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 weight Distribution in Indica All Population:

Phenotype Information Table:

Note: -9 means missing value.

Cultivar Name Cultivar ID Subpopulation Grain weight
Sadu-cho C001 Indica I 21.6
Shan-Huang_Zhan-2-1_ C006 Indica Intermediate 15.55
Shan-Huang_Zhan-2-2_ C007 Indica Intermediate 15.21
Swarna C008 Indica Intermediate 14.91
MOROBEREKAN C009 Indica Intermediate 22.85
MILYANG_23 C011 Indica II 23.0
Aijiaonante C019 Indica I 20.85
Guangluai-4-1 C020 Indica I 22.12
xiangaizao10 C021 Indica I 19.24
JinnanteB C022 Indica I 17.83
zhenshan97B-1 C024 Indica I 21.19
Qingsiai16B C025 Indica Intermediate 20.8
Dianrui409B C027 Indica Intermediate 22.93
88B-1 C030 Indica Intermediate 21.8
88B-2 C031 Indica Intermediate 21.22
Lucaihao C033 Indica I 21.69
Shufeng101 C036 Indica Intermediate 26.48
Chengduai3hao C037 Indica I 23.07
Sankecui C038 Indica Intermediate 22.26
Gongju73 C039 Indica I 23.95
Jiabala C040 Indica I 21.86
Taishannuo C041 Indica I 22.96
Guichao2hao C042 Indica Intermediate 23.42
Huke3hao C043 Indica I 25.71
Teqingxuanhui C044 Indica Intermediate 22.63
Huangsiguizhan C045 Indica Intermediate 16.7
Xiangwanxian3hao C046 Indica Intermediate 21.94
Hanmadao-2 C047 Indica I 22.72
Jinyou1hao C049 Indica Intermediate 23.92
Chengnongshuijing C050 Indica II 24.93
Momi C053 Indica Intermediate 24.77
Sanbaili C055 Indica I 23.17
Liusha1hao C058 Indica I 22.03
Bawangbian1 C059 Indica I 23.66
Dongtingwanxian C060 Indica I 21.68
Yangdao2hao C061 Indica II 25.7
WH62 C062 Indica I 28.92
Hongwan1hao C065 Indica Intermediate 22.68
Liushizao C066 Indica I 19.43
Taizhongxianxuan2 C068 Indica II 20.49
Dangyu5hao C069 Indica II 24.21
Nantehao C072 Indica I 23.67
Esiniu C073 Indica I 19.28
Benbanggu-1 C076 Indica I 24.35
Benbanggu-2 C077 Indica I 21.51
Qitoubaigu C078 Indica Intermediate 23.95
Hanmadao-1 C080 Indica I 22.58
Heidu4 C081 Indica I 21.83
Nangaogu-2 C088 Indica I 22.39
Sanlicun C090 Indica Intermediate 24.25
Meihuanuo-1 C091 Indica I 21.35
Meihuanuo-2 C092 Indica I 21.18
Menjiagao1 C094 Indica Intermediate 19.99
Xiaohonggu C095 Indica I 22.23
Jinxibai-1 C096 Indica Intermediate 22.59
Jinbaoyin C097 Indica Intermediate 21.04
Hongainuo C098 Indica Intermediate 21.07
WH099 C099 Indica Intermediate 22.67
WH100 C100 Indica Intermediate 23.54
Qiyuexian C102 Indica Intermediate 19.36
Mamagu-1 C104 Indica I 21.45
WH105 C105 Indica Intermediate 21.17
Mowanggunei-2 C107 Indica III 22.82
Mamagu-2 C108 Indica I 25.09
WH109 C109 Indica I 23.49
Xianggu C110 Indica I 23.22
Jinnante43B C112 Indica I 16.0
Xiangzaoxian7hao C113 Indica Intermediate 16.6
80B C114 Indica Intermediate 22.24
WH115 C115 Indica II 21.47
Jiangnongzao1hao C117 Indica Intermediate 25.42
Gu154 C118 Indica II 19.92
XiangaiB C121 Indica Intermediate 24.27
Aituogu151 C122 Indica I 21.81
menjiading2 C124 Indica Intermediate 23.58
Jiefangxian C125 Indica I 25.55
Baikehualuo C127 Indica I 23.22
Liuyezhan C128 Indica I 24.09
Aihechi C129 Indica Intermediate 23.89
Xuanenchangtan C131 Indica I 19.54
Jinzhinuo C132 Indica Intermediate 26.83
Xibaizhan C135 Indica I 19.13
Zegu C136 Indica I 20.49
WH139 C139 Indica I 21.96
Wuzuhonggu C140 Indica I 20.35
Nangaogu-1 C141 Indica I 22.09
Mowanggunei-1 C142 Indica III 20.43
Qitougu C143 Indica I 25.61
Zhenshan97B C145 Indica I 23.14
Minghui63 C147 Indica II 26.96
9311 C148 Indica II 27.93
Nanjing11 C151 Indica I 21.9
Erjiunan1hao C155 Indica I 19.16
ChaoyangyihaoB C156 Indica I 19.73
L301B C157 Indica I 18.7
Guangluai15 C158 Indica I 21.41
ZhuzhenB C159 Indica I 26.88
Baoxie-7B C160 Indica Intermediate 20.64
Gzhenshan97B C161 Indica I 26.95
Nanxiongzaoyou C162 Indica Intermediate 22.0
Zaoshuxianghei C163 Indica II 23.98
IR661-1 C164 Indica II 24.96
Nanjing11-2 C165 Indica I 22.86
Gui630 C166 Indica Intermediate 22.5
76--1 C167 Indica Intermediate 24.64
Xugunuo C168 Indica Intermediate 24.58
Taizhongzailai1 C169 Indica Intermediate 23.18
Xiangwanxian1hao C170 Indica I 22.38
Aimakang C173 Indica I 22.77
JWR221 C174 Indica II 27.66
Zhengxian232 C175 Indica Intermediate 20.9
Chenwan3hao C176 Indica Intermediate 24.13
Aimi C178 Indica I 22.05
Wanlixian C180 Indica I 23.92
Hengxianliangchun C182 Indica I 23.02
Leihuozhan C183 Indica I 26.12
Baikezaohe C184 Indica I 24.83
Xiangdao C190 Indica I 19.97
Younian C191 Indica I 22.35
Wukezhan C192 Indica Intermediate 21.96
Zhongnong4hao C193 Indica I 19.75
Minbeiwanxian C194 Indica Intermediate 23.06
Maweinian C197 Indica I 22.36
Zinuo C198 Indica Intermediate 22.12
Beizinuo C199 Indica I 22.55
Biwusheng C200 Indica I 21.39
Yizhixiang C201 Indica Intermediate 18.93
Xiaobaimi C202 Indica I 20.8
Zaoxian240 C203 Indica I 20.18
Mayang_Khang W001 Indica I 25.31
BERLIN W009 Indica III 26.08
Warrangal_Culture_1252 W023 Indica III 19.5
Won_Son_Zo_No._11 W026 Indica I 24.1
Ai_Chueh_Ta_Pai_Ku W029 Indica Intermediate 19.94
Thang_10 W030 Indica Intermediate 21.34
Sipirasikkam W031 Indica I 19.55
TJ W032 Indica I 21.2
PD_46 W033 Indica I 23.4
K8C-263-3 W035 Indica Intermediate 23.44
Chun_118-33 W036 Indica I 23.06
Manga_Kely_694 W037 Indica Intermediate 27.85
Nam_Dawk_Mai W039 Indica I 26.83
INIAP_7 W040 Indica II 30.97
Red W042 Indica Intermediate 23.41
Dichroa_Alef_Uslkij W043 Indica Intermediate 22.77
BKN_6987-68-14 W044 Indica II 26.88
IR_9660-48-1-1-2 W046 Indica II 24.4
RP2151-173-1-8 W051 Indica II 24.74
Toga W054 Indica Intermediate 21.92
Kao_Chio_Lin_Chou W058 Indica I 23.28
IR_238 W066 Indica Intermediate 19.72
Shui_Ya_Jien W070 Indica Intermediate 22.03
AKP_4 W071 Indica Intermediate 23.04
IR_2061-214-2-3 W073 Indica II 23.46
TAINUNG_45 W074 Indica Intermediate 25.68
Sapundali_Local W075 Indica Intermediate 22.51
B805D-MR-16-8-3 W078 Indica Intermediate 24.69
UZ_ROS_59 W080 Indica I 24.56
CNTLR80076-44-1-1-1 W083 Indica Intermediate 27.1
IR_58614-B-B-8-2 W084 Indica Intermediate 23.56
KECHENGNUO_NO._4 W085 Indica Intermediate 25.28
4484 W086 Indica II 25.07
YOU-I_B W087 Indica I 23.06
Egyptian_Wild_Type W089 Indica III 20.82
Srav_Prapay W093 Indica III 26.86
AMANE W101 Indica Intermediate 27.49
JP_5 W107 Indica Intermediate 28.59
Sereno W111 Indica III 23.62
ARC_10633 W112 Indica III 24.44
Heo_Trang W114 Indica III -9.0
Kin_Shan_Zim W124 Indica I 17.51
Pan_Ju W126 Indica I 21.19
Hsin_Hsing_Pai_Ku W132 Indica I 20.68
TD_70 W133 Indica Intermediate 24.18
Shimla_Early W135 Indica Intermediate 22.36
CM1;_HAIPONG W137 Indica Intermediate 30.73
4595 W138 Indica I 20.25
Ao_Chiu_2_Hao W144 Indica I 22.09
GUYANE_1 W145 Indica Intermediate 22.47
10340 W146 Indica I 23.86
BR11 W147 Indica Intermediate 24.58
BR24 W148 Indica Intermediate 24.58
93072 W149 Indica Intermediate 27.85
108S W150 Indica II 24.92
C418 W151 Indica II 22.28
CDR22 W152 Indica II 25.31
Chenghui448 W153 Indica II 25.89
Fengaizhan W154 Indica II 17.66
Gang46B W155 Indica Intermediate 22.38
Gumei2hao W156 Indica I 30.99
Huajingxian74 W157 Indica Intermediate 24.07
R644 W159 Indica II 22.47
Y134 W161 Indica II 23.15
Yuexiangzhan W163 Indica Intermediate 19.38
Zaoxian14 W164 Indica Intermediate 21.43
Zhong413 W165 Indica Intermediate 23.5
Zhongyouzao81 W166 Indica Intermediate 24.64
Zihui100 W167 Indica Intermediate 23.92
Bg90-2 W168 Indica II 26.62
IR72 W169 Indica II 21.34
PR106 W170 Indica II 24.83
TKM9 W171 Indica Intermediate 21.85
Amo13_(Sana) W172 Indica II 24.92
Gayabyeo W174 Indica II 19.81
Milyang23 W176 Indica II 23.11
MR185 W177 Indica II 22.86
Manawthukha W178 Indica III 15.95
Shwe_Thwe_Yin_Hyv W179 Indica II 19.1
Bg300 W180 Indica Intermediate 24.07
Bg94-1 W181 Indica Intermediate 24.64
CR203 W182 Indica II 21.86
OM997 W183 Indica II 22.31
PSB_RC_28 W184 Indica II 23.13
PSB_RC_66 W185 Indica II 25.12
TEQING W186 Indica Intermediate -9.0
IR68552-55-3-2 W187 Indica Intermediate -9.0
IR66897B W188 Indica II 20.96
IR58025B W189 Indica II 23.73
F6 W194 Indica II 20.55
452 W195 Indica II 26.17
Ai-Zi-DAO W197 Indica II 19.14
Babaomi W198 Indica Intermediate 29.08
Diantun502 W199 Indica Intermediate 31.15
Heiheaihui W200 Indica Intermediate 24.42
Jiangxisimiao W201 Indica Intermediate 25.13
Laohudao W202 Indica Intermediate 25.69
Linjintangdao W203 Indica Intermediate 23.92
Mengguandamagu W204 Indica I 21.77
Pengshantieganzhan W205 Indica I 21.67
Wumanggaonuo W206 Indica Intermediate 31.48
Khao_Daeng W210 Indica I 24.09
Basmati370 W211 Indica II 17.04
Bhavani W212 Indica Intermediate 21.66
IR50 W213 Indica Intermediate 19.28
Type3 W216 Indica II 23.9
IRAT352 W217 Indica Intermediate 16.9
TB154E-TB-2 W218 Indica Intermediate 18.54
MR77_(seberang) W221 Indica Intermediate 17.38
ir6 W222 Indica II 24.84
At354 W223 Indica II 26.79
BG304 W224 Indica II 19.69
OM1706 W227 Indica Intermediate 25.32
OM1723 W228 Indica II 28.29
X21 W229 Indica II 23.16
X22 W230 Indica II 22.5
X23 W231 Indica II 23.39
C70 W233 Indica Intermediate 24.53
Q5 W234 Indica Intermediate 24.47
Suiyangnian W235 Indica I 21.16
Pokhreli W236 Indica II 27.19
Govnd W237 Indica II 22.87
UPR191-66 W238 Indica II 21.17
ASD18 W239 Indica Intermediate 19.81
TGMS29 W240 Indica Intermediate 29.03
Phalguna W241 Indica II 24.02
Ajaya W242 Indica Intermediate 25.57
Dodda W243 Indica II 26.25
Palung_2 W244 Indica II 26.09
TKM6 W245 Indica Intermediate 18.41
RUSTYLATE/Zhong_413 W246 Indica Intermediate 24.88
Yenfangghu W247 Indica I 24.34
Heimichut W248 Indica I 21.78
Up15 W259 Indica II 26.55
Bintapan W262 Indica I 23.59
SADAJIRA-19-303 W263 Indica Intermediate 17.4
CHOROFA W264 Indica Intermediate 24.1
La110 W265 Indica Intermediate 21.59
Yunjiang35 W266 Indica III -9.0
Yunhui72 W267 Indica Intermediate 22.59
Wudadaozhong W268 Indica Intermediate 23.17
IR65600-27-1-2-2 W269 Indica Intermediate 21.27
Yetuozai W270 Indica Intermediate 19.72
P59279 W271 Indica Intermediate 25.21
Tsao_wan_ching W272 Indica Intermediate 26.31
Er_chiu_ching W274 Indica I 23.41
Pathma_wee W276 Indica III 23.54
Ma_ba_you_zhan W282 Indica Intermediate -9.0
IR_661-1-140-3-117 W289 Indica II 24.3
IR_2071-625-1-252 W291 Indica II -9.0
IR_8 W293 Indica II 25.96
LEBONNET W295 Indica II 22.97
IR_36 W298 Indica II 20.0
JAYA W299 Indica Intermediate 18.74
IR_64 W301 Indica II 23.06
AGNO_(PSBRC28) W307 Indica II -9.0
PSBRC82 W308 Indica II 23.56
NSICRC122 W309 Indica II 23.85
BRRI_DHAN_29 W310 Indica Intermediate 19.36
PR_116 W311 Indica II 23.9
CIGEULIS W312 Indica II 23.56
OM_2517 W313 Indica II 21.36
BRRI_DHAN_28 W314 Indica II 20.63
CIBOGO W315 Indica II 23.8
NEDA W316 Indica II 25.91
CIHERANG W317 Indica II 24.0
Qiuqianbai W318 Indica I 23.02
Wenxiangnuo W320 Indica Intermediate 26.82
Laozaogu W321 Indica III 22.66
Lengshuinuo W322 Indica Intermediate 23.37

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
vg0114516704 sf0114515678 1 14516704 1.29E-10 NA
vg0202024716 sf0202024716 2 2024716 1.21E-09 NA
vg0920006932 sf0920006451 9 20006932 2.63E-09 NA
vg0201211730 sf0201211730 2 1211730 7.48E-09 NA
vg0825382886 sf0825380172 8 25382886 8.72E-09 NA
vg0500333563 sf0500333563 5 333563 2.22E-08 1.60E-06
vg1002106037 sf1002105014 10 2106037 3.12E-07 3.97E-06
vg0721887753 sf0721886760 7 21887753 8.17E-07 NA
vg0723665620 sf0723664627 7 23665620 2.80E-06 7.74E-06
vg0501545838 sf0501545822 5 1545838 4.56E-06 NA
vg1201249880 sf1201248880 12 1249880 8.60E-06 2.57E-06
vg0316905224 sf0316904098 3 16905224 9.95E-06 NA
vg0505363587 sf0505363565 5 5363587 NA 6.86E-07
vg0920176425 sf0920175944 9 20176425 NA 9.44E-07
vg0920145322 sf0920144841 9 20145322 NA 1.30E-06
vg0823317285 sf0823314572 8 23317285 NA 1.84E-06
vg0911571250 sf0911570249 9 11571250 NA 2.06E-06
vg0913504136 sf0913503135 9 13504136 NA 2.33E-06
vg0523308922 sf0523246343 5 23308922 NA 3.75E-06