Introduction Oryza sativa 2005 2003 2006 2004 2004 2004 Arabidopsis thaliana 2003 Ds 2006 Oryza sativa Japonica Tos17 2003 Tos17 1996 Tos17 Tos17 Tos17 Tos17 Tos Tos17 Tos Tos17s Tos17 Tos17 2003 Tos17 2000 2003 2003 Ds 2003 2004 En/Spm 2005 Tos Tos17 2004 2001 Tos17 Tos17 Tos17 Materials and methods Plant materials 1990 2 1 Tos17 Phenotyping Ten to twenty-five seeds were planted per line. Germination rates and seedling phenotypes were observed in the nursery. After 1 month from seeding, the seedlings were transferred to the paddy field. Phenotypes in the field were observed at the vegetative stage, near the heading stage, at the seed maturation stage, and at harvest. Lines segregating abnormal plants at about 25% frequency were digitally photographed and assigned a phenotype ID. Database http://www.postgresql.org/ http://www.freebsd.org/ Tos17 Tos17 SOM analysis http://www.cis.hut.fi/research/som_pak/ Results Flow of phenotypic analysis 2 2 Each line was designated by “N” for “Nipponbare” followed by a letter A-G that indicates the yearly lot, and four figures, e.g. NA1234. Lines named with “NA” and “NB” were used in a small-scale pilot study and “NC” to “NG” were used in large-scale studies. Tos Tos17 Tos17 1998 Classification of phenotypes 1 Germination. This trait was evaluated by measuring germination rate under defined conditions. Since wild type (cv. Nipponbare) showed a germination rate higher than 95%, lines that showed germination rates less than 75% were recorded in the present project. Since several laboratories measured germination rates of all lines, all primary data are also stored in the database. In total, 3489 lines showed a low germination rate, and 525 lines showed germination rates less than 50%. Some of the lines with low germination rates may be embryo mutants. 1 1 2004 2005 1 1 1 1 1 1 1 1 1 1 1 1 Heading date. In this category, lines whose heading date deviated more than 7 days from normal were classified as heading date mutants. This category includes “Early heading”, “Late heading”, and “Non-heading?” mutants. A small number of lines segregated as “Non-heading?” mutants that did not form panicles even at harvest (five to 6 months after sowing). The number of “Early heading” lines (1797) is a little larger than that of “Late heading” lines (1244). 1 1 Tos17 Seed. Only “Large grain”, “Small grain”, and “Slender grain” were distinguished in this category. The frequency of “Small grain” was two and four times higher than the frequency of “Large grain” and “Slender grain”, respectively. Among the “Others”, white or dull kernel phenotypes were often observed. Table 1 Summary of phenotype data  Class Phenotype ID code NC ND NE NF NG Total 1 Germination Low germination rate 1 327 531 1326 1005 300 3489 2 Growth Lethal 2 135 300 689 271 234 1629 Abnormal shoot 3 189 172 219 823 384 1787 Weak 4 114 204 341 556 390 1605 3 Leaf color Albino 11 264 384 230 275 254 1407 Yellow 12 96 139 186 317 71 809 Dark green  13 295 285 354 58 69 1061 Pale green  14 270 429 372 265 395 1731 Virescent 15 35 278 206 131 184 834 Stripe 16 46 40 64 132 102 384 Zebra 17 12 15 13 39 29 108 Others 18 9 15 23 22 16 85 4 Leaf shape Wide leaf 21 38 28 51 4 21 142 Narrow leaf 22 165 324 432 204 251 1376 Long leaf 23 3 3 14 4 5 29 Short leaf 24 2 4 25 8 1 40 Drooping leaf 25 8 140 35 12 31 226 Rolled leaf 26 31 52 153 23 83 342 Spiral leaf 27 10 23 55 3 18 109 Brittle leaf/culm 28 5 14 40 53 10 122 Abnormal lamina joint angle 29 14 27 13 14 28 96 Withering 30 112 270 251 88 147 868 Others 31 37 54 46 113 93 343 5 Culm shape Semi-dwarf 41 645 822 661 633 900 3661 Dwarf 42 803 1550 1351 882 1123 5709 Severely dwarf 43 248 411 355 143 217 1374 Long culm 44 258 217 50 68 83 676 Fine culm 45   1 16 1 18 Thick culm 46 31 24 2 1 4 62 Others 47  1 1 4 2 8 6 Spotted leaf/lesion mimic Spotted leaf/lesion mimic 51 115 211 197 269 302 1094 7 Tillering High tillering 61 11 27 25 21 27 111 Low tillering 62 418 678 696 609 421 2822 Lazy 63 70 115 53 80 56 374 8 Heading date Early heading 65 352 976 99 297 65 1789 Late heading 66 111 561 247 215 110 1244 Non-heading? 67 2 2 42 32 18 96 9 Spikelet Abnormal hull 71 41 268 36 52 111 508 Abnormal floral organ 72 12 128 43 11 17 211 10 Panicle Long panicle 81 1 3 19 3 3 29 Short panicle 82 51 79 426 92 104 752 Lax panicle 83 18 16 15 23 32 104 Dense panicle 84 41 18 97 65 43 264 Viviparous 85 85 473 267 142 138 1105 Shattering 86 1 3 2   6 Neck leaf 87 38 51 48 10 24 171 Abnormal panicle shape 88 21 43 265 79 25 433 11 Sterility Sterile 91 441 1026 818 658 882 3825 Low fertility 92 2877 3127 935 2991 2612 12542 12 Seed Large grain 101 55 78 3 34 25 195 Small grain 102 47 95 96 145 44 427 Slender grain 103 20 28 18 21 14 101 Others 104 979 1117 883 143 347 3469 Lots NC through NG were harvested in 1997 through 2001, respectively. Numbers of mutant lines with the corresponding phenotypes are listed Fig. 1 Tos  Correlation between phenotypes 1995 2 Fig. 2 Self-organizing map for correlation of phenotypes. Lines that showed two or more abnormal phenotypes were analyzed by SOM. Distances between phenotypes indicate the magnitude of correlation of phenotypes. Col_Oth., Color Others; Lg_lf, Long leaf; L_joint, Abnormal lamina joint angle; Lg_pa, Long panicle; Ab_floral_organ, Abnormal floral organ; Sl_grain, Slender grain; Thick_cm, Thick culm. Grayscale levels of each node represents the distance between references  2 2 Tos17 Tos17 Tos17 2006 2 Tos17 Os06g027500 3 Tos17 Tos17 Os06g027500 Hd1 2000 Os07g0656500 3 2003 Tos17 Tos17 Table 2 Tos17 Locus name Description Phenotypes Os01g0113200 LRK14 Pale green leaf, low fertility Os01g0113300 Receptor-like kinase ARK1AS Dwarf, spotted leaf/lesion mimic Os01g0147800 Protein of unknown function DUF547 domain containing protein Pale green leaf, semi-dwarf, long culm, short panicle, sterile, low fertile Os01g0685900 65 kD Microtubule associated protein Narrow leaf, semi-dwarf Os02g0552600 8-Oxoguanine DNA glycosylase Lethal Os04g0464200 Betaine-aldehyde dehydrogenase (EC 1.2.1.8) (BADH) Low fertility Os04g0680400 Allantoinase (EC 3.5.2.5) Dwarf, low fertility Os05g0318600 Protein kinase domain containing protein Narrow leaf Os05g0548900 Phosphoethanolamine methyltransferase Early heading Os05g0552400 Zn-finger, RING domain containing protein Early heading Os06g0176800 2OG-Fe(II) oxygenase domain containing protein Dark green leaf, dwarf, severely dwarf Os06g0275000 Hd1 Dwarf, early heading Os06g0680500 Glutamate receptor 3.1 precursor (Ligand-gated ion channel 3.1) (AtGLR2) Low fertility Os07g0197100 Hexokinase Dwarf, sterile Os07g0646500 SWIM Zn-finger domain containing protein Late heading Os07g0656500 Protoporphyrin IX Mg-chelatase subunit precursor Lethal, albino, dwarf Os09g0278300 Phosphatidylinositol-4-phosphate 5-kinase family protein Semi-dwarf, dwarf, low tillering, sterile, low fertility Os10g0567100 Chlorophyll b synthase (Fragment) Dark green leaf, pale green leaf, withering, semi-dwarf, severely dwarf, early heading, late heading, low fertility Os12g0127600 WRKY transcription factor 57 Sterile, low fertility Os12g0566000 HCO3-Transporter domain containing protein Severely dwarf Os12g0572500 Protein of unknown function XH domain containing protein Early heading Locus name and description are from RAP data Fig. 3 Tos17 A Hd1 B Tos17 Tos17 Tos17s  2 Tos17 Tos17 Discussion 2 Tos17 2 Tos17s Tos17 Tos17 Tos17 1995 2 2004 2006 2006 2006 2005 Tos17 In this study, we collected a large amount of phenotypic data in seven fields under natural conditions. If phenotypes are observed under other conditions such as drought or temperature stress conditions or under pathogen pressure, phenotypic description of this population would be much more enriched. In addition, the present study evaluated only a limited number of traits easily scored on above-ground organs. Thus, other traits such as roots and seed storage composition remain to be investigated in the future. Expansion of this study to include new traits would enable investigators to find new correlations with disrupted genes. Furthermore, integration of phenotype data with those of microarray experiments, metabolic profiling, and other approaches will be a powerful tool for revealing new aspects of plant physiology. Tos17 http://www.rgrc.dna.affrc.go.jp/