Molecular mapping and breeding with microsatellite markers

Methods in Molecular Biology

Volumn 1006, Issue , 2013, Pages 297-317

  Lightfoot, David A ^a   Iqbal, Muhammad J ^a,b  

^a SOUTHERN ILLINOIS UNIVERSITY   (United States)

^b NORTH DAKOTA STATE UNIVERSITY   (United States)

Author keywords

BES; Bulked segregants; Genome; Marker assisted selection; Motif; QTL; Trait indexing

Indexed keywords

ALLELE; ARTICLE; BREEDING METHOD; CODOMINANCE; DINUCLEOTIDE REPEAT; DNA MARKER; GENE IDENTIFICATION; GENE ISOLATION; GENE SEQUENCE; GENETIC LINKAGE; GENETIC RESOURCE; GENOME; GENOTYPE; HIGH THROUGHPUT SCREENING; HIGH THROUGHPUT SEQUENCING; MARKER ASSISTED BREEDING; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MICROSATELLITE MARKER; NONHUMAN; PATENT; PHENOTYPE; PLANT BREEDING; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS MAPPING; RECOMBINANT INBRED STRAIN; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SIMPLE SEQUENCE REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84877154486     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-389-3_20     Document Type: Article

References (88)

1. Iqbal MJ, Lightfoot DA (2004) Application of DNA markers: Soybean improvement. In: L″rz H, Wenzel G (eds) Molecular marker systems in plant breeding and crop improvement. Springer, New York, p 475
2. Stefaniak TR, Hyten DL, Pantalone VR, Klarer A, Pfeiffer TW (2006) Soybean cultivars resulted from more recombination events than unselected lines in the same population. Crop Sci 46:43-51
3. Lightfoot DA (2008) Soybean genomics: Developments through the use of cultivar Forrest. Int J Plant Genomics 2008:1-22. doi: 10.1155/2008/793158
4. Anand SC (1992) Registration of 'Hartwig' soybean. Crop Sci 32:1060-1070
5. Arelli AP (1994) Inheritance of resistance to Heterodera glycines race 3 in soybean accessions. Plant Dis 78:898-900
6. Hnetkovsky N, Chang SJC, Doubler TW, Gibson PT, Lightfoot DA (1996) Genetic mapping of loci underlying fi eld resistance to soybean sudden death syndrome (SDS). Crop Sci 36:393-400
7. Prabhu RR, Njiti VN, Bell-Johnson B, Johnson JE, Schmidt ME, Klein JH, Lightfoot DA (1999) Selecting soybean cultivars for dual resistance to soybean cyst nematode and sudden death syndrome using two DNA markers. Crop Sci 39:982-987
8. Njiti VN, Johnson JE, Torto TA, Gray LE, Lightfoot DA (2001) Inoculum rate in fl uences selection for fi eld resistance to soybean sudden death syndrome in the greenhouse. Crop Sci 41:1726-1731
9. Kassem MA, Shultz J, Meksem K, Cho Y, Wood AJ, Iqbal MJ, Lightfoot DA (2006) An updated 'Essex' by 'Forrest' linkage map and fi rst composite interval map of QTL underlying six soybean traits. Theor Appl Genet 113:1015-1026
10. Shultz JL, Kazi S, Afzal JA, Bashir R, Lightfoot DA (2007) The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. Theor Appl Genet 114:1081-1090
11. Webb DM, Baltazar BM, Rao-Arelli AP, Schupp J, Keim P, Clayton K, Ferreira AR, Owens T, Beavis WD (1995) QTLs affecting soybean cyst-nematode resistance. Theor Appl Genet 91:574-581
12. Webb DM (1996) Soybean cyst nematode resistant soybeans and methods of breeding and identifying resistant plants. US Patent 5,491,081
13. Hauge BM, Wang ML, Parsons JD, Parnell LD (2001) Nucleic acid molecules and other molecules associated with soybean cyst nematode resistance. US patent WO 0151627-A 19-JUL-2001
14. Lightfoot DA (2001) Soybean sudden death syndrome resistant soybeans, soybean cyst nematode resistant soybeans and methods of breeding and identifying resistant plants. US Patent 6,300,541
15. Lightfoot DA, Meksem K (2011) Isolated soybean cyst nematode and sudden death syndrome polypeptides. US Patent 7,902,337
16. Webb DM (2000) Positional cloning of soybean cyst nematode resistance genes. US Patent 6,162,967
17. Webb DM (2003) Quantitative trait loci associated with soybean cyst nematode resistance and uses thereof. US Patent 6,538,175
18. Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB (2004) A new integrated genetic linkage map of the soybean. Theor Appl Genet 109:122-128
19. Shultz JL, Jayaraman D, Shopinski KL, Iqbal MJ, Kazi S, Zobrist K, Bashir R, Yaegashi S, Lavu N, Afzal AJ, Yesudas CR, Kassem MA, Wu C, Zhang HB, Town CD, Meksem K, Lightfoot DA Molecular Mapping and Breeding with Microsatellite Markers 315 (2006) The soybean genome database (SoyGD): A browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of glycine max. Nucleic Acid Res 34:D758-D765
20. Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT (2010) SNP discovery by high-throughput sequencing in soybean. BMC Genomics 11:469
21. 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
22. Lam HM, Xu X, Liu X et al (2010) Resequencing of 31 wild and cultivated soybean genomes identi fi es patterns of genetic diversity and selection. Nat Genet 42:1053-1062
23. Lightfoot DA, Njiti VN, Gibson PT, Kassem MA, Iqbal MJ, Meksem K (2005) Registration of Essex × Forrest recombinant inbred line (RIL) mapping population. Crop Sci 45:1678-1681
24. Kazi S, Njiti VN, Doubler TW, Yuan J, Iqbal MJ, Cianzio S, Lightfoot DA (2007) Registration of the Flyer by Hartwig recombinant inbred line mapping population. J Plant Reg 1:175-178
25. Njiti VN, Doubler TW, Suttner RJ, Gray LE, Gibson PT, Lightfoot DA (1998) Resistance to soybean sudden death syndrome and root colonization by Fusarium solani f. sp. glycines in near-isogeneic lines. Crop Sci 38:472-477
26. Njiti VN, Myers O, Schroeder D, Lightfoot DA (2003) Glyphosate on roundup ready soybean: Effects on root infection by Fusarium solani f. sp. Glycines and sudden death syndrome. Agron J 95:1140-1145
27. Njiti VN, Lightfoot DA (2006) Genetic analysis infers Dt loci underlie resistance to SDS caused by Fusarium virguliforme in indeterminate soybeans. Can J Plant Sci 41:83-89
28. Afzal AJ, Srour A, Hemmati N, Saini N, Shemy E, Lightfoot DA (2012) Recombination suppression at the dominant Rhg1/Rfs2 locus underlying soybean resistance to the cyst nematode. Theor Appl Genet 124:1027-1039
29. Mansur LM, Orf JH, Chase K, Jarvick T, Cregan PB, Lark KG (1996) Genetic mapping of agronomic traits using recombinant inbred lines of soybean. Crop Sci 36:1327-1336
30. Shoemaker RC, Specht JE (1995) Integration of the soybean molecular and classical genetic linkage groups. Crop Sci 35:436-446
31. Akkaya MS, Bhagwat AA, Cregan PB (1992) Length polymorphism of simple sequence repeat DNA in soybean. Genetics 132:1131-1139
32. Morgante M, Olivieri AM (1993) PCRampli fi ed microsatellites as markers in plant genetics. Plant J 3:175-182
33. Rongwen J, Akkaya MS, Bhagwat AA, Lavi U, Cregan PB (1995) The use of microsatellite DNA markers for soybean genotype identi fi cation. Theor Appl Genet 90:43-48
34. Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP, and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225-238
35. Diwan N, Cregan PB (1997) Automated sizing of fl uorescent-labeled simple sequence repeat (SSR) markers to assay genetic variation in soybean. Theor Appl Genet 95:723-733
36. Marek LF, Mudge J, Darnielle L, Grant D, Hanson N, Paz M, Huihuang Y, Denny R, Larson K, Foster-Hartnett D, Cooper A, Danesh D, Larsen D, Schmidt T, Staggs R, Crow JA, Retzel E, Young ND, Shoemaker RC (2001) Soybean genomic survey: BACend sequences near RFLP and SSR markers. Genome 44:572-581
37. Akkaya MS, Shoemaker RC, Specht JE, Bhagwat AA, Cregan PB (1995) Integration of simple sequence repeat DNA markers into a soybean linkage map. Crop Sci 35:1439-1445
38. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178-183
39. McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom RJ, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199-207
40. Rota ML, Kantety RV, Yu JK, Sorrells ME (2005) Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 6:23-32
41. Witsenboer H, Vogel J, Michelmore RW (1998) Identi fi cation, genetic localization and allelic diversity of selectively ampli fi ed microsatellite polymorphic loci (SAMPL) in lettuce and wild relatives (Lactuca spp.). Genome 40:923-936
42. Cregan PB, Mudge J, Fickus EW, Danesh D, Denny R, Young ND (1999) Two simple sequence repeat markers to select for soybean cyst nematode resistance conditioned by the rhg1 locus. Theor Appl Genet 99:811-818
43. Chen CH, Potter NT, Taranenko NT (2003) Detection of trinucleotide repeat containing genes by matrix-assisted laser desorption/ ionization (MALDI) mass spectrometry. Methods Mol Biol 217:91-100
44. Meksem K, Ruben E, Hyten D, Triwitayakorn K, Lightfoot DA (2001) Conversion of AFLP 316 David A. Lightfoot and Muhammad J. Iqbal bands into high-throughput DNA markers. Mol Genet Genomics 265:207-214
45. Ruben E, Aziz J, Afzal AJ, Njiti VN, Triwitayakorn K, Iqbal MJ, Yaegashi S, Arelli P, Town C, Meksem K, Lightfoot DA (2006) Genomic analysis of the 'Peking' rhg1 locus: Candidate genes that underlie soybean resistance to the cyst nematode. Mol Genet Genomics 276:320-330
46. Meksem K, Doubler TW, Chang SJC, Chancharoenchai K, Suttner R, Cregan P, Rao-Arelli P, Gibson PT, Lightfoot DA (1999) Clustering among genes underlying QTL for fi eld resistance to Sudden Death Syndrome and cyst nematode race 3. Theor Appl Genet 99:1131-1142
47. Triwitayakorn K, Njiti VN, Iqbal MJ, Yaegashi S, Town C, Lightfoot DA (2005) Genomic analysis of a region encompassing QRfs1 and QRfs2: Genes that underlie soybean resistance to sudden death syndrome. Genome 48:125-138
48. Meksem K, Hyten D, Ruben E, Lightfoot DA (2001) High-throughput genotyping for a polymorphism linked to soybean cyst nematode resistance gene Rhg4 by using Taqman probes. Mol Breed 77:63-71
49. Srour A, Afzal AJ, Saini N, Blahut-Beatty L, Hemmati N, Simmonds DH, El Shemy H, Town CD, Sharma H, Liu X, Li W, Lightfoot DA (2012) The receptor like kinase transgene from the Rhg1/Rfs2 locus caused pleiotropic resistances to soybean cyst nematode and sudden death syndrome. BMC Genomics 13:368
50. Landegren U, Schallmeiner E, Nilsson M, Fredriksson S, Banr J, Gullberg M, Jarvius J, Gustafsdottir S, Dahl F, Sderberg O, Ericsson O, Stenberg J (2004) Molecular tools for a molecular medicine: Analyzing genes, transcripts and proteins using padlock and proximity probes. J Mol Recognit 17:194-197
51. Mein CA, Barratt BJ, Dunn MG, Siegmund T, Smith AN, Esposito L, Nutland S, Stevens HE, Wilson AJ, Philips MS, Jarvis N, Law S, de Arruda M, Todd JA (2000) Evaluation of single nucleotide polymorphism typing with invader on PCR ampli fi cation and its automation. Genome Res 3:330-343
52. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376
53. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379
54. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genomewide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499-510
55. Truong HT, Ramos AM, Yalcin F, de Ruiter M, van der Poel HJA, Huvenaars KHJ, Hogers RCJ, van Enckevort LJG, Janssen A, van Orsouw NJ, van Eijk MJT (2012) Sequencebased genotyping for marker discovery and co615 dominant scoring in germplasm and populations. PLoS One 7:e37565
56. Poland JA, Brown PJ, Sorrells ME, Jannink JL (2012) Development of high-density genetic maps for barley and wheat using a novel twoenzyme genotyping-by-sequencing approach. PLoS One 7:e32253
57. Wang S, Meyer E, McKay JK, Matz MV (2012) 2b-RAD: A simple and fl exible method for genome-wide genotyping. Nat Methods 9: 808-810
58. Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133-141
59. Futschik A, Schltterer C (2010) The next generation of molecular markers from massively parallel sequencing of pooled DNA samples. Genetics 186:207-218
60. You FM, Huo N, Deal KR, Gu YQ, Luo M-C, McGuire PE, Dvorak J, Anderson OD (2011) Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation s 639 sequencing without a reference genome sequence. BMC Genomics 12:59
61. Nielsen R, Paul JS, Albrechtsen A, Song YS (2011) Genotype and SNP calling from nextgeneration sequencing data. Nat Rev Genet 12:443-451
62. Xu X, Pan S, Cheng S, Zhang B, Mu D et al (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189-195
63. Wang X, Wang H, Wang J, Sun R, Wu J et al (2011) The genome of the mesopolyploid crop species Brassica rapa Nat Genet 43:1035-1039
64. Lander E, Green P, Abrahamson J, Barlow A, Daley M, Lincoln S, Newburg L (1987) MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174-181
65. Basten CJ, Weir BS, Zeng Z (2001) QTL cartographer version 2.0. Department of Statistics, North Carolina State University, Raleigh, NC
66. Hartwig EE, Epps JM (1973) Registration of forest soybeans. Crop Sci 13:287
67. Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding: New tools for an old science. Bio-technology 7:257-264
68. Frisch M, Bohn M, Melchinger AE (1999) Comparison of selection strategies for markerassisted backcrossing of a gene. Crop Sci 39: 1295-1301
69. Iqbal MJ, Meksem K, Njiti VN, Kassem MA, Lightfoot DA (2001) Microsatellite markers identify three additional quantitative trait loci for resistance to soybean sudden death syndrome (SDS) in Essex × Forrest RILs. Theor Appl Genet 102:187-192
70. Yuan Z, Njiti VN, Meksem K, Iqbal MJ, Triwitayakorn K, Kassem MA, Davis GT, Schmidt ME, Lightfoot DA (2002) Identi fi cation of yield loci in soybean populations that segregate for disease resistance. Crop Sci 42:271-277
71. Kazi S, Shultz J, Bashir R, Afzal J, Njiti VN, Lightfoot DA (2008) Separate loci underlie resistance to soybean sudden death syndrome in 'Hartwig' by 'Flyer'. Theor Appl Genet 116:967-977
72. Kazi S, Shultz J, Afzal J, Hashmi R, Jasim M, Bond J, Arelli PR, Lightfoot DA (2010) Isolines and inbred-lines con fi rmed loci that underlie resistance from cultivar 'Hartwig' to three soybean cyst nematode populations. Theor Appl Genet 120:633-640
73. Karangula UB, Kassem MA, Gupta L, El-Shemy HA, Lightfoot DA (2009) Locus interactions underlie seed yield in soybeans resistant to Heterodera glycines. Curr Issues Mol Biol 11(suppl 1):i73-i84
74. Njiti VN, Gray L, Lightfoot DA (1997) Ratereducing resistance to Fusarium solani f. sp. phaseoli (nee: Glycines) underlies fi eld resistance to soybean sudden-death syndrome (SDS). Crop Sci 37:1-12
75. Njiti VN, Meksem K, Iqbal MJ, Johnson JE, Kassem MA, Zobrist KF, Kilo VY, Lightfoot DA (2002) Common loci underlie fi eld resistance to soybean sudden death syndrome in Forrest, Pyramid, Essex, and Douglas. Theor Appl Genet 104:294-300
76. Liu X, Liu S, Jamai A, Bendahmane A, Lightfoot DA, Mitchum MG, Meksem K (2011) Soybean cyst nematode resistance in soybean is independent of the Rhg4 locus LRR RLK gene. Funct Integr Genomics. doi: 10.1007/s10142-011-0225-4
77. Mudge J, Cregan PB, Kenworthy JP, Kenworthy WJ, Orf JH, Young ND (1997) Two microsatellite markers that fl ank the major soybean cyst nematode resistance locus. Crop Sci 37:1611-1615
78. Iqbal MJ, Yaegashi S, Njiti VN, Ahsan R, Cryder KL, Lightfoot DA (2002) Resistance locus pyramids alter transcript abundance in soybean roots inoculated with Fusarium solani f. sp. glycines Mol Genet Genomics 268:407-417
79. Iqbal MJ, Afzal AJ, Yaegashi S, Ruben E, Triwitayakorn K, Njiti VN, Ahsan R, Wood AJ, Lightfoot DA (2002) A pyramid of loci for partial resistance to Fusarium solani f. sp. glycines maintains myo-inositol-1-phoshate synthase expression in soybean roots. Theor Appl Genet 105:1115-1123
80. Iqbal MJ, Yaegashi S, Ahsan R, Shopinski KL, Lightfoot DA (2005) Root response to Fusarium solani f. sp. glycines: Temporal accumulation of transcripts in partially resistant and susceptible soybean. Theor Appl Genet 110: 1429-1438
81. Aoki T, O'Donnell K, Homma Y, Lattanzi AR (2003) Sudden-death syndrome of soybean is caused by two morphologically and phylogenetically distinct species within the Fusarium solani species complex F. virguliforme in North America and F. tucumaniae in South America. Mycologia 95:660-684
82. Xin Z, Velten JP, Oliver MJ, Burke JJ (2003) High-throughput DNA extraction method suitable for PCR. Biotechniques 34: 820-826
83. Yuan J, Haroon M, Lightfoot DA, Pelletier Y, Liu Q, Bizimungu B, Li XQ (2009) Highresolution DNA melting analysis of allelic expression. Curr Issues Mol Biol 11(S1):1-9
84. Landegren U, Nilsson M, Kwok PW (1998) Reading bits of genetic information: Methods for single nucleotide polymorphism analysis. Genome Res 8:769-776
85. Kazi S (2005) Minimum tile derive microsatellite markers improve the physical map of the soybean genome and the Flyer by Hartwig genetic map at Rhg, Rfs and yield loci. MS Thesis SIUC Carbondale IL, USA, pp 212
86. Hashmi RY (2004) Inheritance of resistance to soybean sudden death syndrome (SDS) in Ripley x Spencer F5 derived lines. PhD dissertation, Plant Biology, SIUC, Carbondale, USA
87. Chang SJC, Doubler TW, Kilo V, Suttner RJ, Klein JH, Schmidt ME, Gibson PT and Lightfoot DA (1996) Two additional loci underlying durable fi eld resistance to soybean sudden-death syndrome (SDS). Crop Sci 36: 1624-1628
88. Sanithchon J, Vanavichit A, Chanprame S, Toojinda T, Triwitayakorn T, Njiti, VM, SrinivesP (2004) Identi fi cation of simple sequence repeat markers linked to sudden death syndrome resistance in soybean. Science Asia 30:205-209