Phân tích phân tử về khả năng kháng bệnh đốm nâu đậu nành ở giống đậu nành PI 561356 và phân tích SNP haplotype trong vùng Rpp1 ở các nguồn giống đa dạng

Born H, Diver S (2005) Asian soybean rust: notes and organic control options for farmers. http://www.agrisk.umn.edu/cache/ARL02950.htm Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331 Bromfield KR (1984) Soybean rust. Monograph no. 11. American Phytopathological Society, St. Paul Caldwell P, McLaren NW (2004) Soybean rust research in South Africa. In: Proc. VII world soybean res. conf. IV int. soybean processing and utilization conference, III Brazilian soybean congress, Foz do Iguassu, PR, Brazil, pp 354–360 Chakraborty N, Curley J, Frederick RD, Hyten DL, Nelson RL, Hartman GL, Diers BW (2009) Mapping and confirmation of a new allele at Rpp 1 from soybean PI 594538A conferring RB lesion-type resistance to soybean rust. Crop Sci 49:783–790 Fan JB, Chee MS, Gunderson KL (2006) Highly parallel genomic assays. Nat Rev Genet 7:632–644 Fehr WR, Caviness CE, Burmood DT, Pennington JS (1971) Stage of development descriptions for soybeans, Glycine max (L.) Merrill. Crop Sci 11:929–931 Garcia A, Calvo ES, Kiihl RS, Harada A, Hiromoto DM, Vieira LGE (2008) Molecular mapping of soybean rust (Phakopsora pachyrhizi) resistance genes: discovery of a novel locus and alleles. Theor Appl Genet 117:545–553 Gizlice Z, Carter TE, Burton JW (1994) Genetic base for North American public soybean cultivars released between 1947 and 1988. Crop Sci 34:1143–1151 Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES (2009) A first-generation haplotype map of maize. Science 326:1115–1117 Hartman GL, Wang TC, Tschanz AT (1991) Soybean rust development and the quantitative relationship between rust severity and soybean yield. Plant Dis 75:596–600 Hartman GL, Miles MR, Frederick RD (2005) Breeding for resistance to soybean rust. Plant Dis 89:664–666 Hartman GL, Hill CB, Twizeyimana M, Miles MR, Bandyopadhyay R (2011) Interaction of soybean and Phakopsora pachyrhizi, the cause of soybean rust. CAB Rev Perspect Agric Vet Sci Nutr Nat Resour 6. doi:10.1079/PAVSNNR20116025 Hennings VP (1903) A few new Japanese Uredinaceae. Hedwigia 42:S107–S108 Hershman D, Sikora E, Giesler L (2011) Soybean rust PIPE: Past, present, and future. J Integr Pest Manag 2. doi:10.1603/IPM11001 Hyten DL, Song Q, Zhu Y, Choi IY, Nelson RL, Costa JM, Specht JE, Shoemaker RC, Cregan PB (2006) Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci USA 103:16666–16671 Hyten DL, Hartman GL, Nelson RL, Frederick RD, Concibido VC, Narvel JM, Cregan PB (2007) Map location of the Rpp 1 locus that confers resistance to soybean rust in soybean. Crop Sci 47:837–840 Hyten DL, Smith JR, Frederick RD, Tuker ML, Song Q, Cregan PB (2009) Bulk segregate analysis using the GoldenGate assay to locate the Rpp 3 locus that confers resistance to Phakopsora pachyrhizi (soybean rust) in soybean. Crop Sci 49:265–271 Isard SA, Gage SH, Comtois P, Russo JM (2005) Principles of the atmospheric pathway for invasive species applied to soybean rust. Bioscience 55:851–862 Johnson GC, Esposito L, Barratt BJ, Smith AN, Heward J, Genova GD, Ueda H, Cordell HJ, Eaves IA, Dudbridge F, Twells RC, Payne F, Hughes W, Nutland S, Stevens H, Carr P, Tuomilehto-Wolf E, Tuomilehto J, Gough SC, Clayton DG, Todd JA (2001) Haplotype tagging for the identification of common disease genes. Nat Genet 29:233–237 Keim P, Olson T, Shoemaker RC (1988) A rapid protocol for isolating soybean DNA. Soybean Genet Newsl 15:150–152 Killgore E, Heu R (1994) First report of soybean rust in Hawaii. Plant Dis 78:1216 Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun SS, Zhang G (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42:1053–1059 Li S, Smith JR, Ray JD, Frederick RD (2012) Identification of a new soybean rust resistance genes in PI 567102B. Theor Appl Genet 125:133–142 Melching JS, Bromfield KR, Kingsolver CH (1983) The plant pathogen containment facility at Frederick, Maryland. Plant Dis 67:717–722 Meyer JDF, Silva DCG, Yang C, Pedley KF, Zhang C, van de Mortel M, Hill JH, Shoemaker RC, Abdelnoor RV, Whitham SA, Graham MA (2009) Identification and analyses of candidate genes for Rpp 4-mediated resistance to Asian soybean rust in soybean (Glycine max (L.) Merr.). Plant Physiol 150:295–307 Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832 Miles MR, Frederick RD, Hartman GL (2003) Soybean rust: is the U.S. soybean crop at risk? APS Net Plant Pathol. doi:10.1094/APSnetFeature-2003-060 Miles MR, Frederick RD, Hartman GL (2006) Evaluation of soybean germplasm for resistance to Phakopsora pachyrhizi. Plant Health Prog. doi:10.1094/PHP-2006-0104-01-RS Miles MR, Bonde MR, Nester SE, Berner DK, Frederick RD, Hartman GL (2011) Characterizing resistance to Phakopsora pachyrhizi in soybean. Plant Dis 95:577–581 Monteros MJ, Missaoui AM, Phillips DV, Walker DR, Boerma HR (2007) Mapping and confirmation of the ‘Hyuuga’ red-brown lesion resistance gene for Asian soybean rust. Crop Sci 47:829–836 Monteros MJ, Ha BK, Phillips DV, Boerma HR (2010) SNP assay to detect the ‘Hyuuga’ red-brown lesion resistance gene for Asian soybean rust. Theor Appl Genet 121:1023–1032 Mueller TA, Miles MR, Morel W, Marios JJ, Wright DL, Kemerait RC, Levy C, Hartman GL (2009) Effect of fungicide and timing of application on soybean rust severity and yield. Plant Dis 93:243–248 Pathan MS, Sleper DA (2008) Advances in soybean breeding. In: Stacey G (ed) Genetics and genomics of soybean. Springer, NY Pham TA, Miles MR, Frederick RD, Hill CB, Hartman GL (2009) Differential responses of resistant soybean entries to isolates of Phakopsora pachyrhizi. Plant Dis 93:224–228 Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100 Ray JD, Morel W, Smith JR, Frederick RD, Miles MR (2009) Genetics and mapping of adult plant rust resistance in soybean PI 587886 and PI 587880A. Theor Appl Genet 119:271–280 Ribeiro AS, Ubirajara J, Moreira V, Pierozzi EB, Rachid BF, Toledo JFF, Arias CAA, Soares RM, Godoy CV (2007) Genetic control of Asian rust in soybean. Euphytica 157:15–25 SAS Institute (2002) The SAS system for Windows. Release 9.2. SAS Institute, Cary Schmutz J, Cannon S, Schlueter J, Ma J, Mitros T, Nelson W, Hyten D, Song Q, Thelen J, Cheng J, Xu D, Hellsten U, May G, Yu Y, Sakurai T, Umezawa T, Bhattacharyya M, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang X, Shinozaki K, Nguyen H, Wing R, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker R, Jackson S (2010) Genome sequence of the paleopolyploid soybean. Nature 463:178–183 Schneider RW, Hollier CA, Whitman HK, Palm ME, McKenny JM, Hernández JR, Levy L, Devries-Paterson R (2005) First report of soybean rust caused by Phakopsora pachyrhizi in the continental United States. Plant Dis 89:774 Shastry BS (2004) Role of SNP/haplotype map in gene discovery and drug development: an overview. Drug Dev Res 62:143–150 Silva DCG, Yamanaka N, Brogin RL, Arias CAA, Nepomuceno AL, Di Mauro AO, Pereira SS, Nogueira LM, Passianotto ALL, Abdelnoor RV (2008) Molecular mapping of two loci that confer resistance to Asian rust in soybean. Theor Appl Genet 117:57–63 Song QJ, Jia GF, Zhu YL, Grant D, Nelson RT, Hwang EY, Hyten DL, Cregan PB (2010) Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean. Crop Sci 50:1950–1960 Song QJ, Hyten DL, Jia GF, Quigley C, Fickus E, Cregan PB (2012) Development and Evaluation of a high-density Illumina Infinium iSelect Beadchip SoySNP50K. In: Plant and animal genome conference XX. San Diego, CA, USA. http://pag.confex.com/pag/xx/webprogram/Paper4683.html Tamura K, Dudley J, Ne Mi, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24(8):1596–1599 USDA-ARS (2012) National Genetic Resources Program. Germplasm Resources Information Network—(GRIN). (Online Database) National Germplasm Resources Laboratory, Beltsville, Maryland. Retrieved from http://www.ars-grin.gov/npgs/index.html Utomo HS, Linscombe SD (2009) Current patents and future development underlying marker-assisted breeding in major grain crops. Rec Pat DNA Gene Seq 3:53–62 Van Ooijen JW, Voorrips RW (2001) Joinmap 3.0. Software for the calculation of genetic linkage maps. Plant Research International, Wageningen Van Ooijen JW, Boer MP, Jansen RC, Maliepaard C (2002) MapQTL 4.0. Software for the calculation of QTL positions on genetic maps. Plant Research International, Wageningen Wang D, Shi J, Carlson SR, Cregan PB, Ward RW, Diers BW (2003) A low-cost, high-throughput polyacrylamide gel electrophoresis system for genotyping with microsatellite DNA markers. Crop Sci 43:1828–1832 Yorinori JT, Paiva WM, Frederick RD, Costamilan LM, Bertagnoli PF, Hartman GL, Godoy CV, Nunes JJ (2005) Epidemics of soybean rust (Phakopsora pachyrhizi) in Brazil and Paraguay from 2001 to 2003. Plant Dis 89:675–677 Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134 Zhu Q, Zheng X, Luo J, Gaut BS, Ge S (2007) Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol 24:875–888