Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean

Plant Physiology

Volumn 156, Issue 1, 2011, Pages 240-253

  Bolon, Yung Tsi ^a   Haun, William J ^b   Xu, Wayne W ^b   Grant, David ^a   Stacey, Minviluz G ^c   Nelson, Rex T ^a   Gerhardt, Daniel J ^d   Jeddeloh, Jeffrey A ^d   Stacey, Gary ^c   Muehlbauer, Gary J ^b   Orf, James H ^b   Naeve, Seth L ^b   Stupar, Robert M ^b   Vance, Carroll P ^a,b  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

^c UNIVERSITY OF MISSOURI   (United States)

^d Roche NimbleGen Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCINE MAX;

VEGETABLE PROTEIN;

COMPARATIVE GENOMIC HYBRIDIZATION; DNA SEQUENCE; EXOME; FAST NEUTRON RADIATION; GENE DELETION; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; PLANT GENOME; PLANT SEED; PROCEDURES; SOYBEAN;

COMPARATIVE GENOMIC HYBRIDIZATION; EXOME; FAST NEUTRONS; GENOME, PLANT; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PLANT PROTEINS; SEEDS; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION; SOYBEANS;

EID: 79956046982     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.110.170811     Document Type: Article

References (62)

1. Alonso JM, Ecker JR (2006) Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat Rev Genet 7: 524-536
2. Alonso JM, Stepanova AN, Solano R, Wisman E, Ferrari S, Ausubel FM, Ecker JR (2003) Five components of the ethylene-response pathway identified in a screen for weak ethylene-insensitive mutants in Arabidopsis. Proc Natl Acad Sci USA 100: 2992-2997
3. Alt JL, Fehr WR, Welke GA, Sandhu D (2005) Phenotypic and molecular analysis of oleate content in the mutant soybean line M23. Crop Sci 45: 1997-2000
4. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410
5. Anai T, Yamada T, Hideshima R, Kinoshita T, Rahman SM, Takagi Y (2008) Two high-oleic-acid soybean mutants, M23 and KK21, have disrupted microsomal omega-6 fatty acid desaturase, encoded by GmFAD2-1a. Breed Sci 58: 447-452
6. Ané JM, Kiss GB, Riely BK, Penmetsa RV, Oldroyd GE, Ayax C, Lévy J, Debellé F, Baek JM, Kalo P, et al (2004) Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes. Science 303: 1364-1367
7. Bolon YT, Joseph B, Cannon SB, Graham MA, Diers BW, Farmer AD, May GD, Muehlbauer GJ, Specht JE, Tu ZJ, et al (2010) Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean. BMC Plant Biol 10: 41
8. Caldwell DG, McCallum N, Shaw P, Muehlbauer GJ, Marshall DF, Waugh R (2004) A structured mutant population for forward and reverse genetics in barley (Hordeum vulgare L.). Plant J 40: 143-150
9. Carter NP (2007) Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet (Suppl) 39: S16-S21
10. Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, Nayir A, Bakkaloǧlu A, Ozen S, Sanjad S, et al (2009) Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci USA 106: 19096-19101
11. Cooper JL, Till BJ, Laport RG, Darlow MC, Kleffner JM, Jamai A, El-Mellouki T, Liu S, Ritchie R, Nielsen N, et al (2008) TILLING to detect induced mutations in soybean. BMC Plant Biol 8: 9
12. Fernandes J, Dong Q, Schneider B, Morrow DJ, Nan GL, Brendel V, Walbot V (2004) Genome-wide mutagenesis of Zea mays L. using RescueMu transposons. Genome Biol 5: R82
13. Gong JM, Waner DA, Horie T, Li SL, Horie R, Abid KB, Schroeder JI (2004) Microarray-based rapid cloning of an ion accumulation deletion mutant in Arabidopsis thaliana. Proc Natl Acad Sci USA 101: 15404-15409
14. Grant D, Nelson RT, Cannon SB, Shoemaker RC (2009) SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res 38: D843-D846
15. Haas BJ, Delcher AL, Wortman JR, Salzberg SL (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20: 3643-3646
16. Haun WJ, Hyten DL, Xu WW, Gerhardt DJ, Albert TJ, Richmond T, Jeddeloh JA, Jia G, Springer NM, Vance CP, et al (2011) The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82. Plant Physiol 155: 645-655
17. Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW, Middle CM, Rodesch MJ, Albert TJ, Hannon GJ, et al (2007) Genome-wide in situ exon capture for selective resequencing. Nat Genet 39: 1522-1527
18. Hoffmann D, Jiang Q, Men A, Kinkema M, Gresshoff PM (2007) Nodulation deficiency caused by fast neutron mutagenesis of the model legume Lotus japonicus. J Plant Physiol 164: 460-469
19. Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW, Shoemaker RC, Specht JE, Farmer AD, May GD, Cregan PB (2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11: 38
20. Kaló P, Gleason C, Edwards A, Marsh J, Mitra RM, Hirsch S, Jakab J, Sims S, Long SR, Rogers J, et al (2005) Nodulation signaling in legumes requires NSP2, a member of the GRAS family of transcriptional regulators. Science 308: 1786-1789
21. Koornneef M, Dellaert LW, van der Veen JH (1982) EMS-and radiationinduced mutation frequencies at individual loci in Arabidopsis thaliana (L.) Heynh. Mutat Res 93: 109-123
22. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, et al (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science 318: 420-426
23. Kuromori T, Takahashi S, Kondou Y, Shinozaki K, Matsui M (2009) Phenome analysis in plant species using loss-of-function and gain-offunction mutants. Plant Cell Physiol 50: 1215-1231
24. Kuromori T, Wada T, Kamiya A, Yuguchi M, Yokouchi T, Imura Y, Takabe H, Sakurai T, Akiyama K, Hirayama T, et al (2006) A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis. Plant J 47: 640-651
25. Larmande P, Gay C, Lorieux M, Périn C, Bouniol M, Droc G, Sallaud C, Perez P, Barnola I, Biderre-Petit C, et al (2008) Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. Nucleic Acids Res 36: D1022-D1027
26. Lawrence CJ, Schaeffer ML, Seigfried TE, Campbell DA, Harper LC (2007) MaizeGDB's new data types, resources and activities. Nucleic Acids Res 35: D895-D900
27. Li X, Lassner M, Zhang Y (2002) Deleteagene: a fast neutron deletion mutagenesis-based gene knockout system for plants. Comp Funct Genomics 3: 158-160
28. Li X, Song Y, Century K, Straight S, Ronald P, Dong X, Lassner M, Zhang Y (2001) A fast neutron deletion mutagenesis-based reverse genetics system for plants. Plant J 27: 235-242
29. Li X, Zhang Y (2002) Reverse genetics by fast neutron mutagenesis in higher plants. Funct Integr Genomics 2: 254-258
30. Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, He J, Xu D, May G, Stacey G (2010) An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J 63: 86-99
31. Martienssen RA (1998) Functional genomics: probing plant gene function and expression with transposons. Proc Natl Acad Sci USA 95: 2021-2026
32. Medvedev P, Stanciu M, Brudno M (2009) Computational methods for discovering structural variation with next-generation sequencing. Nat Methods (Suppl) 6: S13-S20
33. Meinke DW, Meinke LK, Showalter TC, Schissel AM, Mueller LA, Tzafrir I (2003) A sequence-based map of Arabidopsis genes with mutant phenotypes. Plant Physiol 131: 409-418
34. Men AE, Laniya ST, Searle IR, Iturbe-Ormaetxe I, Gresshoff I, Jiang Q, Carroll BJ, Gresshoff PM (2002) Fast neutron mutagenesis of soybean (Glycine soja L.) produces a supernodulating mutant containing a large deletion in linkage group H. Genome Lett 3: 147-155
35. Menda N, Semel Y, Peled D, Eshed Y, Zamir D (2004) In silico screening of a saturated mutation library of tomato. Plant J 38: 861-872
36. 2+/calmodulin-dependent protein kinase required for symbiotic nodule development: gene identification by transcriptbased cloning. Proc Natl Acad Sci USA 101: 4701-4705
37. Miyao A, Iwasaki Y, Kitano H, Itoh J, Maekawa M, Murata K, Yatou O, Nagato Y, Hirochika H (2007) A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes. Plant Mol Biol 63: 625-635
38. Noh B, Lee SH, Kim HJ, Yi G, Shin EA, Lee M, Jung KJ, Doyle MR, Amasino RM, Noh YS (2004) Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time. Plant Cell 16: 2601-2613
39. Oldroyd GE, Long SR (2003) Identification and characterization of nodulation-signaling pathway 2, a gene of Medicago truncatula involved in Nod factor signaling. Plant Physiol 131: 1027-1032
40. Orf JH, Denny RL (2004) Registration of 'MN1302' soybean. Crop Sci 44: 693
41. Østergaard L, Yanofsky MF (2004) Establishing gene function by mutagenesis in Arabidopsis thaliana. Plant J 39: 682-696
42. Pham AT, Lee JD, Shannon JG, Bilyeu KD (2010) Mutant alleles of FAD2-1A and FAD2-1B combine to produce soybeans with the high oleic acid seed oil trait. BMC Plant Biol 10: 195
43. Rahman SM, Takagi Y, Kubota K, Miyamoto K, Kawakita T (1994) High oleic acid mutant in soybean induced by x-ray irradiation. Biosci Biotechnol Biochem 58: 1070-1072
44. Rogers C, Wen J, Chen R, Oldroyd G (2009) Deletion-based reverse genetics in Medicago truncatula. Plant Physiol 151: 1077-1086
45. Sandhu D, Alt JL, Scherder CW, Fehr WR, Bhattacharyya MK (2007) Enhanced oleic acid content in the soybean mutant M23 is associated with the deletion in the Fad2-1a gene encoding a fatty acid desaturase. J Am Oil Chem Soc 84: 229-235
46. Scherder CW, Fehr WR, Shannon JG (2008) Stability of oleate content in soybean lines derived from M23. Crop Sci 48: 1749-1754
47. Schlueter JA, Vasylenko-Sanders IF, Deshpande S, Yi J, Siegfried M, Roe BA, Schlueter SD, Scheffler BE, Shoemaker RC (2007) The FAD2 gene family of soybean. Crop Sci 47: S-14-S-26
48. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183
49. Searle IR, Men AE, Laniya TS, Buzas DM, Iturbe-Ormaetxe I, Carroll BJ, Gresshoff PM (2003) Long-distance signaling in nodulation directed by a CLAVATA1-like receptor kinase. Science 299: 109-112
50. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Månér S, Massa H, Walker M, Chi M, et al (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525-528
51. Severin AJ, Woody JL, Bolon YT, Joseph B, Diers BW, Farmer AD, Muehlbauer GJ, Nelson RT, Grant D, Specht JE, et al (2010) RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol 10: 160
52. Sundaresan V, Springer P, Volpe T, Haward S, Jones JD, Dean C, Ma H, Martienssen R (1995) Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. Genes Dev 9: 1797-1810
53. Tadege M, Wen J, He J, Tu H, Kwak Y, Eschstruth A, Cayrel A, Endre G, Zhao PX, Chabaud M, et al (2008) Large-scale insertional mutagenesis using the Tnt1 retrotransposon in the model legume Medicago truncatula. Plant J 54: 335-347
54. Tzafrir I, Dickerman A, Brazhnik O, Nguyen Q, McElver J, Frye C, Patton D, Meinke D (2003) The Arabidopsis SeedGenes Project. Nucleic Acids Res 31: 90-93
55. Tzafrir I, Pena-Muralla R, Dickerman A, Berg M, Rogers R, Hutchens S, Sweeney TC, McElver J, Aux G, Patton D, et al (2004) Identification of genes required for embryo development in Arabidopsis. Plant Physiol 135: 1206-1220
56. Wang H, Li G, Chen R (2006) Fast neutron bombardment (FNB) mutagenesis for forward and reverse genetic studies in plants. In JA Teixeira da Silva, ed, Floriculture, Ornamental and Plant Biotechnology: Advances and Special Issues, Vol 1. Global Science Books, pp 629-639
57. Waugh R, Leader DJ, McCallum N, Caldwell D (2006) Harvesting the potential of induced biological diversity. Trends Plant Sci 11: 71-79
58. Wei W-H, Chen B, Yan X-H, Wang L-J, Zhang H-F, Cheng J-P, Zhou X-A, Sha A-H, Shen H (2008) Identification of differentially expressed genes in soybean seeds differing in oil content. Plant Sci 175: 663-673
59. Wu JL, Wu C, Lei C, Baraoidan M, Bordeos A, Madamba MR, Ramos-Pamplona M, Mauleon R, Portugal A, Ulat VJ, et al (2005) Chemicaland irradiation-induced mutants of indica rice IR64 for forward and reverse genetics. Plant Mol Biol 59: 85-97
60. Xin Z, Wang ML, Barkley NA, Burow G, Franks C, Pederson G, Burke J (2008) Applying genotyping (TILLING) and phenotyping analyses to elucidate gene function in a chemically induced sorghum mutant population. BMC Plant Biol 8: 103
61. Zhang J, Li C, Wu C, Xiong L, Chen G, Zhang Q, Wang S (2006a) RMD: a rice mutant database for functional analysis of the rice genome. Nucleic Acids Res 34: D745-D748
62. Zhang L, Fetch T, Nirmala J, Schmierer D, Brueggeman R, Steffenson B, Kleinhofs A (2006b) Rpr1, a gene required for Rpg1-dependent resistance to stem rust in barley. Theor Appl Genet 113: 847-855