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 Grain thickness Distribution in Indica All Population:

Phenotype Information Table:

Note: -9 means missing value.

Cultivar Name Cultivar ID Subpopulation Grain thickness
Sadu-cho C001 Indica I 1.96
Shan-Huang_Zhan-2-1_ C006 Indica Intermediate 1.69
Shan-Huang_Zhan-2-2_ C007 Indica Intermediate 1.72
Swarna C008 Indica Intermediate 1.75
MOROBEREKAN C009 Indica Intermediate 2.06
MILYANG_23 C011 Indica II 1.94
Aijiaonante C019 Indica I 1.96
Guangluai-4-1 C020 Indica I 2.1
xiangaizao10 C021 Indica I 1.98
JinnanteB C022 Indica I 1.83
zhenshan97B-1 C024 Indica I 2.0
Qingsiai16B C025 Indica Intermediate 1.94
Dianrui409B C027 Indica Intermediate 1.99
88B-1 C030 Indica Intermediate 2.01
88B-2 C031 Indica Intermediate 1.87
Lucaihao C033 Indica I 2.02
Shufeng101 C036 Indica Intermediate 2.04
Chengduai3hao C037 Indica I 2.02
Sankecui C038 Indica Intermediate 2.04
Gongju73 C039 Indica I 2.0
Jiabala C040 Indica I 1.96
Taishannuo C041 Indica I 1.98
Guichao2hao C042 Indica Intermediate 2.18
Huke3hao C043 Indica I 1.98
Teqingxuanhui C044 Indica Intermediate 2.0
Huangsiguizhan C045 Indica Intermediate 1.81
Xiangwanxian3hao C046 Indica Intermediate 1.9
Hanmadao-2 C047 Indica I 2.03
Jinyou1hao C049 Indica Intermediate 1.94
Chengnongshuijing C050 Indica II 1.87
Momi C053 Indica Intermediate 1.91
Sanbaili C055 Indica I 2.0
Liusha1hao C058 Indica I 1.99
Bawangbian1 C059 Indica I 2.03
Dongtingwanxian C060 Indica I 1.94
Yangdao2hao C061 Indica II 1.99
WH62 C062 Indica I 2.27
Hongwan1hao C065 Indica Intermediate 2.05
Liushizao C066 Indica I 2.08
Taizhongxianxuan2 C068 Indica II 1.88
Dangyu5hao C069 Indica II 1.94
Nantehao C072 Indica I 2.08
Esiniu C073 Indica I 1.89
Benbanggu-1 C076 Indica I 2.16
Benbanggu-2 C077 Indica I 2.01
Qitoubaigu C078 Indica Intermediate 2.07
Hanmadao-1 C080 Indica I 2.01
Heidu4 C081 Indica I 2.03
Nangaogu-2 C088 Indica I 2.2
Sanlicun C090 Indica Intermediate 2.04
Meihuanuo-1 C091 Indica I 1.98
Meihuanuo-2 C092 Indica I 1.94
Menjiagao1 C094 Indica Intermediate 2.04
Xiaohonggu C095 Indica I 2.02
Jinxibai-1 C096 Indica Intermediate 2.02
Jinbaoyin C097 Indica Intermediate 1.82
Hongainuo C098 Indica Intermediate 1.94
WH099 C099 Indica Intermediate 2.01
WH100 C100 Indica Intermediate 1.97
Qiyuexian C102 Indica Intermediate 1.99
Mamagu-1 C104 Indica I 1.95
WH105 C105 Indica Intermediate 1.96
Mowanggunei-2 C107 Indica III 2.06
Mamagu-2 C108 Indica I 2.18
WH109 C109 Indica I 1.92
Xianggu C110 Indica I 1.96
Jinnante43B C112 Indica I 1.91
Xiangzaoxian7hao C113 Indica Intermediate 1.9
80B C114 Indica Intermediate 1.94
WH115 C115 Indica II 1.96
Jiangnongzao1hao C117 Indica Intermediate 2.11
Gu154 C118 Indica II 1.82
XiangaiB C121 Indica Intermediate 2.03
Aituogu151 C122 Indica I 2.0
menjiading2 C124 Indica Intermediate 2.02
Jiefangxian C125 Indica I 2.25
Baikehualuo C127 Indica I 2.04
Liuyezhan C128 Indica I 2.02
Aihechi C129 Indica Intermediate 1.98
Xuanenchangtan C131 Indica I 1.93
Jinzhinuo C132 Indica Intermediate 2.09
Xibaizhan C135 Indica I 1.94
Zegu C136 Indica I 2.07
WH139 C139 Indica I 1.96
Wuzuhonggu C140 Indica I 1.98
Nangaogu-1 C141 Indica I 1.92
Mowanggunei-1 C142 Indica III 2.02
Qitougu C143 Indica I 1.96
Zhenshan97B C145 Indica I 2.0
Minghui63 C147 Indica II 1.95
9311 C148 Indica II 2.06
Nanjing11 C151 Indica I 2.0
Erjiunan1hao C155 Indica I 2.1
ChaoyangyihaoB C156 Indica I 1.98
L301B C157 Indica I 1.85
Guangluai15 C158 Indica I 1.97
ZhuzhenB C159 Indica I 2.15
Baoxie-7B C160 Indica Intermediate 1.95
Gzhenshan97B C161 Indica I 2.14
Nanxiongzaoyou C162 Indica Intermediate 1.98
Zaoshuxianghei C163 Indica II 2.0
IR661-1 C164 Indica II 2.03
Nanjing11-2 C165 Indica I 2.11
Gui630 C166 Indica Intermediate 2.09
76--1 C167 Indica Intermediate 2.19
Xugunuo C168 Indica Intermediate 2.19
Taizhongzailai1 C169 Indica Intermediate 1.97
Xiangwanxian1hao C170 Indica I 1.97
Aimakang C173 Indica I 2.05
JWR221 C174 Indica II 2.11
Zhengxian232 C175 Indica Intermediate 1.87
Chenwan3hao C176 Indica Intermediate 2.1
Aimi C178 Indica I 1.98
Wanlixian C180 Indica I 2.0
Hengxianliangchun C182 Indica I 2.03
Leihuozhan C183 Indica I 2.05
Baikezaohe C184 Indica I 2.1
Xiangdao C190 Indica I 1.96
Younian C191 Indica I 2.08
Wukezhan C192 Indica Intermediate 1.97
Zhongnong4hao C193 Indica I 1.99
Minbeiwanxian C194 Indica Intermediate 1.93
Maweinian C197 Indica I 1.99
Zinuo C198 Indica Intermediate 2.07
Beizinuo C199 Indica I 1.94
Biwusheng C200 Indica I 1.94
Yizhixiang C201 Indica Intermediate 1.92
Xiaobaimi C202 Indica I 2.03
Zaoxian240 C203 Indica I 2.1
Mayang_Khang W001 Indica I 2.09
BERLIN W009 Indica III 2.05
Warrangal_Culture_1252 W023 Indica III 1.83
Won_Son_Zo_No._11 W026 Indica I 1.99
Ai_Chueh_Ta_Pai_Ku W029 Indica Intermediate 2.03
Thang_10 W030 Indica Intermediate 1.84
Sipirasikkam W031 Indica I 1.87
TJ W032 Indica I 1.84
PD_46 W033 Indica I 1.99
K8C-263-3 W035 Indica Intermediate 1.99
Chun_118-33 W036 Indica I 1.99
Manga_Kely_694 W037 Indica Intermediate 2.07
Nam_Dawk_Mai W039 Indica I 2.11
INIAP_7 W040 Indica II 1.98
Red W042 Indica Intermediate 2.07
Dichroa_Alef_Uslkij W043 Indica Intermediate 1.89
BKN_6987-68-14 W044 Indica II 2.09
IR_9660-48-1-1-2 W046 Indica II 1.9
RP2151-173-1-8 W051 Indica II 2.02
Toga W054 Indica Intermediate 1.92
Kao_Chio_Lin_Chou W058 Indica I 2.04
IR_238 W066 Indica Intermediate 1.89
Shui_Ya_Jien W070 Indica Intermediate 1.83
AKP_4 W071 Indica Intermediate 1.96
IR_2061-214-2-3 W073 Indica II 1.9
TAINUNG_45 W074 Indica Intermediate 2.23
Sapundali_Local W075 Indica Intermediate 2.0
B805D-MR-16-8-3 W078 Indica Intermediate 2.07
UZ_ROS_59 W080 Indica I 1.96
CNTLR80076-44-1-1-1 W083 Indica Intermediate 2.02
IR_58614-B-B-8-2 W084 Indica Intermediate 1.98
KECHENGNUO_NO._4 W085 Indica Intermediate 1.95
4484 W086 Indica II 1.89
YOU-I_B W087 Indica I 1.98
Egyptian_Wild_Type W089 Indica III 1.83
Srav_Prapay W093 Indica III 1.72
AMANE W101 Indica Intermediate 2.16
JP_5 W107 Indica Intermediate 2.19
Sereno W111 Indica III 1.98
ARC_10633 W112 Indica III 2.03
Heo_Trang W114 Indica III 1.9
Kin_Shan_Zim W124 Indica I 1.82
Pan_Ju W126 Indica I 1.9
Hsin_Hsing_Pai_Ku W132 Indica I 1.91
TD_70 W133 Indica Intermediate 1.97
Shimla_Early W135 Indica Intermediate 1.98
CM1;_HAIPONG W137 Indica Intermediate 2.01
4595 W138 Indica I 1.85
Ao_Chiu_2_Hao W144 Indica I 2.0
GUYANE_1 W145 Indica Intermediate 2.04
10340 W146 Indica I 2.07
BR11 W147 Indica Intermediate 1.94
BR24 W148 Indica Intermediate 2.03
93072 W149 Indica Intermediate 2.08
108S W150 Indica II 1.97
C418 W151 Indica II 2.0
CDR22 W152 Indica II 1.9
Chenghui448 W153 Indica II 1.97
Fengaizhan W154 Indica II 1.78
Gang46B W155 Indica Intermediate 1.93
Gumei2hao W156 Indica I 2.11
Huajingxian74 W157 Indica Intermediate 1.94
R644 W159 Indica II 1.92
Y134 W161 Indica II 1.92
Yuexiangzhan W163 Indica Intermediate 1.78
Zaoxian14 W164 Indica Intermediate 1.95
Zhong413 W165 Indica Intermediate 2.08
Zhongyouzao81 W166 Indica Intermediate 2.02
Zihui100 W167 Indica Intermediate 1.96
Bg90-2 W168 Indica II 2.06
IR72 W169 Indica II 1.89
PR106 W170 Indica II 1.81
TKM9 W171 Indica Intermediate 1.96
Amo13_(Sana) W172 Indica II 1.94
Gayabyeo W174 Indica II 1.88
Milyang23 W176 Indica II 1.95
MR185 W177 Indica II 1.95
Manawthukha W178 Indica III 1.75
Shwe_Thwe_Yin_Hyv W179 Indica II 1.77
Bg300 W180 Indica Intermediate 2.03
Bg94-1 W181 Indica Intermediate 2.01
CR203 W182 Indica II 1.88
OM997 W183 Indica II 1.88
PSB_RC_28 W184 Indica II 1.88
PSB_RC_66 W185 Indica II 1.98
TEQING W186 Indica Intermediate -9.0
IR68552-55-3-2 W187 Indica Intermediate -9.0
IR66897B W188 Indica II 1.86
IR58025B W189 Indica II 1.91
F6 W194 Indica II 1.85
452 W195 Indica II 1.81
Ai-Zi-DAO W197 Indica II 1.74
Babaomi W198 Indica Intermediate 2.19
Diantun502 W199 Indica Intermediate 2.06
Heiheaihui W200 Indica Intermediate 1.89
Jiangxisimiao W201 Indica Intermediate 1.9
Laohudao W202 Indica Intermediate 1.94
Linjintangdao W203 Indica Intermediate 1.92
Mengguandamagu W204 Indica I 1.89
Pengshantieganzhan W205 Indica I 1.9
Wumanggaonuo W206 Indica Intermediate 2.08
Khao_Daeng W210 Indica I 2.02
Basmati370 W211 Indica II 1.77
Bhavani W212 Indica Intermediate 1.98
IR50 W213 Indica Intermediate 1.8
Type3 W216 Indica II 1.95
IRAT352 W217 Indica Intermediate 1.74
TB154E-TB-2 W218 Indica Intermediate 1.76
MR77_(seberang) W221 Indica Intermediate 1.71
ir6 W222 Indica II 1.98
At354 W223 Indica II 1.99
BG304 W224 Indica II 1.83
OM1706 W227 Indica Intermediate 1.91
OM1723 W228 Indica II 1.99
X21 W229 Indica II 1.95
X22 W230 Indica II 1.94
X23 W231 Indica II 2.01
C70 W233 Indica Intermediate 2.04
Q5 W234 Indica Intermediate 2.05
Suiyangnian W235 Indica I 1.94
Pokhreli W236 Indica II 1.95
Govnd W237 Indica II 1.87
UPR191-66 W238 Indica II 1.83
ASD18 W239 Indica Intermediate 1.81
TGMS29 W240 Indica Intermediate 2.02
Phalguna W241 Indica II 1.94
Ajaya W242 Indica Intermediate 2.02
Dodda W243 Indica II 1.92
Palung_2 W244 Indica II 1.91
TKM6 W245 Indica Intermediate 1.8
RUSTYLATE/Zhong_413 W246 Indica Intermediate 2.09
Yenfangghu W247 Indica I 2.0
Heimichut W248 Indica I 1.92
Up15 W259 Indica II 1.96
Bintapan W262 Indica I 2.07
SADAJIRA-19-303 W263 Indica Intermediate 1.81
CHOROFA W264 Indica Intermediate 2.04
La110 W265 Indica Intermediate 1.78
Yunjiang35 W266 Indica III 1.58
Yunhui72 W267 Indica Intermediate 1.98
Wudadaozhong W268 Indica Intermediate 2.0
IR65600-27-1-2-2 W269 Indica Intermediate 1.91
Yetuozai W270 Indica Intermediate 1.92
P59279 W271 Indica Intermediate 2.04
Tsao_wan_ching W272 Indica Intermediate 2.09
Er_chiu_ching W274 Indica I 2.12
Pathma_wee W276 Indica III 2.06
Ma_ba_you_zhan W282 Indica Intermediate -9.0
IR_661-1-140-3-117 W289 Indica II 1.96
IR_2071-625-1-252 W291 Indica II -9.0
IR_8 W293 Indica II 1.99
LEBONNET W295 Indica II 1.96
IR_36 W298 Indica II 1.81
JAYA W299 Indica Intermediate 1.91
IR_64 W301 Indica II 1.89
AGNO_(PSBRC28) W307 Indica II 1.91
PSBRC82 W308 Indica II 1.99
NSICRC122 W309 Indica II 1.87
BRRI_DHAN_29 W310 Indica Intermediate 1.83
PR_116 W311 Indica II 1.94
CIGEULIS W312 Indica II 1.97
OM_2517 W313 Indica II 1.88
BRRI_DHAN_28 W314 Indica II 1.83
CIBOGO W315 Indica II 1.99
NEDA W316 Indica II 1.96
CIHERANG W317 Indica II 1.99
Qiuqianbai W318 Indica I 1.98
Wenxiangnuo W320 Indica Intermediate 2.19
Laozaogu W321 Indica III 2.07
Lengshuinuo W322 Indica Intermediate 1.94

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
vg0505363587 sf0505363565 5 5363587 8.20E-20 1.38E-12
vg0505363470 sf0505363448 5 5363470 2.21E-19 1.30E-12
vg0113720193 sf0113719167 1 13720193 6.67E-14 NA
vg0140472804 sf0140471761 1 40472804 1.33E-13 NA
vg1125633880 sf1125167719 11 25633880 2.73E-12 NA
vg0231596229 sf0231590360 2 31596229 4.72E-12 NA
vg0114524872 sf0114523846 1 14524872 1.28E-10 1.40E-06
vg1126104826 sf1125633240 11 26104826 2.16E-08 3.44E-07
vg0723665620 sf0723664627 7 23665620 7.53E-08 4.75E-06
vg1126836664 sf1126365051 11 26836664 8.78E-08 NA
vg1110764535 sf1110759080 11 10764535 NA 2.17E-07
vg0809442161 sf0809441165 8 9442161 NA 3.42E-07
vg0403269668 sf0403265271 4 3269668 NA 1.67E-06
vg0333037620 sf0333030490 3 33037620 NA 4.06E-06
vg0812015546 sf0812014551 8 12015546 NA 4.94E-06