Table S4. The comparison of phenotypic classification used in the mutant collections of TRIM, Tos17 and IRRI-IR64. The plant ontology developed by Gramene ( is also listed.

TRIM Category / TRIM ID / TRIM phenotype / TOS17 ID / TOS17 Class / TOS17 Phenotype / Phenotype ID, IRRI / Observable / PO Term ID / Attribute / PATO Term ID / Trait / TO Term ID / Trait Value
Development / 1 / germination rate / 1 / Germination / Germination rate / IRFGC:0050 / Germination / GRO:0007043 / rate / PATO:0007147 / Germination rate / TO:0000430 / slow
2 / lethal / 2 / Growth / Lethal / IRFGC:0080 / Seedling/vegetative stage / GRO:0007047 / viability / PATO:00000168 / Seedling/vegetative vigor (Vg) / TO:0000296 / yellow lethal
3 / abnormal growth / 3 / Growth / abnormal growth / -- / -- / -- / -- / -- / -- / -- / --
4 / weak / 4 / Growth / Weak / IRFGC:0081 / Seedling/vegetative stage / GRO:0007047 / viability / PATO:00000168 / Seedling/vegetative vigor (Vg) / TO:0000296 / weak
Leaf color / 11 / albino / 11 / Leaf color / Albino / IRFGC:0020 / Leaf blade / PO:0020039 / color / PATO:0000033 / Leaf blade color (LBC) / TO:0000326 / albino
12 / yellow / 12 / Leaf color / Yellow / IRFGC:0021 / Leaf blade / PO:0020039 / color / PATO:0000033 / Leaf blade color (LBC) / TO:0000326 / chlorina
12 / yellow / 12 / Leaf color / Yellow / IRFGC:0030 / Leaf blade / PO:0020039 / color / PATO:0000033 / Leaf blade color (LBC) / TO:0000326 / almost white
13 / dark green / 13 / Leaf color / Deep green leaf / IRFGC:0022 / Leaf blade / PO:0020039 / color / PATO:0000033 / Leaf blade color (LBC) / TO:0000326 / dark green
14 / pale green / 14 / Leaf color / Pale green leaf / IRFGC:0023 / Leaf blade / PO:0020039 / color / PATO:0000033 / Leaf blade color (LBC) / TO:0000326 / light green
15 / bluish green / 15 / Leaf color / Virescent / IRFGC:0024 / Leaf blade / PO:0020039 / color / PATO:0000033 / Leaf blade color (LBC) / TO:0000326 / virescent
16 / stripe / 16 / Leaf color / Stripe / IRFGC:0025 / Leaf blade / PO:0020039 / color / PATO:0000033 / Leaf blade color (LBC) / TO:0000326 / fine stripe
16 / stripe / 16 / Leaf color / Stripe / IRFGC:0027 / Leaf blade / PO:0020039 / color / PATO:0000033 / Leaf blade color (LBC) / TO:0000326 / white stripe
16 / stripe / 16 / Leaf color / Stripe / IRFGC:0028 / Leaf blade / PO:0020039 / color / PATO:0000033 / Leaf blade color (LBC) / TO:0000326 / yellow stripe
16 / stripe / 16 / Leaf color / Stripe / IRFGC:0029 / Leaf blade / PO:0020039 / color / PATO:0000033 / Leaf blade color (LBC) / TO:0000326 / white midrib
16 / stripe / 16 / Leaf color / Stripe / IRFGC:0031 / Leaf blade / PO:0020039 / color / PATO:0000033 / Leaf blade color (LBC) / TO:0000326 / light green stripe
17 / zebra / 17 / Leaf color / Zebra / IRFGC:0026 / Leaf blade / PO:0020039 / color / PATO:0000033 / Leaf blade color (LBC) / TO:0000326 / zebra
18 / others / 18 / Leaf color / Others / IRFGC:0006 / Basal leaf sheath / PO:0020040 / color / PATO:0000033 / Basal leaf sheath color (BLSC) / TO:0000367 / purple
18 / others / 18 / Leaf color / Others / IRFGC:0007 / Basal leaf sheath / PO:0020040 / color / PATO:0000033 / Basal leaf sheath color (BLSC) / TO:0000367 / red
18 / others / 18 / Leaf color / Others / IRFGC:0008 / Basal leaf sheath / PO:0020040 / color / PATO:0000033 / Basal leaf sheath color (BLSC) / TO:0000367 / dark brown
18 / others / 18 / Leaf color / Others / IRFGC:0032 / Leaf blade / PO:0020039 / color / PATO:0000033 / Leaf blade color (LBC) / TO:0000326 / white edge
Leaf morphology / 21 / wide / 21 / Leaf shape / Wide leaf / -- / -- / -- / -- / -- / -- / -- / --
22 / narrow / 22 / Leaf shape / Narrow leaf / IRFGC:0042 / Leaf / PO:0009025 / width / PATO:0000084 / Leaf width / TO:0000492 / narrow
23 / long / 23 / Leaf shape / Long leaf / IRFGC:0033 / Leaf / PO:0009025 / length / PATO:0010077 / Leaf length / TO:0000492 / long
23 / long / 23 / Leaf shape / Long leaf / -- / -- / -- / -- / -- / -- / -- / --
24 / short / 24 / Leaf shape / Short leaf / IRFGC:0034 / Leaf / PO:0009025 / length / PATO:0010077 / Leaf length / TO:0000492 / short
25 / drooping / 25 / Leaf shape / Drooping leaf / -- / -- / -- / -- / -- / -- / -- / --
26 / rolled / 26 / Leaf shape / Rolled leaf / IRFGC:0037 / Leaf / PO:0009025 / related trait / Unknown / Leaf related trait / Unknown / semi-rolled
26 / rolled / 26 / Leaf shape / Rolled leaf / IRFGC:0036 / Leaf / PO:0009025 / related trait / Unknown / Leaf related trait / Unknown / rolled
27 / spiral / 27 / Leaf shape / Spiral / IRFGC:0038 / Leaf / PO:0009025 / related trait / Unknown / Leaf related trait / Unknown / crinkled
28 / brittle / 28 / Leaf shape / Brittle / IRFGC:0085 / Stem / PO:0009047 / strength / Unknown / Stem strength / TO:0000051 / brittle
29 / thin lamina joint / 29 / Leaf shape / Lamina joint / IRFGC:0052 / Leaf / PO:0009025 / shape / PATO:0000130 / Leaf shape / TO:0000492 / --
30 / white and withering leaf tip / 30 / Leaf shape / Withering / IRFGC:0040 / Leaf / PO:0009025 / senescence / Unknown / Leaf senescence (Sen) / TO:0000249 / intermediate
30 / white and withering leaf tip / 30 / Leaf shape / Withering / IRFGC:0035 / Leaf / PO:0009025 / related trait / Unknown / Leaf related trait / Unknown / dried leaves
30 / white and withering leaf tip / 30 / Leaf shape / Withering / IRFGC:0039 / Leaf / PO:0009025 / related trait / Unknown / Leaf related trait / Unknown / wilted upper half
31 / others / 31 / Leaf shape / Others / IRFGC:0015 / Flag leaf / PO:0020103 / length / PATO:0010077 / Flag leaf length / Unknown / long
Plant type / 41 / semidwarf / 41 / Height / Semidwarf / IRFGC:0063 / Plant / PO:0009011 / height / PATO:0000074 / Plant height (Ht) / TO:0000207 / semidwarf
42 / dwarf / 42 / Height / Dwarf / IRFGC:0064 / Plant / PO:0009011 / height / PATO:0000074 / Plant height (Ht) / TO:0000207 / dwarf
43 / severe dwarf / 43 / Height / Extremely dwarf / IRFGC:0065 / Plant / PO:0009011 / height / PATO:0000074 / Plant height (Ht) / TO:0000207 / extreme dwarf
44 / long culm / 44 / Height / Long culm / IRFGC:0066 / Plant / PO:0009011 / height / PATO:0000074 / Plant height (Ht) / TO:0000207 / tall
45 / erect / 45 / Height / Erect / IRFGC:0009 / Culm / PO:0009047 / angle / PATO:0000124 / Culm angle (CmA) / TO:0000427 / erect
45 / erect / 45 / Height / Erect / IRFGC:0019 / Leaf / PO:0009025 / angle / PATO:0000124 / Leaf angle (LA) / TO:0000206 / erect
46 / lazy / 46 / Height / Lazy / IRFGC:0011 / Culm / PO:0009047 / angle / PATO:0000124 / Culm angle (CmA) / TO:0000427 / procumbent
47 / thin culm / 47 / Height / Thin culm / IRFGC:0013 / Culm / PO:0009047 / diameter / Unknown / Culm diameter / Unknown / fine
48 / thick culm / 48 / Height / Thick culm / -- / -- / -- / -- / -- / -- / -- / --
49 / others / -- / -- / IRFGC:0014 / Culm / PO:0009047 / senescence / Unknown / Culm senescence / Unknown / premature
49 / others / -- / -- / IRFGC:0086 / Stem / PO:0009047 / strength / Unknown / Stem strength / TO:0000051 / stiff
Lesion / 51 / lesion mimic / 51 / Mimic response / Spl/Lesion mimic / IRFGC:0046 / Plant / PO:0009011 / response, mimic / Unknown / mimic response / TO:0000063 / lesion mimic-spl6 type
51 / lesion mimic / 51 / Mimic response / Spl/Lesion mimic / IRFGC:0047 / Plant / PO:0009011 / response, mimic / Unknown / mimic response / TO:0000063 / lesion mimic-uncharacterized
51 / lesion mimic / 51 / Mimic response / Spl/Lesion mimic / IRFGC:0048 / Plant / PO:0009011 / response, mimic / Unknown / mimic response / TO:0000063 / lesion mimic-spl11 type
51 / lesion mimic / 51 / Mimic response / Spl/Lesion mimic / IRFGC:0049 / Plant / PO:0009011 / response, mimic / Unknown / mimic response / TO:0000063 / lesion mimic-spl1 type
Tiller / 61 / high-position tiller / 61 / Tillering / High tillering / IRFGC:0088 / Tiller / PO:0006343 / yield / PATO:00000153 / Tillering ability (TI) / TO:0000329 / very high
62 / low-position tiller / 62 / Tillering / Low tillering / IRFGC:0089 / Tiller / PO:0006343 / yield / PATO:00000153 / Tillering ability (TI) / TO:0000329 / low
62 / low-position tiller / 62 / Tillering / Low tillering / IRFGC:0090 / Tiller / PO:0006343 / yield / PATO:00000153 / Tillering ability (TI) / TO:0000329 / very low
63 / monoculm / 63 / Tillering / Lazy / IRFGC:0010 / Culm / PO:0009047 / angle / PATO:0000124 / Culm angle (CmA) / TO:0000427 / spreading
64 / few panicle / Tillering-- / -- / -- / Tiller / -- / -- / -- / -- / -- / --
65 / Many panicle / Tillering / -- / -- / Tiller / -- / -- / -- / -- / -- / --
Heading date / 71 / early heading / 65 / Heading date / Early heading / IRFGC:0016 / Heading / GRO:0007044 / relative time / PATO:0000147 / Heading time / TO:0000137 / early
72 / late heading / 66 / Heading date / Late heading / IRFGC:0017 / Heading / GRO:0007044 / relative time / PATO:0000147 / Heading time / TO:0000137 / late
73 / no heading / 67 / Heading date / No heading / -- / -- / -- / -- / -- / -- / -- / --
Glume / 75 / abnormal hull / 71 / Flower / Abnormal hull / IRFGC:0069 / Seed / PO:0009010 / related trait / Unknown / Seed related trait / TO:0000184 / open hull
75 / abnormal hull / 71 / Flower / Abnormal hull / IRFGC:0070 / Seed / PO:0009010 / related trait / Unknown / Seed related trait / TO:0000184 / beaked hull
75 / abnormal hull / 71 / Flower / Abnormal hull / IRFGC:0071 / Seed / PO:0009010 / related trait / Unknown / Seed related trait / TO:0000184 / half hull
75 / abnormal hull / 71 / Flower / Abnormal hull / IRFGC:0072 / Seed / PO:0009010 / related trait / Unknown / Seed related trait / TO:0000184 / double palea
75 / abnormal hull / 71 / Flower / Abnormal hull / IRFGC:0073 / Seed / PO:0009010 / related trait / Unknown / Seed related trait / TO:0000184 / multiple lemma and palea
75 / abnormal hull / 71 / Flower / Abnormal hull / IRFGC:0074 / Seed / PO:0009010 / related trait / Unknown / Seed related trait / TO:0000184 / depressed palea
75 / abnormal hull / 71 / Flower / Abnormal hull / IRFGC:0075 / Seed / PO:0009010 / related trait / Unknown / Seed related trait / TO:0000184 / triangular
76 / abnormal floral organ / 72 / Flower / Abnormal floral organ / IRFGC:0051 / Shoot / PO:0009006 / abnormal / PATO:0000004 / Shoot growth / TO:0000077 / abnormal
76 / abnormal floral organ / 72 / Flower / Abnormal floral organ / IRFGC:0053 / Floret / PO:0006318 / shape / PATO:0000130 / Abnormal floral organ / TO:0000499 / abnormal
77 / awn / 73 / Flower / Awn / IRFGC:0001 / Awning / PO:0006032 / shape / PATO:0000130 / Awning (An) / TO:0000072 / long & partly awned
77 / awn / 73 / Flower / Awn / IRFGC:0002 / Awning / PO:0006032 / shape / PATO:0000130 / Awning (An) / TO:0000072 / short & partly awned
77 / awn / 73 / Flower / Awn / IRFGC:0003 / Awning / PO:0006032 / shape / PATO:0000130 / Awning (An) / TO:0000072 / awned
77 / awn / 73 / Flower / Awn / IRFGC:0004 / Awning / PO:0006032 / shape / PATO:0000130 / Awning (An) / TO:0000072 / long awn
77 / awn / 73 / Flower / Awn / IRFGC:0005 / Awning / PO:0006032 / shape / PATO:0000130 / Awning (An) / TO:0000072 / short awn
78 / abnormal glume / 74 / Flower / Abnormal hull / IRFGC:0076 / Seed / PO:0009010 / related trait / Unknown / Seed related trait / TO:0000184 / extra glume
79 / abnormal lemma color / 75 / Flower / Abnormal lemma color / -- / -- / -- / -- / -- / -- / -- / --
Panicle / 81 / long panicle / 81 / Panicle / Long panicle / -- / -- / -- / -- / -- / -- / -- / --
82 / short panicle / 82 / Panicle / Short panicle / IRFGC:0057 / Panicle / PO:0009049 / length / PATO:0010077 / Panicle length (PnL) / TO:0000040 / short
83 / lax panicle / 83 / Panicle / Lax panicle / IRFGC:0061 / Panicle / PO:0009049 / type / Unknown / Panicle type (PnT) / TO:0000089 / open
84 / dense panicle / 84 / Panicle / Dense panicle / IRFGC:0062 / Panicle / PO:0009049 / type / Unknown / Panicle type (PnT) / TO:0000089 / compact
85 / vivipary / 85 / Panicle / Vivipary / IRFGC:0054 / Panicle / PO:0009049 / status / Unknown / Panicle status / Unknown / viviparous
86 / shattering / 86 / Panicle / Shattering / IRFGC:0059 / Panicle / PO:0009049 / threshability / PATO:0300094 / Panicle threshability (Thr) / TO:0000406 / loose
86 / shattering / 86 / Panicle / Shattering / IRFGC:0060 / Panicle / PO:0009049 / threshability / PATO:0300094 / Panicle threshability (Thr) / TO:0000406 / easy
87 / neck leaf / 87 / Panicle / Neck leaf / IRFGC:0058 / Panicle / PO:0009049 / related trait / Unknown / panicle related trait / Unknown / leafy head
87 / neck leaf / 87 / Panicle / Neck leaf / IRFGC:0056 / Panicle / PO:0009049 / exsertion / Unknown / Panicle exsertion (Exs) / TO:0000165 / partly exserted
88 / abnormal panicle / 88 / Panicle / Abnormal panicle shape / IRFGC:0091 / Internode / PO:0020142 / length / PATO:0010077 / (Uppermost) internode length / TO:0000145 / elongated
89 / others / 89 / Panicle / Abnormal panicle shape / IRFGC:0018 / Internode / PO:0020142 / length / PATO:0010077 / (Uppermost) internode length / TO:0000145 / short
89 / others / 89 / Panicle / Abnormal panicle shape / IRFGC:0055 / Panicle / PO:0009049 / axis / Unknown / Panicle axis (PnA) / TO:0000342 / straight
Fertility / 91 / sterile / 91 / Sterility / Sterile / IRFGC:0082 / Spikelet / PO:0009051 / fertility / PATO:00000171 / Spikelet fertility (SpFert) / TO:0000180 / completely sterile
91 / sterile / 91 / Sterility / Sterile / IRFGC:0083 / Spikelet / PO:0009051 / fertility / PATO:00000171 / Spikelet fertility (SpFert) / TO:0000180 / highly sterile
92 / low fertility / 92 / Sterility / Low Fertile / IRFGC:0084 / Spikelet / PO:0009051 / fertility / PATO:00000171 / Spikelet fertility (SpFert) / TO:0000180 / partly sterile
Grain / 101 / large grain / 101 / Seed / Large grain / IRFGC:0012 / Culm / PO:0009047 / diameter / Unknown / Culm diameter / Unknown / big
101 / large grain / 101 / Seed / Large grain / IRFGC:0077 / Seed / PO:0009010 / size / PATO:0000058 / Seed size / TO:0000391 / big
102 / small grain / 102 / Seed / Small grain / IRFGC:0078 / Seed / PO:0009010 / size / PATO:0000058 / Seed size / TO:0000391 / small
102 / small grain / 102 / Seed / Small grain / IRFGC:0041 / Leaf / PO:0009025 / width / PATO:0000084 / Leaf width / TO:0000492 / wide
102 / small grain / 102 / Seed / Small grain / IRFGC:0079 / Seed / PO:0009010 / width / PATO:0000084 / Seed width / TO:0000149 / wide
103 / slender grain / 103 / Seed / Slender grain / -- / -- / -- / -- / -- / -- / -- / --
104 / others / 104 / Seed / Others / IRFGC:0068 / Seed / PO:0009010 / length / PATO:0010077 / Seed length / TO:0000146 / short
104 / others / 104 / Seed / Others / IRFGC:0043 / Floret / PO:0006318 / color / PATO:0000033 / Lemma and palea color (LmPC) / TO:0000264 / brown
104 / others / 104 / Seed / Others / IRFGC:0044 / Floret / PO:0006318 / color / PATO:0000033 / Lemma and palea color (LmPC) / TO:0000264 / gold
104 / others / 104 / Seed / Others / IRFGC:0045 / Floret / PO:0006318 / color / PATO:0000033 / Lemma and palea color (LmPC) / TO:0000264 / brown spots on straw
104 / others / 104 / Seed / Others / IRFGC:0067 / Seed / PO:0009010 / length / PATO:0010077 / Seed length / TO:0000146 / long
104 / others / 104 / Seed / Others / IRFGC:0087 / Sterile lemma / PO:0009040 / length / PATO:0010077 / Sterile lemma length (SLmL) / TO:0000240 / long