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 Yield Distribution in Indica All Population:

Phenotype Information Table:

Note: -9 means missing value.

Cultivar Name Cultivar ID Subpopulation Yield
Sadu-cho C001 Indica I 24.13
Shan-Huang_Zhan-2-1_ C006 Indica Intermediate 13.96
Shan-Huang_Zhan-2-2_ C007 Indica Intermediate 20.44
Swarna C008 Indica Intermediate 6.03
MOROBEREKAN C009 Indica Intermediate 29.62
MILYANG_23 C011 Indica II 24.11
Aijiaonante C019 Indica I 14.97
Guangluai-4-1 C020 Indica I 21.41
xiangaizao10 C021 Indica I 24.08
JinnanteB C022 Indica I 21.1
zhenshan97B-1 C024 Indica I 21.54
Qingsiai16B C025 Indica Intermediate 25.69
Dianrui409B C027 Indica Intermediate 27.54
88B-1 C030 Indica Intermediate 33.03
88B-2 C031 Indica Intermediate 28.48
Lucaihao C033 Indica I 25.18
Shufeng101 C036 Indica Intermediate 28.86
Chengduai3hao C037 Indica I 27.65
Sankecui C038 Indica Intermediate 20.55
Gongju73 C039 Indica I 30.07
Jiabala C040 Indica I 25.01
Taishannuo C041 Indica I 26.12
Guichao2hao C042 Indica Intermediate 27.47
Huke3hao C043 Indica I 22.34
Teqingxuanhui C044 Indica Intermediate 20.22
Huangsiguizhan C045 Indica Intermediate 27.6
Xiangwanxian3hao C046 Indica Intermediate 28.5
Hanmadao-2 C047 Indica I 22.12
Jinyou1hao C049 Indica Intermediate 16.2
Chengnongshuijing C050 Indica II 23.95
Momi C053 Indica Intermediate 27.49
Sanbaili C055 Indica I 21.49
Liusha1hao C058 Indica I 16.26
Bawangbian1 C059 Indica I 24.25
Dongtingwanxian C060 Indica I 25.52
Yangdao2hao C061 Indica II 25.1
WH62 C062 Indica I 14.31
Hongwan1hao C065 Indica Intermediate 27.86
Liushizao C066 Indica I 22.28
Taizhongxianxuan2 C068 Indica II 31.13
Dangyu5hao C069 Indica II 27.13
Nantehao C072 Indica I 28.47
Esiniu C073 Indica I 15.67
Benbanggu-1 C076 Indica I 18.58
Benbanggu-2 C077 Indica I 14.78
Qitoubaigu C078 Indica Intermediate 18.63
Hanmadao-1 C080 Indica I 23.69
Heidu4 C081 Indica I 15.53
Nangaogu-2 C088 Indica I 15.18
Sanlicun C090 Indica Intermediate 31.86
Meihuanuo-1 C091 Indica I 18.66
Meihuanuo-2 C092 Indica I 18.02
Menjiagao1 C094 Indica Intermediate 12.4
Xiaohonggu C095 Indica I 12.28
Jinxibai-1 C096 Indica Intermediate 12.05
Jinbaoyin C097 Indica Intermediate 13.57
Hongainuo C098 Indica Intermediate 15.41
WH099 C099 Indica Intermediate 18.19
WH100 C100 Indica Intermediate 12.15
Qiyuexian C102 Indica Intermediate 16.6
Mamagu-1 C104 Indica I 13.31
WH105 C105 Indica Intermediate 15.0
Mowanggunei-2 C107 Indica III 20.04
Mamagu-2 C108 Indica I 16.56
WH109 C109 Indica I 8.97
Xianggu C110 Indica I 20.66
Jinnante43B C112 Indica I 18.27
Xiangzaoxian7hao C113 Indica Intermediate 12.22
80B C114 Indica Intermediate 22.13
WH115 C115 Indica II 23.74
Jiangnongzao1hao C117 Indica Intermediate 27.28
Gu154 C118 Indica II 23.85
XiangaiB C121 Indica Intermediate 37.33
Aituogu151 C122 Indica I 38.68
menjiading2 C124 Indica Intermediate 19.71
Jiefangxian C125 Indica I 14.01
Baikehualuo C127 Indica I 28.27
Liuyezhan C128 Indica I 37.31
Aihechi C129 Indica Intermediate 38.8
Xuanenchangtan C131 Indica I 21.29
Jinzhinuo C132 Indica Intermediate 13.14
Xibaizhan C135 Indica I 17.25
Zegu C136 Indica I 21.26
WH139 C139 Indica I 17.37
Wuzuhonggu C140 Indica I 10.51
Nangaogu-1 C141 Indica I 21.38
Mowanggunei-1 C142 Indica III 18.58
Qitougu C143 Indica I 6.52
Zhenshan97B C145 Indica I 27.41
Minghui63 C147 Indica II 27.15
9311 C148 Indica II 26.72
Nanjing11 C151 Indica I 24.3
Erjiunan1hao C155 Indica I 17.93
ChaoyangyihaoB C156 Indica I 15.13
L301B C157 Indica I 11.06
Guangluai15 C158 Indica I 26.08
ZhuzhenB C159 Indica I 32.72
Baoxie-7B C160 Indica Intermediate 21.27
Gzhenshan97B C161 Indica I 25.21
Nanxiongzaoyou C162 Indica Intermediate 12.92
Zaoshuxianghei C163 Indica II 16.16
IR661-1 C164 Indica II 23.03
Nanjing11-2 C165 Indica I 20.14
Gui630 C166 Indica Intermediate 20.12
76--1 C167 Indica Intermediate 18.49
Xugunuo C168 Indica Intermediate 29.36
Taizhongzailai1 C169 Indica Intermediate 30.26
Xiangwanxian1hao C170 Indica I 22.92
Aimakang C173 Indica I 19.72
JWR221 C174 Indica II 27.65
Zhengxian232 C175 Indica Intermediate 27.96
Chenwan3hao C176 Indica Intermediate 16.33
Aimi C178 Indica I 23.51
Wanlixian C180 Indica I 19.29
Hengxianliangchun C182 Indica I 15.27
Leihuozhan C183 Indica I 13.52
Baikezaohe C184 Indica I 16.07
Xiangdao C190 Indica I 22.79
Younian C191 Indica I 28.88
Wukezhan C192 Indica Intermediate 11.77
Zhongnong4hao C193 Indica I 22.5
Minbeiwanxian C194 Indica Intermediate 11.93
Maweinian C197 Indica I 11.31
Zinuo C198 Indica Intermediate 21.4
Beizinuo C199 Indica I 21.81
Biwusheng C200 Indica I 15.08
Yizhixiang C201 Indica Intermediate 24.53
Xiaobaimi C202 Indica I 16.82
Zaoxian240 C203 Indica I 13.12
Mayang_Khang W001 Indica I 22.49
BERLIN W009 Indica III 30.1
Warrangal_Culture_1252 W023 Indica III 42.76
Won_Son_Zo_No._11 W026 Indica I 46.69
Ai_Chueh_Ta_Pai_Ku W029 Indica Intermediate 33.16
Thang_10 W030 Indica Intermediate 42.82
Sipirasikkam W031 Indica I 38.67
TJ W032 Indica I 38.75
PD_46 W033 Indica I 25.69
K8C-263-3 W035 Indica Intermediate 28.86
Chun_118-33 W036 Indica I 52.97
Manga_Kely_694 W037 Indica Intermediate 26.79
Nam_Dawk_Mai W039 Indica I 48.93
INIAP_7 W040 Indica II 37.75
Red W042 Indica Intermediate 36.42
Dichroa_Alef_Uslkij W043 Indica Intermediate 41.84
BKN_6987-68-14 W044 Indica II 30.48
IR_9660-48-1-1-2 W046 Indica II 34.03
RP2151-173-1-8 W051 Indica II 41.35
Toga W054 Indica Intermediate 39.47
Kao_Chio_Lin_Chou W058 Indica I 54.37
IR_238 W066 Indica Intermediate 28.08
Shui_Ya_Jien W070 Indica Intermediate 56.93
AKP_4 W071 Indica Intermediate 32.24
IR_2061-214-2-3 W073 Indica II 31.0
TAINUNG_45 W074 Indica Intermediate 36.26
Sapundali_Local W075 Indica Intermediate 49.48
B805D-MR-16-8-3 W078 Indica Intermediate 26.95
UZ_ROS_59 W080 Indica I 54.17
CNTLR80076-44-1-1-1 W083 Indica Intermediate 32.77
IR_58614-B-B-8-2 W084 Indica Intermediate 27.97
KECHENGNUO_NO._4 W085 Indica Intermediate 39.59
4484 W086 Indica II 33.73
YOU-I_B W087 Indica I 28.51
Egyptian_Wild_Type W089 Indica III 43.14
Srav_Prapay W093 Indica III 27.89
AMANE W101 Indica Intermediate 43.36
JP_5 W107 Indica Intermediate 27.58
Sereno W111 Indica III 29.52
ARC_10633 W112 Indica III 43.85
Heo_Trang W114 Indica III 28.55
Kin_Shan_Zim W124 Indica I 29.85
Pan_Ju W126 Indica I 59.9
Hsin_Hsing_Pai_Ku W132 Indica I 47.57
TD_70 W133 Indica Intermediate 37.09
Shimla_Early W135 Indica Intermediate 49.14
CM1;_HAIPONG W137 Indica Intermediate 34.35
4595 W138 Indica I 64.86
Ao_Chiu_2_Hao W144 Indica I 39.58
GUYANE_1 W145 Indica Intermediate 25.75
10340 W146 Indica I 64.45
BR11 W147 Indica Intermediate 65.87
BR24 W148 Indica Intermediate 53.04
93072 W149 Indica Intermediate 45.4
108S W150 Indica II 36.18
C418 W151 Indica II 51.34
CDR22 W152 Indica II 47.87
Chenghui448 W153 Indica II 48.48
Fengaizhan W154 Indica II 60.98
Gang46B W155 Indica Intermediate 44.83
Gumei2hao W156 Indica I 40.36
Huajingxian74 W157 Indica Intermediate 46.17
R644 W159 Indica II 48.61
Y134 W161 Indica II 49.92
Yuexiangzhan W163 Indica Intermediate 78.87
Zaoxian14 W164 Indica Intermediate 56.01
Zhong413 W165 Indica Intermediate 52.53
Zhongyouzao81 W166 Indica Intermediate 66.81
Zihui100 W167 Indica Intermediate 45.93
Bg90-2 W168 Indica II 42.14
IR72 W169 Indica II 47.84
PR106 W170 Indica II 36.14
TKM9 W171 Indica Intermediate 36.34
Amo13_(Sana) W172 Indica II 40.94
Gayabyeo W174 Indica II 41.87
Milyang23 W176 Indica II 49.18
MR185 W177 Indica II 39.95
Manawthukha W178 Indica III 30.93
Shwe_Thwe_Yin_Hyv W179 Indica II 38.47
Bg300 W180 Indica Intermediate 37.7
Bg94-1 W181 Indica Intermediate 67.62
CR203 W182 Indica II 50.03
OM997 W183 Indica II 41.2
PSB_RC_28 W184 Indica II 45.16
PSB_RC_66 W185 Indica II 43.83
TEQING W186 Indica Intermediate -9.0
IR68552-55-3-2 W187 Indica Intermediate -9.0
IR66897B W188 Indica II 51.46
IR58025B W189 Indica II 47.6
F6 W194 Indica II 53.24
452 W195 Indica II 68.19
Ai-Zi-DAO W197 Indica II 64.98
Babaomi W198 Indica Intermediate 39.96
Diantun502 W199 Indica Intermediate 48.37
Heiheaihui W200 Indica Intermediate 48.88
Jiangxisimiao W201 Indica Intermediate 51.03
Laohudao W202 Indica Intermediate 52.28
Linjintangdao W203 Indica Intermediate 55.14
Mengguandamagu W204 Indica I 50.0
Pengshantieganzhan W205 Indica I 44.07
Wumanggaonuo W206 Indica Intermediate 32.66
Khao_Daeng W210 Indica I 92.66
Basmati370 W211 Indica II 25.22
Bhavani W212 Indica Intermediate 66.98
IR50 W213 Indica Intermediate 31.38
Type3 W216 Indica II 47.57
IRAT352 W217 Indica Intermediate 20.5
TB154E-TB-2 W218 Indica Intermediate 22.26
MR77_(seberang) W221 Indica Intermediate 25.91
ir6 W222 Indica II 55.67
At354 W223 Indica II 52.59
BG304 W224 Indica II 45.4
OM1706 W227 Indica Intermediate 50.01
OM1723 W228 Indica II 41.88
X21 W229 Indica II 55.19
X22 W230 Indica II 25.57
X23 W231 Indica II 40.06
C70 W233 Indica Intermediate 36.4
Q5 W234 Indica Intermediate 43.17
Suiyangnian W235 Indica I 56.42
Pokhreli W236 Indica II 50.76
Govnd W237 Indica II 72.55
UPR191-66 W238 Indica II 36.2
ASD18 W239 Indica Intermediate 54.41
TGMS29 W240 Indica Intermediate 45.03
Phalguna W241 Indica II 51.51
Ajaya W242 Indica Intermediate 44.32
Dodda W243 Indica II 53.58
Palung_2 W244 Indica II 38.07
TKM6 W245 Indica Intermediate 12.75
RUSTYLATE/Zhong_413 W246 Indica Intermediate 51.53
Yenfangghu W247 Indica I 49.59
Heimichut W248 Indica I 34.34
Up15 W259 Indica II 57.48
Bintapan W262 Indica I 42.45
SADAJIRA-19-303 W263 Indica Intermediate 32.59
CHOROFA W264 Indica Intermediate 44.62
La110 W265 Indica Intermediate 43.5
Yunjiang35 W266 Indica III -9.0
Yunhui72 W267 Indica Intermediate 49.72
Wudadaozhong W268 Indica Intermediate 47.52
IR65600-27-1-2-2 W269 Indica Intermediate 53.08
Yetuozai W270 Indica Intermediate 43.21
P59279 W271 Indica Intermediate 48.11
Tsao_wan_ching W272 Indica Intermediate 49.72
Er_chiu_ching W274 Indica I 27.06
Pathma_wee W276 Indica III 42.41
Ma_ba_you_zhan W282 Indica Intermediate -9.0
IR_661-1-140-3-117 W289 Indica II 31.8
IR_2071-625-1-252 W291 Indica II -9.0
IR_8 W293 Indica II 41.4
LEBONNET W295 Indica II 47.32
IR_36 W298 Indica II 39.21
JAYA W299 Indica Intermediate 36.96
IR_64 W301 Indica II 38.48
AGNO_(PSBRC28) W307 Indica II -9.0
PSBRC82 W308 Indica II 30.02
NSICRC122 W309 Indica II 50.16
BRRI_DHAN_29 W310 Indica Intermediate 54.69
PR_116 W311 Indica II 53.65
CIGEULIS W312 Indica II 55.13
OM_2517 W313 Indica II 42.46
BRRI_DHAN_28 W314 Indica II 45.76
CIBOGO W315 Indica II 29.4
NEDA W316 Indica II 37.4
CIHERANG W317 Indica II 42.61
Qiuqianbai W318 Indica I 61.22
Wenxiangnuo W320 Indica Intermediate 13.07
Laozaogu W321 Indica III 30.24
Lengshuinuo W322 Indica Intermediate 36.91

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
vg0622856929 sf0622855932 6 22856929 1.08E-08 5.36E-07
vg0305009028 sf0305008030 3 5009028 1.53E-08 NA
vg0818303489 sf0818300776 8 18303489 2.74E-08 NA
vg0102386398 sf0102385398 1 2386398 5.02E-08 8.89E-06
vg0102416437 sf0102415437 1 2416437 5.11E-08 4.94E-06
vg0819041897 sf0819039184 8 19041897 5.91E-08 NA
vg0818493390 sf0818490677 8 18493390 1.66E-07 NA
vg0122974440 sf0122973396 1 22974440 3.68E-07 3.44E-06
vg0216275518 sf0216269648 2 16275518 2.46E-06 1.40E-06
vg0121868877 sf0121867832 1 21868877 8.55E-06 8.98E-07
vg1116079879 sf1115614751 11 16079879 9.05E-06 4.11E-06