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 Plant Height (cm) Distribution in Indica All Population:

Phenotype Information Table:

Note: -9 means missing value.

Cultivar Name Cultivar ID Subpopulation Plant Height (cm)
Sadu-cho C001 Indica I 144.13
Shan-Huang_Zhan-2-1_ C006 Indica Intermediate 108.23
Shan-Huang_Zhan-2-2_ C007 Indica Intermediate 107.97
Swarna C008 Indica Intermediate 87.47
MOROBEREKAN C009 Indica Intermediate 106.8
MILYANG_23 C011 Indica II 100.43
Aijiaonante C019 Indica I 80.25
Guangluai-4-1 C020 Indica I 78.17
xiangaizao10 C021 Indica I 80.83
JinnanteB C022 Indica I 77.3
zhenshan97B-1 C024 Indica I 85.33
Qingsiai16B C025 Indica Intermediate 82.83
Dianrui409B C027 Indica Intermediate 100.47
88B-1 C030 Indica Intermediate 99.57
88B-2 C031 Indica Intermediate 96.27
Lucaihao C033 Indica I 132.04
Shufeng101 C036 Indica Intermediate 95.07
Chengduai3hao C037 Indica I 105.33
Sankecui C038 Indica Intermediate 101.33
Gongju73 C039 Indica I 109.43
Jiabala C040 Indica I 102.46
Taishannuo C041 Indica I 113.1
Guichao2hao C042 Indica Intermediate 103.67
Huke3hao C043 Indica I 106.33
Teqingxuanhui C044 Indica Intermediate 104.33
Huangsiguizhan C045 Indica Intermediate 106.23
Xiangwanxian3hao C046 Indica Intermediate 172.37
Hanmadao-2 C047 Indica I 97.53
Jinyou1hao C049 Indica Intermediate 103.13
Chengnongshuijing C050 Indica II 108.81
Momi C053 Indica Intermediate 116.63
Sanbaili C055 Indica I 119.03
Liusha1hao C058 Indica I 103.7
Bawangbian1 C059 Indica I 113.43
Dongtingwanxian C060 Indica I 114.73
Yangdao2hao C061 Indica II 109.37
WH62 C062 Indica I 105.5
Hongwan1hao C065 Indica Intermediate 109.07
Liushizao C066 Indica I 120.27
Taizhongxianxuan2 C068 Indica II 109.6
Dangyu5hao C069 Indica II 115.8
Nantehao C072 Indica I 158.07
Esiniu C073 Indica I 167.83
Benbanggu-1 C076 Indica I 127.36
Benbanggu-2 C077 Indica I 149.8
Qitoubaigu C078 Indica Intermediate 172.4
Hanmadao-1 C080 Indica I 170.53
Heidu4 C081 Indica I 155.8
Nangaogu-2 C088 Indica I 135.4
Sanlicun C090 Indica Intermediate 177.29
Meihuanuo-1 C091 Indica I 170.07
Meihuanuo-2 C092 Indica I 168.47
Menjiagao1 C094 Indica Intermediate 154.87
Xiaohonggu C095 Indica I 163.37
Jinxibai-1 C096 Indica Intermediate 166.4
Jinbaoyin C097 Indica Intermediate 172.2
Hongainuo C098 Indica Intermediate 178.27
WH099 C099 Indica Intermediate 176.8
WH100 C100 Indica Intermediate 166.45
Qiyuexian C102 Indica Intermediate 150.67
Mamagu-1 C104 Indica I 179.14
WH105 C105 Indica Intermediate 170.17
Mowanggunei-2 C107 Indica III 193.67
Mamagu-2 C108 Indica I 156.8
WH109 C109 Indica I 162.1
Xianggu C110 Indica I 159.33
Jinnante43B C112 Indica I 77.43
Xiangzaoxian7hao C113 Indica Intermediate 73.77
80B C114 Indica Intermediate 86.87
WH115 C115 Indica II 80.4
Jiangnongzao1hao C117 Indica Intermediate 110.43
Gu154 C118 Indica II 88.27
XiangaiB C121 Indica Intermediate 150.67
Aituogu151 C122 Indica I 118.1
menjiading2 C124 Indica Intermediate 110.27
Jiefangxian C125 Indica I 145.65
Baikehualuo C127 Indica I 152.54
Liuyezhan C128 Indica I 158.23
Aihechi C129 Indica Intermediate 166.87
Xuanenchangtan C131 Indica I 165.07
Jinzhinuo C132 Indica Intermediate 169.67
Xibaizhan C135 Indica I 136.39
Zegu C136 Indica I 182.14
WH139 C139 Indica I 185.33
Wuzuhonggu C140 Indica I 164.4
Nangaogu-1 C141 Indica I 190.93
Mowanggunei-1 C142 Indica III 198.57
Qitougu C143 Indica I 170.36
Zhenshan97B C145 Indica I 92.33
Minghui63 C147 Indica II 108.1
9311 C148 Indica II 117.2
Nanjing11 C151 Indica I 107.73
Erjiunan1hao C155 Indica I 69.47
ChaoyangyihaoB C156 Indica I 73.13
L301B C157 Indica I 75.1
Guangluai15 C158 Indica I 85.17
ZhuzhenB C159 Indica I 95.8
Baoxie-7B C160 Indica Intermediate 83.68
Gzhenshan97B C161 Indica I 93.5
Nanxiongzaoyou C162 Indica Intermediate 97.77
Zaoshuxianghei C163 Indica II 104.17
IR661-1 C164 Indica II 95.53
Nanjing11-2 C165 Indica I 96.03
Gui630 C166 Indica Intermediate 94.73
76--1 C167 Indica Intermediate 108.23
Xugunuo C168 Indica Intermediate 104.87
Taizhongzailai1 C169 Indica Intermediate 118.07
Xiangwanxian1hao C170 Indica I 94.87
Aimakang C173 Indica I 114.4
JWR221 C174 Indica II 111.43
Zhengxian232 C175 Indica Intermediate 111.2
Chenwan3hao C176 Indica Intermediate 97.67
Aimi C178 Indica I 107.67
Wanlixian C180 Indica I 147.15
Hengxianliangchun C182 Indica I 161.2
Leihuozhan C183 Indica I 160.57
Baikezaohe C184 Indica I 156.17
Xiangdao C190 Indica I 160.9
Younian C191 Indica I 171.27
Wukezhan C192 Indica Intermediate 185.07
Zhongnong4hao C193 Indica I 158.4
Minbeiwanxian C194 Indica Intermediate 173.4
Maweinian C197 Indica I 175.77
Zinuo C198 Indica Intermediate 173.77
Beizinuo C199 Indica I 187.53
Biwusheng C200 Indica I 189.1
Yizhixiang C201 Indica Intermediate 194.93
Xiaobaimi C202 Indica I 176.33
Zaoxian240 C203 Indica I 77.33
Mayang_Khang W001 Indica I 146.4
BERLIN W009 Indica III 193.8
Warrangal_Culture_1252 W023 Indica III 165.8
Won_Son_Zo_No._11 W026 Indica I 160.6
Ai_Chueh_Ta_Pai_Ku W029 Indica Intermediate 147.8
Thang_10 W030 Indica Intermediate 172.6
Sipirasikkam W031 Indica I 159.6
TJ W032 Indica I 159.6
PD_46 W033 Indica I 155.0
K8C-263-3 W035 Indica Intermediate 196.2
Chun_118-33 W036 Indica I 157.8
Manga_Kely_694 W037 Indica Intermediate 173.8
Nam_Dawk_Mai W039 Indica I 152.0
INIAP_7 W040 Indica II 108.4
Red W042 Indica Intermediate 185.4
Dichroa_Alef_Uslkij W043 Indica Intermediate 105.4
BKN_6987-68-14 W044 Indica II 98.8
IR_9660-48-1-1-2 W046 Indica II 96.0
RP2151-173-1-8 W051 Indica II 107.4
Toga W054 Indica Intermediate 190.2
Kao_Chio_Lin_Chou W058 Indica I 150.6
IR_238 W066 Indica Intermediate 102.2
Shui_Ya_Jien W070 Indica Intermediate 160.4
AKP_4 W071 Indica Intermediate 104.6
IR_2061-214-2-3 W073 Indica II 98.8
TAINUNG_45 W074 Indica Intermediate 162.2
Sapundali_Local W075 Indica Intermediate 186.2
B805D-MR-16-8-3 W078 Indica Intermediate 96.8
UZ_ROS_59 W080 Indica I 141.4
CNTLR80076-44-1-1-1 W083 Indica Intermediate 116.4
IR_58614-B-B-8-2 W084 Indica Intermediate 114.4
KECHENGNUO_NO._4 W085 Indica Intermediate 118.6
4484 W086 Indica II 103.4
YOU-I_B W087 Indica I 77.2
Egyptian_Wild_Type W089 Indica III 136.4
Srav_Prapay W093 Indica III 133.0
AMANE W101 Indica Intermediate 149.8
JP_5 W107 Indica Intermediate 163.2
Sereno W111 Indica III 203.6
ARC_10633 W112 Indica III 167.2
Heo_Trang W114 Indica III 181.4
Kin_Shan_Zim W124 Indica I 134.0
Pan_Ju W126 Indica I 157.6
Hsin_Hsing_Pai_Ku W132 Indica I 156.0
TD_70 W133 Indica Intermediate 157.8
Shimla_Early W135 Indica Intermediate 172.8
CM1;_HAIPONG W137 Indica Intermediate 125.6
4595 W138 Indica I 102.0
Ao_Chiu_2_Hao W144 Indica I 168.4
GUYANE_1 W145 Indica Intermediate 177.4
10340 W146 Indica I 127.4
BR11 W147 Indica Intermediate 117.6
BR24 W148 Indica Intermediate 168.4
93072 W149 Indica Intermediate 112.6
108S W150 Indica II 104.6
C418 W151 Indica II 98.0
CDR22 W152 Indica II 110.0
Chenghui448 W153 Indica II 103.8
Fengaizhan W154 Indica II 102.4
Gang46B W155 Indica Intermediate 98.4
Gumei2hao W156 Indica I 99.2
Huajingxian74 W157 Indica Intermediate 95.2
R644 W159 Indica II 95.2
Y134 W161 Indica II 102.0
Yuexiangzhan W163 Indica Intermediate 91.4
Zaoxian14 W164 Indica Intermediate 88.6
Zhong413 W165 Indica Intermediate 103.8
Zhongyouzao81 W166 Indica Intermediate 137.8
Zihui100 W167 Indica Intermediate 135.2
Bg90-2 W168 Indica II 101.4
IR72 W169 Indica II 93.6
PR106 W170 Indica II 90.6
TKM9 W171 Indica Intermediate 96.8
Amo13_(Sana) W172 Indica II 100.2
Gayabyeo W174 Indica II 84.0
Milyang23 W176 Indica II 101.4
MR185 W177 Indica II 100.0
Manawthukha W178 Indica III 97.8
Shwe_Thwe_Yin_Hyv W179 Indica II 93.8
Bg300 W180 Indica Intermediate 108.0
Bg94-1 W181 Indica Intermediate 105.8
CR203 W182 Indica II 101.2
OM997 W183 Indica II 96.6
PSB_RC_28 W184 Indica II 98.0
PSB_RC_66 W185 Indica II 95.6
TEQING W186 Indica Intermediate 98.2
IR68552-55-3-2 W187 Indica Intermediate 105.2
IR66897B W188 Indica II 102.0
IR58025B W189 Indica II 114.2
F6 W194 Indica II 108.8
452 W195 Indica II 123.8
Ai-Zi-DAO W197 Indica II 112.8
Babaomi W198 Indica Intermediate 180.0
Diantun502 W199 Indica Intermediate 125.2
Heiheaihui W200 Indica Intermediate 115.4
Jiangxisimiao W201 Indica Intermediate 108.2
Laohudao W202 Indica Intermediate 112.0
Linjintangdao W203 Indica Intermediate 185.6
Mengguandamagu W204 Indica I 154.2
Pengshantieganzhan W205 Indica I 161.8
Wumanggaonuo W206 Indica Intermediate 112.0
Khao_Daeng W210 Indica I 166.4
Basmati370 W211 Indica II 97.0
Bhavani W212 Indica Intermediate 159.6
IR50 W213 Indica Intermediate 137.4
Type3 W216 Indica II 113.8
IRAT352 W217 Indica Intermediate 133.8
TB154E-TB-2 W218 Indica Intermediate 133.6
MR77_(seberang) W221 Indica Intermediate 112.4
ir6 W222 Indica II 115.6
At354 W223 Indica II 103.6
BG304 W224 Indica II 116.0
OM1706 W227 Indica Intermediate 106.6
OM1723 W228 Indica II 115.0
X21 W229 Indica II 119.4
X22 W230 Indica II -9.0
X23 W231 Indica II 117.0
C70 W233 Indica Intermediate 114.2
Q5 W234 Indica Intermediate 112.8
Suiyangnian W235 Indica I 148.4
Pokhreli W236 Indica II 101.8
Govnd W237 Indica II 115.8
UPR191-66 W238 Indica II 95.4
ASD18 W239 Indica Intermediate 109.8
TGMS29 W240 Indica Intermediate 111.6
Phalguna W241 Indica II 119.2
Ajaya W242 Indica Intermediate 106.2
Dodda W243 Indica II 105.6
Palung_2 W244 Indica II 102.4
TKM6 W245 Indica Intermediate 121.6
RUSTYLATE/Zhong_413 W246 Indica Intermediate 151.0
Yenfangghu W247 Indica I 170.2
Heimichut W248 Indica I 145.4
Up15 W259 Indica II 106.0
Bintapan W262 Indica I 83.8
SADAJIRA-19-303 W263 Indica Intermediate 114.8
CHOROFA W264 Indica Intermediate 91.4
La110 W265 Indica Intermediate 120.4
Yunjiang35 W266 Indica III 132.6
Yunhui72 W267 Indica Intermediate 114.4
Wudadaozhong W268 Indica Intermediate 91.4
IR65600-27-1-2-2 W269 Indica Intermediate 96.0
Yetuozai W270 Indica Intermediate 99.0
P59279 W271 Indica Intermediate 95.8
Tsao_wan_ching W272 Indica Intermediate 155.6
Er_chiu_ching W274 Indica I 70.8
Pathma_wee W276 Indica III 160.2
Ma_ba_you_zhan W282 Indica Intermediate 134.8
IR_661-1-140-3-117 W289 Indica II 104.4
IR_2071-625-1-252 W291 Indica II 96.6
IR_8 W293 Indica II 83.4
LEBONNET W295 Indica II 99.6
IR_36 W298 Indica II 95.2
JAYA W299 Indica Intermediate 90.8
IR_64 W301 Indica II 95.6
AGNO_(PSBRC28) W307 Indica II 101.0
PSBRC82 W308 Indica II 109.4
NSICRC122 W309 Indica II 112.2
BRRI_DHAN_29 W310 Indica Intermediate 111.2
PR_116 W311 Indica II 100.6
CIGEULIS W312 Indica II 111.6
OM_2517 W313 Indica II 110.4
BRRI_DHAN_28 W314 Indica II 111.2
CIBOGO W315 Indica II 102.0
NEDA W316 Indica II 99.0
CIHERANG W317 Indica II 110.4
Qiuqianbai W318 Indica I 139.3
Wenxiangnuo W320 Indica Intermediate 177.2
Laozaogu W321 Indica III 160.6
Lengshuinuo W322 Indica Intermediate 109.0

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
vg0138428840 sf0138427797 1 38428840 2.61E-35 7.79E-06
vg0138424728 sf0138423685 1 38424728 1.41E-34 8.59E-07
vg0131754198 sf0131753154 1 31754198 2.24E-33 NA
vg0135647613 sf0135646570 1 35647613 1.88E-31 5.70E-08
vg0135617816 sf0135616773 1 35617816 1.28E-30 7.17E-11
vg0123720143 sf0123719099 1 23720143 3.11E-30 NA
vg0300353676 sf0300352674 3 353676 1.64E-28 5.49E-06
vg0137838382 sf0137837339 1 37838382 3.76E-23 4.85E-06
vg0133440209 sf0133439165 1 33440209 2.15E-22 2.09E-09
vg0138608956 sf0138607913 1 38608956 2.33E-21 1.24E-07
vg0626847484 sf0626846487 6 26847484 7.13E-21 NA
vg0617735644 sf0617734647 6 17735644 3.78E-19 2.20E-07
vg0614016173 sf0614015174 6 14016173 1.34E-16 5.73E-07
vg0139946773 sf0139945730 1 39946773 2.19E-14 2.52E-07
vg0314203662 sf0314202351 3 14203662 NA 6.77E-08
vg0206403097 sf0206403097 2 6403097 NA 2.79E-07
vg1215352517 sf1215349815 12 15352517 NA 7.23E-07
vg0133271810 sf0133270766 1 33271810 NA 1.25E-06
vg0618029961 sf0618028964 6 18029961 NA 1.30E-06
vg0707215921 sf0707214926 7 7215921 NA 1.43E-06
vg0626149778 sf0626148781 6 26149778 NA 1.50E-06
vg0724905355 sf0724904361 7 24905355 NA 1.59E-06
vg0310272191 sf0310271107 3 10272191 NA 1.77E-06
vg0703359540 sf0703358541 7 3359540 NA 1.84E-06
vg0402468319 sf0402463917 4 2468319 NA 4.08E-06
vg1016355947 sf1016284723 10 16355947 NA 4.86E-06