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 Japonica All Population:

Phenotype Information Table:

Note: -9 means missing value.

Cultivar Name Cultivar ID Subpopulation Plant Height (cm)
Gerdeh C003 Japonica Intermediate 141.57
Li-Jiang-Xin-Tuan-Hei-Gu_ C004 Temperate Japonica 140.4
AZUCENA C005 Tropical Japonica 163.33
CYPRESS C010 Tropical Japonica 106.7
Tainong67 C012 Temperate Japonica 114.1
M202 C014 Japonica Intermediate 82.43
Laoguangtou83 C016 Temperate Japonica 77.73
AnnongwangengB-1 C017 Temperate Japonica 92.67
AnnongwangengB-2 C018 Temperate Japonica 78.27
Funingzipi C023 Temperate Japonica 89.39
Weiguo C026 Temperate Japonica 104.7
Liaogeng287 C028 Temperate Japonica 86.97
Huhui628 C029 Japonica Intermediate 94.0
Longhuamaohu C032 Temperate Japonica 107.8
Zhonglouyihao1 C034 Temperate Japonica 110.5
Yelicanghua C035 Temperate Japonica 102.58
Zaoshunonghu6 C048 Temperate Japonica 97.33
Guihuahuang C052 Temperate Japonica 107.0
Xiushui115 C054 Temperate Japonica 97.9
Jindao1hao C056 Temperate Japonica 99.03
Dandongludao C057 Japonica Intermediate 123.63
Geng87-304 C063 Temperate Japonica 115.54
Sugeng2hao C064 Temperate Japonica 103.3
Muxiqiu C067 Temperate Japonica 117.93
Youmangzaogeng C070 Temperate Japonica 97.8
Laohuzhong C071 Temperate Japonica 128.2
cunsanli C074 Temperate Japonica 143.65
Huangkezaonian C075 Temperate Japonica 131.3
Muguanuo-1 C079 Temperate Japonica 143.32
Gaoyangdiandao C082 Temperate Japonica 156.46
chikenuo C083 Temperate Japonica 174.7
Haobuka C084 Japonica Intermediate 157.62
Shanjiugu C085 Japonica Intermediate 147.1
Lixingeng C087 Temperate Japonica 141.27
Tieganwu C089 Temperate Japonica 142.43
Xiangnuo-2 C093 Temperate Japonica 164.73
Babaili C101 Temperate Japonica 192.07
Yuyannuo-1 C103 Temperate Japonica 202.07
Hongkezhenuo C106 Temperate Japonica 191.0
Ximaxian C111 Temperate Japonica 206.13
LimingB C116 Temperate Japonica 87.03
Ninghui21 C119 Temperate Japonica 86.17
Shuiyuan300li C120 Temperate Japonica 97.63
Taidongludao C123 Tropical Japonica 118.83
Xiangnuo-1 C130 Temperate Japonica 155.4
Muguanuo-2 C133 Temperate Japonica 170.8
Wuzidui C134 Temperate Japonica 172.46
Cungunuo C137 Temperate Japonica 170.0
Lengshuigu C138 Temperate Japonica 190.9
Huangpinuo C144 Temperate Japonica 206.73
Nipponbare C146 Temperate Japonica 74.7
Zhonghua11 C149 Temperate Japonica 102.47
Balilla C150 Temperate Japonica 90.32
02428 C152 Temperate Japonica 100.0
IRAT109 C153 Tropical Japonica 105.07
Heigeng2hao C154 Temperate Japonica 77.43
Xingguo C171 Temperate Japonica 140.61
Zhonghua8hao C172 Temperate Japonica 102.37
Maguzi C177 Temperate Japonica 112.87
Haobayong1 C179 Temperate Japonica 133.53
Feidongtangdao C181 Temperate Japonica 137.9
Haomake(K) C185 Japonica Intermediate 145.0
Sanbangqishiluo C186 Japonica Intermediate 180.0
Niankenuo C187 Temperate Japonica 144.47
Yangkenuo C188 Temperate Japonica 137.8
Putaohuang C189 Temperate Japonica 162.36
Hongmisandan C195 Temperate Japonica 171.79
Yuyannuo-2 C196 Temperate Japonica 193.0
E_B_Gopher W002 Tropical Japonica 157.4
C_5560 W003 Tropical Japonica 140.4
Quinimpol W004 Tropical Japonica 158.2
TAICHU_MOCHI_59 W005 Tropical Japonica 133.8
WC_2811 W006 Tropical Japonica 149.8
Criollo_Chivacoa_2 W007 Tropical Japonica 150.8
Secano_do_Brazil W008 Tropical Japonica 147.0
Sel._No._388 W010 Japonica Intermediate 135.0
SHIMIZU_MOCHI W011 Temperate Japonica 116.8
KRASNODARSKIJ_424 W012 Temperate Japonica 100.8
Pergonil_15 W013 Temperate Japonica 98.6
NORIN_11 W016 Temperate Japonica 78.8
R_75 W017 Tropical Japonica 126.2
UZ_ROSZ_M38 W018 Temperate Japonica 93.4
H57-3-1 W019 Japonica Intermediate 124.8
Khao_Luang W021 Japonica Intermediate 142.4
C_8429 W022 Tropical Japonica 146.0
Padi_Pohon_Batu W024 Tropical Japonica 139.8
Chacareiro_Uruguay W027 Temperate Japonica 116.8
BLUE_STICK W038 Temperate Japonica 138.0
Onu_B W041 Tropical Japonica 169.4
KUBANETS_508 W045 Temperate Japonica 98.0
Jumli_dhan W047 Japonica Intermediate 203.2
HB-6-2 W052 Temperate Japonica 98.6
GPNO_1106 W053 Tropical Japonica 152.6
Tamanishiki W056 Temperate Japonica 129.0
Grassy W057 Tropical Japonica 182.2
Niwahutaw_Mochi W059 Temperate Japonica 115.8
Somewake W060 Temperate Japonica 119.4
Ardito W061 Japonica Intermediate 121.8
NANTON_NO._131 W062 Tropical Japonica 153.4
Vary_Tarva_Osla W063 Japonica Intermediate 114.2
CSORNUJ W064 Temperate Japonica 106.2
R_67 W065 Tropical Japonica 149.4
Mitak W067 Tropical Japonica 152.6
Gazan W068 Temperate Japonica 139.8
Celiaj W082 Temperate Japonica 125.0
CHUNJIANGZAO_NO._1 W088 Temperate Japonica 70.6
Padi_Tarab_Arab W102 Tropical Japonica 182.6
WIR_911 W109 Temperate Japonica 99.4
Lua_Chua_Chan W110 Tropical Japonica 154.4
Simpor W113 Tropical Japonica 141.0
WC_10253 W116 Tropical Japonica 175.4
KRASNODARSKIJ_3352 W117 Temperate Japonica 98.6
EMBRAPA_1200 W118 Tropical Japonica 84.2
WAB462-10-3-1 W119 Tropical Japonica 95.4
Bombilla W120 Temperate Japonica 109.6
BHIM_DHAN W122 Japonica Intermediate 169.8
WC_3532 W123 Tropical Japonica 140.8
Buphopa W127 Japonica Intermediate 142.6
LUSITANO W130 Temperate Japonica 92.6
A_5 W139 Temperate Japonica 96.4
Jyanak W143 Japonica Intermediate 196.8
Shennong265 W160 Temperate Japonica 96.0
Yuanjing7 W162 Temperate Japonica 98.4
Khazar W173 Tropical Japonica 121.6
Dianjing W193 Temperate Japonica 121.4
Yunguang8hao W207 Temperate Japonica 114.6
Zhongchao123 W208 Temperate Japonica 119.6
Gizal159 W209 Temperate Japonica 142.4
Lemont W225 Tropical Japonica 90.2
M401 W226 Temperate Japonica 93.2
Teksichut W249 Temperate Japonica 125.8
Eiko W250 Temperate Japonica 123.2
RUBIO W251 Tropical Japonica 129.8
Sereendan_Kuning W253 Tropical Japonica 146.2
SAI-BUI-BAO W254 Tropical Japonica 143.4
Latisai1 W257 Tropical Japonica 171.6
Uz-Rosz_275 W260 Tropical Japonica 134.0
Anambae_ndanggalasi W273 Tropical Japonica 156.2
Heen_goda_wee W275 Tropical Japonica 148.2
Sholay W281 Temperate Japonica 150.0
Daegujo W283 Temperate Japonica 68.4
Paikasa W284 Tropical Japonica 135.4
Uwi W285 Tropical Japonica 134.6
Dourado_Precoce W288 Tropical Japonica 144.2
Aichi_Asahi W290 Temperate Japonica 116.4
NEW_BONNET W300 Tropical Japonica 107.2
KUNTLAN W302 Tropical Japonica 166.8
British_Honduras_Creole W303 Tropical Japonica 157.8
AKITAKOMACHI W305 Temperate Japonica 74.0
Guangkexiangnuo W319 Temperate Japonica 174.2
Feienuo2 W323 Japonica Intermediate 136.4
Zimangfeie W324 Japonica Intermediate 156.0
Guantuibaihe W325 Temperate Japonica 135.8
Haolvguangnian W326 Japonica Intermediate 155.4
JinghuB W327 Temperate Japonica 89.8
GPNO_5055 W329 Tropical Japonica 147.4

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
vg0140366212 sf0140365169 1 40366212 5.71E-24 NA
vg0427936324 sf0427751187 4 27936324 2.06E-22 NA
vg0801829820 sf0801828823 8 1829820 3.06E-22 NA
vg0112928822 sf0112927796 1 12928822 5.12E-22 NA
vg0728390085 sf0728389093 7 28390085 5.75E-22 NA
vg0431158473 sf0430973364 4 31158473 9.02E-18 NA
vg0528325523 sf0528262878 5 28325523 1.66E-14 NA
vg0713713694 sf0713712701 7 13713694 3.50E-13 NA
vg0808250957 sf0808249961 8 8250957 1.98E-12 NA
vg0904237248 sf0904236248 9 4237248 NA 2.50E-08
vg0114706624 sf0114705598 1 14706624 NA 2.04E-07
vg0525619564 sf0525556985 5 25619564 NA 2.18E-06
vg0421353471 sf0421181525 4 21353471 NA 2.74E-06
vg1125863777 sf1125397696 11 25863777 NA 3.67E-06
vg0719775322 sf0719774329 7 19775322 NA 8.97E-06