Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome
Tóm tắt
Từ khóa
Tài liệu tham khảo
Anderson MJ (2003) PCO: a FORTRAN computer program for principal component analysis. Department of Statistics, University of Auckland, Auckland, New Zealand
Bonin A, Bellemain E, Bronken Eidesen P, Pompanon F, Brochmann C, Taberlet P (2004) How to track and assess genotyping errors in population genetics studies. Mol Ecol 13:3261–3273
Botstein D, White R, Skolnick M, Davis R (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331
Bryan GJ, Collins AJ, Stephenson P, Orry A, Smith JB, Gale MD (1997) Isolation and characterisation of microsatellites from hexaploid bread wheat. Theor Appl Genet 94:557–563
Caldwell KS, Dvorak J, Lagudah ES, Akhunov E, Luo MC, Wolters P, Powell W (2004) Sequence polymorphism in polyploid wheat and their D-genome diploid ancestor. Genetics 167:941–947
Chalmers KJ, Campbell AW, Kretschmer J, Karakousis A, Henschke PH, Pierens S, Harker N, Pallotta M, Cornish GB, Shariflou MR, Rampling LR, McLauchlan A, Daggard G, Sharp PJ, Holton TA, Sutherland MW, Appels R, Langridge P (2001) Construction of three linkage maps in bread wheat. Triticum aestivum. Aust J Agric Res 52:1089–1119
Chee M, Yang R, Hubbell E, Berno A, Huang XC, Stern D, Winkler J, Lockhart DJ, Morris MS, Fodor SPA (1996) Accessing genetic information with high-density DNA arrays. Science 274:610–614
Cohen AC Jr (1960) Estimating the parameter in a conditional Poisson distribution. Biometrics 16:203–211
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:1–15
Dreisigacker S, Zhang P, Warburton ML, Van Ginkel M, Hoisington D, Bohn M, Melchinger AE (2004) SSR and pedigree analyses of genetic diversity among CIMMYT wheat lines targeted to different megaenvironments. Crop Sci 44:381–388
Feuillet C, Keller B (2002) Comparative genomics in the grass family: molecular characterisation of grass genome structure and evolution. Ann Bot (Lond) 89:3–10
Hayden MJ, Good G, Sharp PJ (2002) Sequence tagged microsatellite profiling (STMP): improved isolation of DNA sequence flanking target SSRs. Nucleic Acids Res 30:e129
Hayden MJ, Stephenson P, Logojan AM, Khatkar D, Rogers C, Koebner RMD, Snape JW, Sharp PJ (2004) A new approach to extending the wheat marker pool by anchored PCR amplification of compound SSRs. Theor Appl Genet 108:733–742
Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29:e25
Kammholz SJ, Campbell AW, Sutherland MW, Hollamby GJ, Martin PJ, Eastwood RF, Barclay I, Wilson RE, Brennan PS, Sheppard JA (2001) Establishment and characterisation of wheat genetic mapping populations. Aust J Agric Res 52:1079–1088
Kilian A, Huttner E, Wenzl P, Jaccoud D, Carling J, Caig V, Evers M, Heller-Uszynska, Cayla C, Patarapuwadol S, Xia L, Yang S, Thomson B (2005) The fast and the cheap: SNP and DArT-based whole genome profiling for crop improvement. In: Tuberosa R, Phillips RL, Gale M (eds) Proceedings of the international congress “In the wake of the double helix: from the green revolution to the gene revolution”, 27–31 May, 2003, Avenue Media, Bologna, Italy, pp 443–461
Langridge P, Lagudah ES, Holton TA, Appels R, Sharp PJ, Chalmers KJ (2001) Trends in genetic and genome analysis in wheat: a review. Aust J Agric Res 52:1043–1077
Lehmensiek A, Eckermann PJ, Verbyla AP, Appels R, Sutherland MW, Daggard GE (2005) Curation of wheat maps to improve map accuracy and QTL detection. Aust J Agric Res 56:1347–1354
Lezar S, Myburg AA, Berger DK, Wingfield MJ, Wingfield BD (2004) Development and assessment of microarray-based DNA fingerprinting in Eucalyptus grandis. Theor Appl Genet 109:1329–1336
Liu BH, Knapp SJ (1990) GMENDEL: a program for Mendelian segregation and linkage analysis of individual or multiple progeny populations using log-likelihood ratios. J Hered 81:407–418
McIntosh RA, Wellings CR, Park RF (1995) Wheat rusts: an atlas of resistance genes. CSIRO, Melbourne, Vic., Australia
Mochida K, Yamazaki Y, Ogihara Y (2004) Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags. Mol Genet Genomics 270:371–377
van Ooijen JW, Voorrips RE (2001) Joinmap 3.0, software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The Netherlands
van Os H, Stam P, Visser RGF, van Eck HJ (2005) RECORD: a novel method for ordering loci on a genetic linkage map. Theor Appl Genet 112:30–40
Parker GD, Fox PN, Langridge P, Chalmers K, Whan B, Ganter PF (2002) Genetic diversity within Australian wheat breeding programs based on molecular and pedigree data. Euphytica 124:293–306
Paull JG, Chalmers KJ, Karakousis A, Kretschmer JM, Manning S, Langridge P (1998) Genetic diversity in Australian wheat varieties and breeding material based on RFLP data. Theor Appl Genet 96:435–446
Pestsova E, Ganal MW, Röder MS (2000) Isolation and mapping of microsatellite markers specific for the D genome of bread wheat. Genome 43:689–697
Roussel V, Leisova L, Exbrayat F, Stehno Z, Balfourier F (2005) SSR allelic diversity changes in 480 European bread wheat varieties released from 1840 to 2000. Theor Appl Genet 111:162–170
Schut JW, Qi X, Stam P (1997) Association between relationship measures based on AFLP markers, pedigree data and morphological traits in barley. Theor Appl Genet 95:1161–1168
Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739–744
Tanksley SD, Ganal MW, Prince JP, de Vicente MC (1992) High density molecular linkage maps of the tomato and potato genomes: biological inferences and practical applications. Genetics 132:1141–1160
Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78
Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Fritjers A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414
Vuylsteke M, Mank R, Antonise R, Bastiaans E, Senior ML, Stuber CW, Melchinger AE, Lübberstedt T, Xia XC, Stam P, Zabeau M, Kuiper M (1999) Two high-density AFLP linkage maps of Zea mays L.: analysis of distribution of AFLP markers. Theor Appl Genet 99:921–935
Weber J, May P (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388–396
Wenzl P, Carling J, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A, Kilian A (2004) Diversity arrays technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci USA 101:9915–9920
Williams J, Kubelik A, Livak K, Rafalski J, Tingey S (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535
Wittenberg AHJ, van der Lee T, Cayla C, Kilian A, Visser RGF, Schouten HJ (2005) Validation of the high-throughput marker technology DArT using the model plant Arabidopsis thaliana. Mol Genet Genomics 274:30–39
Xia L, Peng K, Yang S, Wenzl P, de Vicente C, Fregene M, Kilian A (2005) DArT for high-throughput genotyping of cassava (Manihot esculenta) and its wild relatives. Theor Appl Genet 110:1092–1098