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 Heading Date (day) Distribution in Japonica All Population:

Phenotype Information Table:

Note: -9 means missing value.

Cultivar Name Cultivar ID Subpopulation Heading Date (day)
Gerdeh C003 Japonica Intermediate 82
Li-Jiang-Xin-Tuan-Hei-Gu_ C004 Temperate Japonica 84
AZUCENA C005 Tropical Japonica 102
CYPRESS C010 Tropical Japonica 96
Tainong67 C012 Temperate Japonica 97
M202 C014 Japonica Intermediate 78
Laoguangtou83 C016 Temperate Japonica 53
AnnongwangengB-1 C017 Temperate Japonica 50
AnnongwangengB-2 C018 Temperate Japonica 60
Funingzipi C023 Temperate Japonica 73
Weiguo C026 Temperate Japonica 80
Liaogeng287 C028 Temperate Japonica 81
Huhui628 C029 Japonica Intermediate 88
Longhuamaohu C032 Temperate Japonica 72
Zhonglouyihao1 C034 Temperate Japonica 83
Yelicanghua C035 Temperate Japonica 75
Zaoshunonghu6 C048 Temperate Japonica 89
Guihuahuang C052 Temperate Japonica 95
Xiushui115 C054 Temperate Japonica 102
Jindao1hao C056 Temperate Japonica 75
Dandongludao C057 Japonica Intermediate 84
Geng87-304 C063 Temperate Japonica 106
Sugeng2hao C064 Temperate Japonica 109
Muxiqiu C067 Temperate Japonica 85
Youmangzaogeng C070 Temperate Japonica 76
Laohuzhong C071 Temperate Japonica 108
cunsanli C074 Temperate Japonica 89
Huangkezaonian C075 Temperate Japonica 86
Muguanuo-1 C079 Temperate Japonica 85
Gaoyangdiandao C082 Temperate Japonica 90
chikenuo C083 Temperate Japonica 91
Haobuka C084 Japonica Intermediate 105
Shanjiugu C085 Japonica Intermediate 91
Lixingeng C087 Temperate Japonica 104
Tieganwu C089 Temperate Japonica 114
Xiangnuo-2 C093 Temperate Japonica 100
Babaili C101 Temperate Japonica 110
Yuyannuo-1 C103 Temperate Japonica 146
Hongkezhenuo C106 Temperate Japonica 107
Ximaxian C111 Temperate Japonica 147
LimingB C116 Temperate Japonica 85
Ninghui21 C119 Temperate Japonica 88
Shuiyuan300li C120 Temperate Japonica 73
Taidongludao C123 Tropical Japonica 82
Xiangnuo-1 C130 Temperate Japonica 98
Muguanuo-2 C133 Temperate Japonica 87
Wuzidui C134 Temperate Japonica 109
Cungunuo C137 Temperate Japonica 92
Lengshuigu C138 Temperate Japonica 99
Huangpinuo C144 Temperate Japonica 111
Nipponbare C146 Temperate Japonica 83
Zhonghua11 C149 Temperate Japonica 78
Balilla C150 Temperate Japonica 82
02428 C152 Temperate Japonica 94
IRAT109 C153 Tropical Japonica 89
Heigeng2hao C154 Temperate Japonica 58
Xingguo C171 Temperate Japonica 89
Zhonghua8hao C172 Temperate Japonica 80
Maguzi C177 Temperate Japonica 78
Haobayong1 C179 Temperate Japonica 104
Feidongtangdao C181 Temperate Japonica 89
Haomake(K) C185 Japonica Intermediate 108
Sanbangqishiluo C186 Japonica Intermediate 111
Niankenuo C187 Temperate Japonica 101
Yangkenuo C188 Temperate Japonica 103
Putaohuang C189 Temperate Japonica 83
Hongmisandan C195 Temperate Japonica 113
Yuyannuo-2 C196 Temperate Japonica 148
E_B_Gopher W002 Tropical Japonica 107
C_5560 W003 Tropical Japonica 96
Quinimpol W004 Tropical Japonica 106
TAICHU_MOCHI_59 W005 Tropical Japonica 109
WC_2811 W006 Tropical Japonica 104
Criollo_Chivacoa_2 W007 Tropical Japonica 105
Secano_do_Brazil W008 Tropical Japonica 105
Sel._No._388 W010 Japonica Intermediate 97
SHIMIZU_MOCHI W011 Temperate Japonica 73
KRASNODARSKIJ_424 W012 Temperate Japonica 67
Pergonil_15 W013 Temperate Japonica 72
NORIN_11 W016 Temperate Japonica 45
R_75 W017 Tropical Japonica 112
UZ_ROSZ_M38 W018 Temperate Japonica 60
H57-3-1 W019 Japonica Intermediate 91
Khao_Luang W021 Japonica Intermediate 105
C_8429 W022 Tropical Japonica 112
Padi_Pohon_Batu W024 Tropical Japonica 107
Chacareiro_Uruguay W027 Temperate Japonica 85
BLUE_STICK W038 Temperate Japonica 120
Onu_B W041 Tropical Japonica 95
KUBANETS_508 W045 Temperate Japonica 52
Jumli_dhan W047 Japonica Intermediate 97
HB-6-2 W052 Temperate Japonica 103
GPNO_1106 W053 Tropical Japonica 105
Tamanishiki W056 Temperate Japonica 110
Grassy W057 Tropical Japonica 100
Niwahutaw_Mochi W059 Temperate Japonica 90
Somewake W060 Temperate Japonica 72
Ardito W061 Japonica Intermediate 81
NANTON_NO._131 W062 Tropical Japonica 124
Vary_Tarva_Osla W063 Japonica Intermediate 85
CSORNUJ W064 Temperate Japonica 51
R_67 W065 Tropical Japonica 92
Mitak W067 Tropical Japonica 102
Gazan W068 Temperate Japonica 90
Celiaj W082 Temperate Japonica 77
CHUNJIANGZAO_NO._1 W088 Temperate Japonica 67
Padi_Tarab_Arab W102 Tropical Japonica 95
WIR_911 W109 Temperate Japonica 48
Lua_Chua_Chan W110 Tropical Japonica 128
Simpor W113 Tropical Japonica 110
WC_10253 W116 Tropical Japonica 99
KRASNODARSKIJ_3352 W117 Temperate Japonica 69
EMBRAPA_1200 W118 Tropical Japonica 103
WAB462-10-3-1 W119 Tropical Japonica 95
Bombilla W120 Temperate Japonica 90
BHIM_DHAN W122 Japonica Intermediate 98
WC_3532 W123 Tropical Japonica 99
Buphopa W127 Japonica Intermediate 112
LUSITANO W130 Temperate Japonica 69
A_5 W139 Temperate Japonica 45
Jyanak W143 Japonica Intermediate 112
Shennong265 W160 Temperate Japonica 89
Yuanjing7 W162 Temperate Japonica 105
Khazar W173 Tropical Japonica 93
Dianjing W193 Temperate Japonica 101
Yunguang8hao W207 Temperate Japonica 99
Zhongchao123 W208 Temperate Japonica 100
Gizal159 W209 Temperate Japonica 109
Lemont W225 Tropical Japonica 105
M401 W226 Temperate Japonica 85
Teksichut W249 Temperate Japonica 80
Eiko W250 Temperate Japonica 83
RUBIO W251 Tropical Japonica 91
Sereendan_Kuning W253 Tropical Japonica 101
SAI-BUI-BAO W254 Tropical Japonica 102
Latisai1 W257 Tropical Japonica 102
Uz-Rosz_275 W260 Tropical Japonica 90
Anambae_ndanggalasi W273 Tropical Japonica 109
Heen_goda_wee W275 Tropical Japonica 113
Sholay W281 Temperate Japonica 105
Daegujo W283 Temperate Japonica 73
Paikasa W284 Tropical Japonica 117
Uwi W285 Tropical Japonica 116
Dourado_Precoce W288 Tropical Japonica 103
Aichi_Asahi W290 Temperate Japonica 102
NEW_BONNET W300 Tropical Japonica 97
KUNTLAN W302 Tropical Japonica 105
British_Honduras_Creole W303 Tropical Japonica 96
AKITAKOMACHI W305 Temperate Japonica 82
Guangkexiangnuo W319 Temperate Japonica 127
Feienuo2 W323 Japonica Intermediate 115
Zimangfeie W324 Japonica Intermediate 125
Guantuibaihe W325 Temperate Japonica 117
Haolvguangnian W326 Japonica Intermediate 125
JinghuB W327 Temperate Japonica 88
GPNO_5055 W329 Tropical Japonica 107

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
vg0425921230 sf0425736105 4 25921230 1.13E-20 NA
vg0918030519 sf0918029518 9 18030519 1.71E-19 NA
vg0210593156 sf0210593154 2 10593156 2.12E-19 NA
vg0503927501 sf0503927478 5 3927501 1.59E-17 NA
vg1119869771 sf1119403694 11 19869771 2.54E-17 NA
vg0427274146 sf0427089015 4 27274146 2.60E-15 NA
vg1015531611 sf1015460379 10 15531611 9.20E-12 NA
vg0809615964 sf0809614968 8 9615964 1.20E-09 NA
vg0402823495 sf0402819100 4 2823495 NA 2.64E-07
vg1203971725 sf1203970723 12 3971725 NA 1.11E-06
vg0915803839 sf0915802838 9 15803839 NA 1.58E-06
vg0729413494 sf0729412502 7 29413494 NA 1.75E-06
vg0522307170 sf0522244611 5 22307170 NA 3.49E-06
vg1000923572 sf1000922548 10 923572 NA 3.68E-06