007/s00122-009-1101-7
16. Hayes P, Szucs P (2006) Disequilibrium and association in barley: Thinking outside the glass. Proceedings of the National Academy of Sciences of the United States of America 103, 18385-18386. doi: 10.1073/pnas. 0609405103
17. Hearnden PR, Eckermann PJ, McMichael GL, Hayden MJ, Eglinton JK, Chalmers KJ (2007) A genetic map of 1,000 SSR and DArT markers in a wide barley cross. Theoretical and Applied Genetics 115, 383-391. doi: 10.1007/s00122-007-0572-7 (Pubitemid 47087412)
18. Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theoretical and Applied Genetics 33, 54-78.
19. Jefferies SP, Barr AR, Karakousis A, Kretschmer JM, Manning S, Chalmers KJ, Nelson JC, Islam AKMR, Langridge P (1999) Mapping of chromosome regions conferring boron toxicity tolerance in barley (Hordeum vulgare L.). Theoretical and Applied Genetics 98, 1293-1303. doi: 10.1007/s001220051195 (Pubitemid 29324000)
20. Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, et al. (1997) Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Molecular Breeding 3, 381-390. doi: 10.1023/A: 1009612517139
21. Kaneko T, Kihara T, Ito K (2000) Genetic analysis of b-amylase thermostability to develop a DNA marker for malt fermentability improvement in barley, Hordeum vulgare. Plant Breeding 119, 197-201. doi: 10.1046/j.1439-0523. 2000.00496.x (Pubitemid 30411296)
22. Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific markers. The Plant Journal 4, 403-410. doi: 10.1046/j.1365-313X.1993.04020403.x
23. Kota R, Varshney RK, Prasad M, Zhang H, Stein N, Graner A (2008) ESTderived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome. Functional & Integrative Genomics 8, 223-233. doi: 10.1007/s10142-007-0060-9 (Pubitemid 351836952)
24. Lia VV, Bracco M, Gottlieb AM, Poggio L, Confalonieri VA (2007) Complex mutational patterns and size homoplasy at maize microsatellite loci. Theoretical and Applied Genetics 115, 981-991. doi: 10.1007/s00122-007-0625-y (Pubitemid 47561704)
25. Malysheva-Otto LV, Roder MS (2006) Haplotype diversity in the endosperm specific b-amylase gene Bmy1 of cultivated barley (Hordeum vulgare L.). Molecular Breeding 18, 143-156. doi: 10.1007/s11032-006-9023-4 (Pubitemid 44351271)
26. Mantel NA (1967) The detection of disease clustering and a generalized regression approach. Cancer Research 27, 209-220.
27. Matus IA, Hayes PM (2002) Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats. Genome 45, 1095-1106. doi: 10.1139/g02-071 (Pubitemid 351194303)
28. Rafalski JA (2002) Application of single nucleotide polymorphisms in crop genetics. Current Opinion in Plant Biology 5, 94-100. doi: 10.1016/ S1369-5266(02)00240-246
29. Rogowsky PM, Guidet FLY, Langridge P, Shepherd KW, Koebner RMD (1991) Isolation and characterization of wheat-rye recombinants involving chromosome arm 1DS of wheat. Theoretical and Applied Genetics 82, 537-544. doi: 10.1007/BF00226788
30. Rostoks N, Mudie S, Cardle L, Russell J, Ramsay L et al. (2005) Genomewide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Molecular Genetics and Genomics 274, 515-527. doi: 10.1007/s00438-005-0046-z (Pubitemid 41721160)
31. Russell J, Booth A, Fuller J, Harrower B, Hedley P, Machray G, Powell W (2004) A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of barley. Genome 47, 389-398. doi: 10.1139/903-125
32. Russell JR, Fuller JD, Macaulay M, Hatz BG, Jahoor A, Powell W, Waugh R (1997) Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theoretical and Applied Genetics 95, 714-722. doi: 10.1007/s001220050617 (Pubitemid 27433978)
33. Tabone TL, Mather DE, Hayden MJ (2009) Temperature Switch PCR (TSP): Robust assay design for reliable amplification and genotyping of SNPs. BMC Genomics 10, 580. doi: 10.1186/1471-2164-10-580
34. Terzi V, Morcia C, Gorrini A, Stanca M, Shewry PR, Faccioli P (2005) DNAbased methods for identification and quantification of small grain cereal mixtures and fingerprinting of varieties. Journal of Cereal Science 41, 213-220. doi: 10.1016/j.jcs.2004.08.003 (Pubitemid 40406241)
35. Varshney RK, Marcel TC, Ramsay L, Russell J, Roder MS, Stein N, Waugh R, Langridge P, Niks RE, Granar A (2007) A high density barley microsatellite consensus map with 775 SSR loci. Theoretical and Applied Genetics 114, 1091-1103. doi: 10.1007/s00122-007- 0503-507
36. Varshney RK, Thiel T, Sretenovic-Rajicic T, Baum M, Valkoun J, Guo P, Grando S, Ceccarelli S, Graner A (2008) Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley. Molecular Breeding 22, 1-13. doi: 10.1007/s11032-007-9151-5
37. von Korff M, Wang H, Leon J, Pillen K (2006) AB-QTL analysis in spring barley: II. Detection of favorable exotic alleles for agronomic traits introgressed from wild barley (H.vulgare spp. spontaneum). Theoretical and Applied Genetics 112, 1221-1231. doi: 10.1007/ s00122-006-0223-224
38. Von Zitzewitz J, Szucs P, Dubcovsky J, Yan L, Francia E, Pecchioni N, Casas A, Chen THH, Hayes PM, Skinner JS (2005) Molecular and structural characterization of barley vernalization genes. Plant Molecular Biology 59, 449-467. doi: 10.1007/s11103-005-0351-2 (Pubitemid 41464664)
39. Wang J, Dobrowolski MP, Cogan NOI, Forster JW, Smith KF (2009) Assignment of individual genotypes to specific forage cultivars of perennial ryegrass based on SSR markers. Crop Science 49, 49-58. doi: 10.2135/cropsci2008.03.0177
40. Yoon MS, Song QJ, Choi LY, Specht JE, Hyten DL, Cregan PB (2007) BARCSoySNP23: a panel of 23 selected SNPs for soybean cultivar identification. Theoretical and Applied Genetics 114, 885-899. doi: 10.1007/s00122-006-0487-8 (Pubitemid 46339694)