Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The Heading Date (day) Distribution in Indica All Population:

Phenotype Information Table:

Note: -9 means missing value.

Cultivar Name Cultivar ID Subpopulation Heading Date (day)
Sadu-cho C001 Indica I 80
Shan-Huang_Zhan-2-1_ C006 Indica Intermediate 91
Shan-Huang_Zhan-2-2_ C007 Indica Intermediate 91
Swarna C008 Indica Intermediate 143
MOROBEREKAN C009 Indica Intermediate 93
MILYANG_23 C011 Indica II 109
Aijiaonante C019 Indica I 72
Guangluai-4-1 C020 Indica I 71
xiangaizao10 C021 Indica I 71
JinnanteB C022 Indica I 70
zhenshan97B-1 C024 Indica I 74
Qingsiai16B C025 Indica Intermediate 90
Dianrui409B C027 Indica Intermediate 89
88B-1 C030 Indica Intermediate 92
88B-2 C031 Indica Intermediate 95
Lucaihao C033 Indica I 73
Shufeng101 C036 Indica Intermediate 85
Chengduai3hao C037 Indica I 85
Sankecui C038 Indica Intermediate 93
Gongju73 C039 Indica I 86
Jiabala C040 Indica I 88
Taishannuo C041 Indica I 91
Guichao2hao C042 Indica Intermediate 92
Huke3hao C043 Indica I 94
Teqingxuanhui C044 Indica Intermediate 93
Huangsiguizhan C045 Indica Intermediate 90
Xiangwanxian3hao C046 Indica Intermediate 91
Hanmadao-2 C047 Indica I 97
Jinyou1hao C049 Indica Intermediate 93
Chengnongshuijing C050 Indica II 100
Momi C053 Indica Intermediate 110
Sanbaili C055 Indica I 60
Liusha1hao C058 Indica I 87
Bawangbian1 C059 Indica I 95
Dongtingwanxian C060 Indica I 93
Yangdao2hao C061 Indica II 106
WH62 C062 Indica I 94
Hongwan1hao C065 Indica Intermediate 121
Liushizao C066 Indica I 74
Taizhongxianxuan2 C068 Indica II 93
Dangyu5hao C069 Indica II 100
Nantehao C072 Indica I 85
Esiniu C073 Indica I 89
Benbanggu-1 C076 Indica I 90
Benbanggu-2 C077 Indica I 88
Qitoubaigu C078 Indica Intermediate 88
Hanmadao-1 C080 Indica I 91
Heidu4 C081 Indica I 89
Nangaogu-2 C088 Indica I 110
Sanlicun C090 Indica Intermediate 91
Meihuanuo-1 C091 Indica I 88
Meihuanuo-2 C092 Indica I 88
Menjiagao1 C094 Indica Intermediate 108
Xiaohonggu C095 Indica I 112
Jinxibai-1 C096 Indica Intermediate 110
Jinbaoyin C097 Indica Intermediate 114
Hongainuo C098 Indica Intermediate 114
WH099 C099 Indica Intermediate 114
WH100 C100 Indica Intermediate 101
Qiyuexian C102 Indica Intermediate 148
Mamagu-1 C104 Indica I 92
WH105 C105 Indica Intermediate 97
Mowanggunei-2 C107 Indica III 112
Mamagu-2 C108 Indica I 83
WH109 C109 Indica I 88
Xianggu C110 Indica I 107
Jinnante43B C112 Indica I 73
Xiangzaoxian7hao C113 Indica Intermediate 60
80B C114 Indica Intermediate 61
WH115 C115 Indica II 73
Jiangnongzao1hao C117 Indica Intermediate 88
Gu154 C118 Indica II 96
XiangaiB C121 Indica Intermediate 91
Aituogu151 C122 Indica I 93
menjiading2 C124 Indica Intermediate 92
Jiefangxian C125 Indica I 84
Baikehualuo C127 Indica I 84
Liuyezhan C128 Indica I 86
Aihechi C129 Indica Intermediate 110
Xuanenchangtan C131 Indica I 84
Jinzhinuo C132 Indica Intermediate 104
Xibaizhan C135 Indica I 92
Zegu C136 Indica I 88
WH139 C139 Indica I 99
Wuzuhonggu C140 Indica I 111
Nangaogu-1 C141 Indica I 121
Mowanggunei-1 C142 Indica III 113
Qitougu C143 Indica I 103
Zhenshan97B C145 Indica I 72
Minghui63 C147 Indica II 100
9311 C148 Indica II 86
Nanjing11 C151 Indica I 92
Erjiunan1hao C155 Indica I 69
ChaoyangyihaoB C156 Indica I 72
L301B C157 Indica I 69
Guangluai15 C158 Indica I 73
ZhuzhenB C159 Indica I 88
Baoxie-7B C160 Indica Intermediate 75
Gzhenshan97B C161 Indica I 85
Nanxiongzaoyou C162 Indica Intermediate 59
Zaoshuxianghei C163 Indica II 89
IR661-1 C164 Indica II 85
Nanjing11-2 C165 Indica I 87
Gui630 C166 Indica Intermediate 89
76--1 C167 Indica Intermediate 94
Xugunuo C168 Indica Intermediate 92
Taizhongzailai1 C169 Indica Intermediate 97
Xiangwanxian1hao C170 Indica I 91
Aimakang C173 Indica I 89
JWR221 C174 Indica II 104
Zhengxian232 C175 Indica Intermediate 103
Chenwan3hao C176 Indica Intermediate 124
Aimi C178 Indica I 97
Wanlixian C180 Indica I 84
Hengxianliangchun C182 Indica I 88
Leihuozhan C183 Indica I 86
Baikezaohe C184 Indica I 89
Xiangdao C190 Indica I 93
Younian C191 Indica I 99
Wukezhan C192 Indica Intermediate 149
Zhongnong4hao C193 Indica I 83
Minbeiwanxian C194 Indica Intermediate 104
Maweinian C197 Indica I 89
Zinuo C198 Indica Intermediate 91
Beizinuo C199 Indica I 104
Biwusheng C200 Indica I 110
Yizhixiang C201 Indica Intermediate 110
Xiaobaimi C202 Indica I 89
Zaoxian240 C203 Indica I 70
Mayang_Khang W001 Indica I 87
BERLIN W009 Indica III 115
Warrangal_Culture_1252 W023 Indica III 105
Won_Son_Zo_No._11 W026 Indica I 92
Ai_Chueh_Ta_Pai_Ku W029 Indica Intermediate 97
Thang_10 W030 Indica Intermediate 109
Sipirasikkam W031 Indica I 90
TJ W032 Indica I 88
PD_46 W033 Indica I 82
K8C-263-3 W035 Indica Intermediate 105
Chun_118-33 W036 Indica I 105
Manga_Kely_694 W037 Indica Intermediate 110
Nam_Dawk_Mai W039 Indica I 91
INIAP_7 W040 Indica II 109
Red W042 Indica Intermediate 112
Dichroa_Alef_Uslkij W043 Indica Intermediate 110
BKN_6987-68-14 W044 Indica II 107
IR_9660-48-1-1-2 W046 Indica II 105
RP2151-173-1-8 W051 Indica II 55
Toga W054 Indica Intermediate 106
Kao_Chio_Lin_Chou W058 Indica I 85
IR_238 W066 Indica Intermediate 95
Shui_Ya_Jien W070 Indica Intermediate 99
AKP_4 W071 Indica Intermediate 53
IR_2061-214-2-3 W073 Indica II 83
TAINUNG_45 W074 Indica Intermediate 122
Sapundali_Local W075 Indica Intermediate 95
B805D-MR-16-8-3 W078 Indica Intermediate 121
UZ_ROS_59 W080 Indica I 85
CNTLR80076-44-1-1-1 W083 Indica Intermediate 94
IR_58614-B-B-8-2 W084 Indica Intermediate 95
KECHENGNUO_NO._4 W085 Indica Intermediate 89
4484 W086 Indica II 91
YOU-I_B W087 Indica I 65
Egyptian_Wild_Type W089 Indica III 85
Srav_Prapay W093 Indica III 84
AMANE W101 Indica Intermediate 89
JP_5 W107 Indica Intermediate 120
Sereno W111 Indica III 114
ARC_10633 W112 Indica III 114
Heo_Trang W114 Indica III 122
Kin_Shan_Zim W124 Indica I 77
Pan_Ju W126 Indica I 89
Hsin_Hsing_Pai_Ku W132 Indica I 89
TD_70 W133 Indica Intermediate 95
Shimla_Early W135 Indica Intermediate 105
CM1;_HAIPONG W137 Indica Intermediate 104
4595 W138 Indica I 79
Ao_Chiu_2_Hao W144 Indica I 105
GUYANE_1 W145 Indica Intermediate 114
10340 W146 Indica I 77
BR11 W147 Indica Intermediate 100
BR24 W148 Indica Intermediate 107
93072 W149 Indica Intermediate 93
108S W150 Indica II 112
C418 W151 Indica II 81
CDR22 W152 Indica II 101
Chenghui448 W153 Indica II 98
Fengaizhan W154 Indica II 87
Gang46B W155 Indica Intermediate 83
Gumei2hao W156 Indica I 91
Huajingxian74 W157 Indica Intermediate 94
R644 W159 Indica II 90
Y134 W161 Indica II 82
Yuexiangzhan W163 Indica Intermediate 89
Zaoxian14 W164 Indica Intermediate 76
Zhong413 W165 Indica Intermediate 91
Zhongyouzao81 W166 Indica Intermediate 103
Zihui100 W167 Indica Intermediate 107
Bg90-2 W168 Indica II 112
IR72 W169 Indica II 98
PR106 W170 Indica II 95
TKM9 W171 Indica Intermediate 89
Amo13_(Sana) W172 Indica II 96
Gayabyeo W174 Indica II 97
Milyang23 W176 Indica II 105
MR185 W177 Indica II 102
Manawthukha W178 Indica III 119
Shwe_Thwe_Yin_Hyv W179 Indica II 96
Bg300 W180 Indica Intermediate 91
Bg94-1 W181 Indica Intermediate 107
CR203 W182 Indica II 100
OM997 W183 Indica II 110
PSB_RC_28 W184 Indica II 94
PSB_RC_66 W185 Indica II 112
TEQING W186 Indica Intermediate 92
IR68552-55-3-2 W187 Indica Intermediate 92
IR66897B W188 Indica II 92
IR58025B W189 Indica II 96
F6 W194 Indica II 85
452 W195 Indica II 98
Ai-Zi-DAO W197 Indica II 94
Babaomi W198 Indica Intermediate 108
Diantun502 W199 Indica Intermediate 116
Heiheaihui W200 Indica Intermediate 101
Jiangxisimiao W201 Indica Intermediate 98
Laohudao W202 Indica Intermediate 99
Linjintangdao W203 Indica Intermediate 105
Mengguandamagu W204 Indica I 93
Pengshantieganzhan W205 Indica I 93
Wumanggaonuo W206 Indica Intermediate 110
Khao_Daeng W210 Indica I 87
Basmati370 W211 Indica II 94
Bhavani W212 Indica Intermediate 105
IR50 W213 Indica Intermediate 116
Type3 W216 Indica II 108
IRAT352 W217 Indica Intermediate 114
TB154E-TB-2 W218 Indica Intermediate 116
MR77_(seberang) W221 Indica Intermediate 120
ir6 W222 Indica II 105
At354 W223 Indica II 90
BG304 W224 Indica II 91
OM1706 W227 Indica Intermediate 92
OM1723 W228 Indica II 105
X21 W229 Indica II 108
X22 W230 Indica II 117
X23 W231 Indica II 107
C70 W233 Indica Intermediate 93
Q5 W234 Indica Intermediate 94
Suiyangnian W235 Indica I 89
Pokhreli W236 Indica II 94
Govnd W237 Indica II 105
UPR191-66 W238 Indica II 82
ASD18 W239 Indica Intermediate 99
TGMS29 W240 Indica Intermediate 93
Phalguna W241 Indica II 102
Ajaya W242 Indica Intermediate 115
Dodda W243 Indica II 98
Palung_2 W244 Indica II 98
TKM6 W245 Indica Intermediate 92
RUSTYLATE/Zhong_413 W246 Indica Intermediate 105
Yenfangghu W247 Indica I 92
Heimichut W248 Indica I 92
Up15 W259 Indica II 96
Bintapan W262 Indica I 69
SADAJIRA-19-303 W263 Indica Intermediate 112
CHOROFA W264 Indica Intermediate 87
La110 W265 Indica Intermediate 88
Yunjiang35 W266 Indica III 124
Yunhui72 W267 Indica Intermediate 83
Wudadaozhong W268 Indica Intermediate 89
IR65600-27-1-2-2 W269 Indica Intermediate 88
Yetuozai W270 Indica Intermediate 85
P59279 W271 Indica Intermediate 78
Tsao_wan_ching W272 Indica Intermediate 117
Er_chiu_ching W274 Indica I 66
Pathma_wee W276 Indica III 109
Ma_ba_you_zhan W282 Indica Intermediate 124
IR_661-1-140-3-117 W289 Indica II 99
IR_2071-625-1-252 W291 Indica II 105
IR_8 W293 Indica II 113
LEBONNET W295 Indica II 106
IR_36 W298 Indica II 104
JAYA W299 Indica Intermediate 93
IR_64 W301 Indica II 105
AGNO_(PSBRC28) W307 Indica II 94
PSBRC82 W308 Indica II 120
NSICRC122 W309 Indica II 120
BRRI_DHAN_29 W310 Indica Intermediate 111
PR_116 W311 Indica II 111
CIGEULIS W312 Indica II 105
OM_2517 W313 Indica II 94
BRRI_DHAN_28 W314 Indica II 95
CIBOGO W315 Indica II 105
NEDA W316 Indica II 92
CIHERANG W317 Indica II 106
Qiuqianbai W318 Indica I 77
Wenxiangnuo W320 Indica Intermediate 124
Laozaogu W321 Indica III 117
Lengshuinuo W322 Indica Intermediate 93

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0423583513 sf0423398370 4 23583513 1.61E-17 NA
vg0721303635 sf0721302642 7 21303635 1.74E-17 NA
vg0724065640 sf0724064646 7 24065640 4.44E-17 NA
vg0132244134 sf0132243090 1 32244134 1.30E-16 NA
vg0825399481 sf0825396767 8 25399481 2.97E-16 NA
vg1120635547 sf1120169468 11 20635547 1.23E-13 2.88E-06
vg1116565892 sf1116100770 11 16565892 3.59E-12 4.00E-06
vg0802053469 sf0802052472 8 2053469 3.97E-10 8.47E-08
vg0804091298 sf0804090301 8 4091298 5.60E-10 2.38E-06
vg0802712498 sf0802711501 8 2712498 5.76E-10 9.02E-07
vg0922312055 sf0922311574 9 22312055 5.83E-10 NA
vg0601612838 sf0601611839 6 1612838 NA 2.20E-08
vg0600880921 sf0600879922 6 880921 NA 1.53E-07
vg0913675210 sf0913674209 9 13675210 NA 3.52E-07
vg0312437905 sf0312436623 3 12437905 NA 5.53E-07
vg0421937587 sf0421765638 4 21937587 NA 9.25E-07
vg0601074897 sf0601073898 6 1074897 NA 1.38E-06
vg0701510236 sf0701509236 7 1510236 NA 1.85E-06
vg0804004561 sf0804003564 8 4004561 NA 2.28E-06
vg0704291672 sf0704290673 7 4291672 NA 3.03E-06
vg0140349681 sf0140348638 1 40349681 NA 3.55E-06
vg1117529722 sf1117063577 11 17529722 NA 4.98E-06