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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 Japonica All Population:

Phenotype Information Table:

Note: -9 means missing value.

Cultivar Name Cultivar ID Subpopulation Grain weight
Gerdeh C003 Japonica Intermediate 25.75
Li-Jiang-Xin-Tuan-Hei-Gu_ C004 Temperate Japonica 22.08
AZUCENA C005 Tropical Japonica 28.98
CYPRESS C010 Tropical Japonica 21.18
Tainong67 C012 Temperate Japonica 18.18
M202 C014 Japonica Intermediate 22.97
Laoguangtou83 C016 Temperate Japonica 17.12
AnnongwangengB-1 C017 Temperate Japonica 20.9
AnnongwangengB-2 C018 Temperate Japonica 17.85
Funingzipi C023 Temperate Japonica 20.59
Weiguo C026 Temperate Japonica 22.17
Liaogeng287 C028 Temperate Japonica 23.47
Huhui628 C029 Japonica Intermediate 17.76
Longhuamaohu C032 Temperate Japonica 26.32
Zhonglouyihao1 C034 Temperate Japonica 20.3
Yelicanghua C035 Temperate Japonica 21.81
Zaoshunonghu6 C048 Temperate Japonica 25.14
Guihuahuang C052 Temperate Japonica 27.09
Xiushui115 C054 Temperate Japonica 26.84
Jindao1hao C056 Temperate Japonica 25.07
Dandongludao C057 Japonica Intermediate 18.83
Geng87-304 C063 Temperate Japonica 19.8
Sugeng2hao C064 Temperate Japonica 23.65
Muxiqiu C067 Temperate Japonica 20.18
Youmangzaogeng C070 Temperate Japonica 22.09
Laohuzhong C071 Temperate Japonica 26.08
cunsanli C074 Temperate Japonica 30.35
Huangkezaonian C075 Temperate Japonica 22.4
Muguanuo-1 C079 Temperate Japonica 21.12
Gaoyangdiandao C082 Temperate Japonica 23.83
chikenuo C083 Temperate Japonica 23.46
Haobuka C084 Japonica Intermediate 41.48
Shanjiugu C085 Japonica Intermediate 25.52
Lixingeng C087 Temperate Japonica 24.27
Tieganwu C089 Temperate Japonica 20.57
Xiangnuo-2 C093 Temperate Japonica 22.87
Babaili C101 Temperate Japonica 21.04
Yuyannuo-1 C103 Temperate Japonica 25.56
Hongkezhenuo C106 Temperate Japonica 17.61
Ximaxian C111 Temperate Japonica 15.24
LimingB C116 Temperate Japonica 20.1
Ninghui21 C119 Temperate Japonica 19.36
Shuiyuan300li C120 Temperate Japonica 20.78
Taidongludao C123 Tropical Japonica 31.08
Xiangnuo-1 C130 Temperate Japonica 22.14
Muguanuo-2 C133 Temperate Japonica 22.27
Wuzidui C134 Temperate Japonica 19.34
Cungunuo C137 Temperate Japonica 30.57
Lengshuigu C138 Temperate Japonica 25.47
Huangpinuo C144 Temperate Japonica 25.69
Nipponbare C146 Temperate Japonica 21.68
Zhonghua11 C149 Temperate Japonica 25.86
Balilla C150 Temperate Japonica 25.67
02428 C152 Temperate Japonica 23.93
IRAT109 C153 Tropical Japonica 30.41
Heigeng2hao C154 Temperate Japonica 14.01
Xingguo C171 Temperate Japonica 24.1
Zhonghua8hao C172 Temperate Japonica 19.76
Maguzi C177 Temperate Japonica 21.11
Haobayong1 C179 Temperate Japonica 20.05
Feidongtangdao C181 Temperate Japonica 25.98
Haomake(K) C185 Japonica Intermediate 23.36
Sanbangqishiluo C186 Japonica Intermediate 29.77
Niankenuo C187 Temperate Japonica 22.91
Yangkenuo C188 Temperate Japonica 22.23
Putaohuang C189 Temperate Japonica 24.64
Hongmisandan C195 Temperate Japonica 16.71
Yuyannuo-2 C196 Temperate Japonica 23.32
E_B_Gopher W002 Tropical Japonica 22.59
C_5560 W003 Tropical Japonica 29.0
Quinimpol W004 Tropical Japonica 25.99
TAICHU_MOCHI_59 W005 Tropical Japonica 19.12
WC_2811 W006 Tropical Japonica 28.35
Criollo_Chivacoa_2 W007 Tropical Japonica 25.61
Secano_do_Brazil W008 Tropical Japonica 23.93
Sel._No._388 W010 Japonica Intermediate 22.71
SHIMIZU_MOCHI W011 Temperate Japonica 25.41
KRASNODARSKIJ_424 W012 Temperate Japonica 30.31
Pergonil_15 W013 Temperate Japonica 27.34
NORIN_11 W016 Temperate Japonica 22.48
R_75 W017 Tropical Japonica 26.25
UZ_ROSZ_M38 W018 Temperate Japonica 23.74
H57-3-1 W019 Japonica Intermediate 24.64
Khao_Luang W021 Japonica Intermediate 36.65
C_8429 W022 Tropical Japonica 27.26
Padi_Pohon_Batu W024 Tropical Japonica 22.16
Chacareiro_Uruguay W027 Temperate Japonica 21.78
BLUE_STICK W038 Temperate Japonica 20.96
Onu_B W041 Tropical Japonica 26.31
KUBANETS_508 W045 Temperate Japonica 29.56
Jumli_dhan W047 Japonica Intermediate 23.66
HB-6-2 W052 Temperate Japonica 30.65
GPNO_1106 W053 Tropical Japonica 26.72
Tamanishiki W056 Temperate Japonica 18.13
Grassy W057 Tropical Japonica 29.18
Niwahutaw_Mochi W059 Temperate Japonica 23.55
Somewake W060 Temperate Japonica 26.41
Ardito W061 Japonica Intermediate 41.24
NANTON_NO._131 W062 Tropical Japonica 25.7
Vary_Tarva_Osla W063 Japonica Intermediate 34.53
CSORNUJ W064 Temperate Japonica 22.25
R_67 W065 Tropical Japonica 27.67
Mitak W067 Tropical Japonica 29.05
Gazan W068 Temperate Japonica 20.99
Celiaj W082 Temperate Japonica 29.65
CHUNJIANGZAO_NO._1 W088 Temperate Japonica 26.61
Padi_Tarab_Arab W102 Tropical Japonica 25.11
WIR_911 W109 Temperate Japonica 22.16
Lua_Chua_Chan W110 Tropical Japonica 21.3
Simpor W113 Tropical Japonica 19.89
WC_10253 W116 Tropical Japonica 30.95
KRASNODARSKIJ_3352 W117 Temperate Japonica 29.31
EMBRAPA_1200 W118 Tropical Japonica 37.3
WAB462-10-3-1 W119 Tropical Japonica 24.35
Bombilla W120 Temperate Japonica 31.65
BHIM_DHAN W122 Japonica Intermediate 19.83
WC_3532 W123 Tropical Japonica 27.04
Buphopa W127 Japonica Intermediate 25.56
LUSITANO W130 Temperate Japonica 31.05
A_5 W139 Temperate Japonica 25.13
Jyanak W143 Japonica Intermediate 17.89
Shennong265 W160 Temperate Japonica 30.0
Yuanjing7 W162 Temperate Japonica 23.43
Khazar W173 Tropical Japonica 25.35
Dianjing W193 Temperate Japonica 28.62
Yunguang8hao W207 Temperate Japonica 28.67
Zhongchao123 W208 Temperate Japonica 29.16
Gizal159 W209 Temperate Japonica 23.54
Lemont W225 Tropical Japonica 24.79
M401 W226 Temperate Japonica 28.08
Teksichut W249 Temperate Japonica 36.33
Eiko W250 Temperate Japonica 37.46
RUBIO W251 Tropical Japonica 25.95
Sereendan_Kuning W253 Tropical Japonica 30.2
SAI-BUI-BAO W254 Tropical Japonica 29.24
Latisai1 W257 Tropical Japonica 28.82
Uz-Rosz_275 W260 Tropical Japonica 26.63
Anambae_ndanggalasi W273 Tropical Japonica 16.0
Heen_goda_wee W275 Tropical Japonica 15.64
Sholay W281 Temperate Japonica 25.83
Daegujo W283 Temperate Japonica 26.89
Paikasa W284 Tropical Japonica 15.86
Uwi W285 Tropical Japonica 21.49
Dourado_Precoce W288 Tropical Japonica 32.01
Aichi_Asahi W290 Temperate Japonica 23.63
NEW_BONNET W300 Tropical Japonica 19.47
KUNTLAN W302 Tropical Japonica 25.19
British_Honduras_Creole W303 Tropical Japonica 26.79
AKITAKOMACHI W305 Temperate Japonica 25.98
Guangkexiangnuo W319 Temperate Japonica 24.62
Feienuo2 W323 Japonica Intermediate 22.04
Zimangfeie W324 Japonica Intermediate 27.6
Guantuibaihe W325 Temperate Japonica 21.49
Haolvguangnian W326 Japonica Intermediate 28.35
JinghuB W327 Temperate Japonica 26.13
GPNO_5055 W329 Tropical Japonica 26.18

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
vg0219524344 sf0219518476 2 19524344 8.87E-10 NA
vg0620193667 sf0620192670 6 20193667 9.28E-09 NA
vg1224489196 sf1224455650 12 24489196 1.18E-08 NA
vg0810860589 sf0810859594 8 10860589 2.80E-08 NA
vg0718587094 sf0718586101 7 18587094 7.23E-08 NA
vg1020927774 sf1020856253 10 20927774 2.98E-06 NA
vg0902524873 sf0902523873 9 2524873 NA 6.85E-06