Table S1 a Summary of Mutations Induced by Gamma Rays in Rice

Table S1 A summary of mutations induced by gamma rays in rice

No / Name of mutant line or allele / Locus number (RAP-DB /IRGSP) / Mutation type / Size / Reference
1.  / slr1-1 / Os03g0707600 / deletion / 1 bp / Ikeda et al. (2001)
2.  / GA20ox-2 (Calrose 76) / Os01g0883800 / substitution / 1 bp / Ashikari et al. (2002)
3.  / GA20ox-2 (Remei) / Os01g0883800 / substitution / 1 bp / Ashikari et al. (2002)
4.  / phyB-1(elc-1) / Os03g0309200 / insertion / 1 bp / Takano et al. (2005)
5.  / phyB-2(elc-2) / Os03g0309200 / deletion / 11 bp / Takano et al. (2005)
6.  / phyB-3(elc-3) / Os03g0309200 / deletion / 33 bp / Takano et al. (2005)
7.  / phyB-4(elc-4) / Os03g0309200 / deletion / 10 bp / Takano et al. (2005)
8.  / phyB-5*elc-5) / Os03g0309200 / deletion / 8 bp / Takano et al. (2005)
9.  / m8077s (bela ) / Os03g0760200 / deletion / 1 bp / Pan et al. (2006)
10.  / norin8m (belb) / Os03g0760200 / deletion / 1 bp / Pan et al. (2006)
11.  / wx(M-23) / Os06g0133000 / substitution / 1 bp / Sato et al. (2006)
12.  / wx(M-94) / Os06g0133000 / substitution / 1 bp / Sato et al. (2006)
13.  / wx(M-310) / Os06g0133000 / substitution / 1 bp / Sato et al. (2006)
14.  / wx(M-426) / Os06g0133000 / substitution / 1 bp / Sato et al. (2006)
15.  / wx(M-211) / Os06g0133000 / deletion / 2 bp / Sato et al. (2006)
16.  / wx(M-301) / Os06g0133000 / deletion / 2 bp / Sato et al. (2006)
17.  / lsi1 / Os02g0745100 / substitution / 1 bp / Ma et al. (2006)
18.  / Bc7(t) / unknown / deletion / 7 bp / Yan et al. (2007)
19.  / KBNT lpa1-1 / Os02g0819400 / substitution / 1 bp / Kim et al. (2008)
20.  / Os-lpa-XQZ-1 / Os02g0819400 / deletion / 1.4 kbp / Zhao et al. (2008)
21.  / lsi2 / Os03g0107300 / deletion / 15 bp / Huang et al. (2009)
22.  / star1/als1 / Os06g0695800 / deletion / 15 bp / Huang et al. (2009)
23.  / cao-g1 / Os10g0568000 / deletion / 1bp / Morita et al. (2009a)
24.  / cao-g2 / Os10g0568000 / deletion / 3 bp / Morita et al. (2009a)
25.  / cps-g1 / Os02g0278700 / deletion / 1 bp / Morita et al. (2009a)
26.  / ga3ox-g1 / Os01g0177400 / deletion / 1 bp / Morita et al. (2009a)
27.  / ga3ox-g2 / Os01g0177400 / deletion / 3 bp / Morita et al. (2009a)
28.  / gid1-g1 / Os05g0407500 / deletion / 1 bp / Morita et al. (2009a)
29.  / gid2-g1 / Os02g0580300 / deletion / 42.2 kbp / Morita et al. (2009a)
30.  / glb1 / Os05g0499100 / deletion / 62.8 kbp / Morita et al. (2009a)
31.  / glu1 / Os02g0268300 / deletion / 129.7 kbp / Morita et al. (2009a)
32.  / gluA1-g1 / Os01g0762500 / deletion / 1bp / Morita et al. (2009a)
33.  / gluA2-g1 / Os10g0400200 / deletion / 1bp / Morita et al. (2009a)
34.  / gluA2-g2 / Os10g0400200 / substitution / 1bp / Morita et al. (2009a)
35.  / kao-g1 / Os060110000 / deletion / 4 bp / Morita et al. (2009a)
36.  / kao-g2 / Os060110000 / deletion / 16 bp / Morita et al. (2009a)
37.  / pla1-g1 / Os10g0403000 / deletion / 5 bp / Morita et al. (2009a)
38.  / pla1-g2 / Os10g0403000 / substitution / Single base / Morita et al. (2009a)
39.  / pla2-g1 / Os01g0907900 / deletion / 5 bp / Morita et al. (2009a)
40.  / pla2-g2 / Os01g0907900 / Deletion/inversion / 3.2 Mbp / Morita et al. (2009a)
41.  / wx-g1 / Os06g0133000 / deletion / 2 bp / Morita et al. (2009a)
42.  / wx-g2 / Os06g0133000 / deletion / 5bp / Morita et al. (2009a)
43.  / wx-g3 / Os06g0133000 / deletion / 6 bp / Morita et al. (2009a)
44.  / wx-g4 / Os06g0133000 / deletion / 9.4 kbp / Morita et al. (2009a)
45.  / wx-g5 / Os06g0133000 / substitution / Single base / Morita et al. (2009a)
46.  / wx-g6 / Os06g0133000 / Deletion/inversion / 1.2 Mbp / Morita et al. (2009a)
47.  / nol-1 / Os01g0227100 / deletion / 5 bp / Sato et al. (2009)
48.  / nol-2 / Os01g0227100 / deletion / 14 kbp / Sato et al. (2009)
49.  / Nyc3-1 / Os06g0354700 / Inversion / inversion / Morita et al. (2009b)
50.  / dwarf 62 / Os06g0127800 / deletion / 2 bp / Li et al. (2010)
51.  / Os-lpa-XS110-2 / Os03g0142800 / substitution / 1 bp / Xu et al. (2010)
52.  / Os-lpa-XS110-3 / Os03g0142800 / deletion / 5 bp / Xu et al. (2010)
53.  / OASA1 / Os03g0826500 / substitution / 3 bp / Chun et al. (2012)
54.  / esp1 / Os05g0513350 / deletion / 260kb / Duan et al. (2012)
55.  / fzp-10 / Os07g0669500 / deletion / 1 bp / Kato Horibata (2012)
56.  / jiazhe mb / Os03g0760200 / deletion / 1 bp / Wang et al. (2012)
57.  / gz m1s / Os03g0760200 / deletion / 2 bp / Wang et al. (2012)
58.  / gz m2s / Os03g0760200 / deletion / 11 bp / Wang et al. (2012)
59.  / pd2 / Os09g244800 / deletion / 82 kb / Yang et al. (2012)
60.  / tri1 / Os01g0726400 / deletion / 1 bp / Feng et al. (2013a)
61.  / CYP78A11 / Os10g0403000 / deletion / 1 bp / Feng et al. (2013b)
62.  / gsor23 (OsCCD8) / Os01g0746400 / deletion / 1 bp / Yuan et al. (2013)
63.  / OsDFR2 / Os09g0493500 / deletion / 1 bp / Shirasawa et al. (2013)
64.  / Os-lpa-MH86-1 / LOC_04g55800 / deletion / 1 bp / Tan et al. (2013)
65.  / Os-lpa-Z9B-1 / LOC_04g55800 / deletion / 6 bp / Tan et al. (2013)
66.  / Os-lpa-XS110-1 / Os03g0737701 / Insertion / ~7.0 kbp / Zhao et al (2013)

1: The mutations characterized by Chun et al. (2012) for the OASA1 gene were not included in this table because they were identified in regenerated plants after in vitro mutagenesis together with gamma radiation, which made it difficult to determine their true origin: somaclonal variation or radiation induced mutations.

Reference

Ikeda A, Ueguchi-Tanaka M, Sonoda Y, Kitano H, Koshioka M, Futsuhara Y, Matsuoka M, Yamaguchi J (2001) slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8.

Plant Cell 13:999-1010

Ashikari, M., Sasaki, A., Ueguchi-Tanaka, M., Itoh, H., Nishimura, A., Datta, S., Ishiyama, K., Saito, T., Kobayashi, M., Khush, G. S., Kitano, H., and Matsuoka, M. (2002) Loss-of-function of a rice gibberellin biosynthetic gene, GA20 oxidase (GA20ox-2), led to the rice ‘Green Revolution’. Breed. Sci. 52, 143–150.

Takano, M., Inagaki, N., Xie, X., Yuzurihara, N., Hihara, F., Ishizuka, T., Yano, M., Nishimura, M., Miyao, A., Hirochika, H., and Shinomura, T. (2005) Distinct and cooperative functions of phytochromes A, B, and C in the control of deetiolation and flowering in rice. Plant Cell 17, 3311–3325.

Pan G, Zhang X, Liu K, Zhang J, Wu X, Zhu J, Tu J. 2006. Map-based cloning of a novel rice cytochrome P450 gene CYP81A6 that confers resistance to two different classes of herbicides. Plant Mol Biol. 2006 Aug;61(6):933-4.

Sato, Y., Shirasawa, K., Takahashi, Y., Nishimura, M., and Nishio, T. (2006) Mutant selection from progeny of Gamma-ray-irradiated rice by DNA heteroduplex cleavage using Brassica petiole extract. Breed. Sci. 56, 179–183.

Ma J F, Tamai K, Yamaji N, Mitani N, Konishi S, Katsuhara M, Ishiguro M, Murata Y, Yano M. 2006. A silicon transporter in rice. Nature. 2006 Mar 30;440(7084):688-91.

Yan, C., Yan, S., Zeng, X., Zhang, Z., and Gu, M. (2007) Fine mapping and isolation of Bc7(t), allelic to OsCesA4. J. Genet. Genomics 34, 1019–1027.

Kim SI, Andaya CB, Goyal SS, Tai TH (2008) The rice Oslpa1 gene encodes a novel protein involved in phytic acid metabolism. Theor Appl Genet 117:769–779

Zhao HJ, liu Ql, Fu Hl, Xu XH, Wu DX, Shu QY (2008) effect of non-lethal low phytic acid mutations on grain yield and seed viability in rice. Field Crops res 108:206–211.

Huang, C. F., et al. (2009). "A Bacterial-Type ABC Transporter Is Involved in Aluminum Tolerance in Rice." The Plant Cell Online 21(2): 655-667.

Morita, R., Kusaba, M., Iida, S., Yamaguchi, H., Nishio, T., Nishimura, M. 2009a. Molecular characterization of mutations induced by gamma irradiation in rice. Genes & Genetic Systems. Vol. 84, No. 5 P 361-370

Morita, R., Sato, Y., Masuda, Y., Nishimura, M., and Kusaba, M. (2009b) Defect in non-yellow coloring 3, an a/b hydrolase-fold family protein, causes a stay-green phenotype during leaf senescence in rice. The Plant Journal 59, 940–952

Sato, Y., et al. (2009). "Two short-chain dehydrogenase/reductases, NON-YELLOW COLORING 1 and NYC1-LIKE, are required for chlorophyll b and light-harvesting complex II degradation during senescence in rice." Plant J 57(1): 120-131.

Li, W., et al. (2010). "Identification and characterization of dwarf 62, a loss-of-function mutation in DLT/OsGRAS-32 affecting gibberellin metabolism in rice." Planta 232(6): 1383-1396.

Xu F.H., Cheng Z.J., Wang J.L., Wu Z.M., Sun W., Zhang X., Lei C.L., Wang J., Wu F.Q., Guo X.P., Liu L.L., and Wan J.M., 2010, Genetic analysis and fine-mapping of Gws gene using green-white-stripe rice mutant, Zuo wu Xue bao (Acta Agronomica Sinica), 05: 713-720

http://dx.doi.org/10.3724/SP.J.1006.2010.00713

Chun, J. B.; Ha, B.-K.; Jang, D.-S.; Song, M.; Lee, K. J.; Kim, J.-B.; Kim, S. H.; Kang, S.-Y.; Lee, G.-J.; Seo, Y. W.; Kim, D. S., Identification of mutations in OASA1 gene from a gamma-irradiated rice mutant population. Plant Breed 2012, 131 (2), 276-281.

Duan Yuan-lin, Guan Hua-zhong, Zhuo Ming, Chen Zhi-wei, Li Wen-tao, Pan Run-sen, Mao Da-mei, Zhou Yuan-chang and Wu Wei-ren. 2012. Genetic Analysis and Mapping of an Enclosed Panicle Mutant Locus esp1in Rice (Oryza sativaL.). Journal of Integrative Agriculture 2012, 11(12): 1933-1939.

Feng G N, Zhang C Q, Tang M Y, et al. (2013a). Genetic analysis and gene cloning of a triangular hull 1(tri1) mutant in rice (Oryza sativa L.). Chin Sci Bull, 58: 2984-2991, doi: 10.1007/s11434-012-5642-9

Feng G N, Zhang C Q, Zhao D S, Zhu K Z, Tu H Z, Xu C W, Liu Q Q (2013b) Identification and gene cloning of the leafy head mutant pla1-5 in Rice. Chin J Rice Sci 27(2):111-116

Tsuneo Kato and Akira Horibata .2012. A novel frameshift mutant allele, fzp-10, affecting the panicle architecture of rice. EuphyticaInternational Journal of Plant Breeding© Springer Science+Business Media B.V. 201110.1007/s10681-011-0547-2

Wang, Q. Z., Hao W. F., Huang J Z., Zhao H J., Li Y F., Zhang B., Shu Q Y. (2012). Generation and characterization of bentazon susceptible mutants of commercial male sterile lines and evaluation of their utility in hybrid rice production. Field Crops Research 137(0): 12-18.

D. W. Yang, L. B. Lu, C. P. Chen, M. J. Zeng, X. H. Zheng, N. Ye, C. D. Liu, and X. F. Ye, (2012). 'Morphological Characteristics and Gene Mapping of a Palea Degradation(Pd2) Mutant in Rice', Yi Chuan, 34 1064-72.

Shirasawa, S., Kifuji, Y., Komiya, R., Kitashiba, H., Nishimura, M., & Nishio, T. (2013). Identification of a single nucleotide deletion causing frameshift mutation in OsDFR2A in a genic male sterile mutant of rice and its possible application to F1 hybrid breeding. Molecular Breeding, 31(4), 805-814. doi: 10.1007/s11032-013-9835-y

Tan, Y.-Y., Fu, H.-W., Zhao, H.-J., Lu, S., Fu, J.-J., Li, Y.-F., Shu, Q.-Y. (2013). Functional molecular markers and high-resolution melting curve analysis of low phytic acid mutations for marker-assisted selection in rice. Molecular Breeding, 31(3), 517-528. doi: 10.1007/s11032-012-9809-5

Zhao, H. J., Cui, H. R., Xu, X. H., Tan, Y. Y., Fu, J. J., Liu, G. Z., Shu, Q. Y. (2013). Characterization of OsMIK in a rice mutant with reduced phytate content reveals an insertion of a rearranged retrotransposon. Theor Appl Genet. doi: 10.1007/s00122-013-2189-3

Figure S1 Profiles of mutations induced by different chemical mutagens reported in different plant species. Data sources: [1]Greene et al. (2003); [2]Martin et al. 2009; [3]Till et al. (2007); [4]Suzuki et al. (2008); [5]Rawat et al. (2012); [6]Kumar et al. (2013); [7]Talame et al. (2008); [8]Gottwald et al. (2009); [9] Cooper et al. (2008); [10] Uauy et al. (2009); [11] Wang et al. (2005); [12] Harloff et al. (2012); [13] Dong et al. (2009); [14] Chen et al. (2012); [15] Chawade et al. 2010; [16] Jankowicz-Cieslak et al. (2012).