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 Spikelet length Distribution in Japonica All Population:

Phenotype Information Table:

Note: -9 means missing value.

Cultivar Name Cultivar ID Subpopulation Spikelet length
Gerdeh C003 Japonica Intermediate 26.37
Li-Jiang-Xin-Tuan-Hei-Gu_ C004 Temperate Japonica 21.75
AZUCENA C005 Tropical Japonica 30.48
CYPRESS C010 Tropical Japonica 21.55
Tainong67 C012 Temperate Japonica 22.09
M202 C014 Japonica Intermediate 17.51
Laoguangtou83 C016 Temperate Japonica 14.87
AnnongwangengB-1 C017 Temperate Japonica 18.83
AnnongwangengB-2 C018 Temperate Japonica 15.07
Funingzipi C023 Temperate Japonica 20.35
Weiguo C026 Temperate Japonica 19.4
Liaogeng287 C028 Temperate Japonica 15.24
Huhui628 C029 Japonica Intermediate 21.13
Longhuamaohu C032 Temperate Japonica 18.57
Zhonglouyihao1 C034 Temperate Japonica 23.69
Yelicanghua C035 Temperate Japonica 18.86
Zaoshunonghu6 C048 Temperate Japonica 21.75
Guihuahuang C052 Temperate Japonica 17.57
Xiushui115 C054 Temperate Japonica 19.15
Jindao1hao C056 Temperate Japonica 20.85
Dandongludao C057 Japonica Intermediate 23.12
Geng87-304 C063 Temperate Japonica 23.25
Sugeng2hao C064 Temperate Japonica 16.42
Muxiqiu C067 Temperate Japonica 21.95
Youmangzaogeng C070 Temperate Japonica 16.77
Laohuzhong C071 Temperate Japonica 22.68
cunsanli C074 Temperate Japonica 22.39
Huangkezaonian C075 Temperate Japonica 23.21
Muguanuo-1 C079 Temperate Japonica 25.4
Gaoyangdiandao C082 Temperate Japonica 24.25
chikenuo C083 Temperate Japonica 26.01
Haobuka C084 Japonica Intermediate 17.52
Shanjiugu C085 Japonica Intermediate 25.71
Lixingeng C087 Temperate Japonica 24.54
Tieganwu C089 Temperate Japonica 20.09
Xiangnuo-2 C093 Temperate Japonica 26.9
Babaili C101 Temperate Japonica 28.95
Yuyannuo-1 C103 Temperate Japonica 28.38
Hongkezhenuo C106 Temperate Japonica 27.43
Ximaxian C111 Temperate Japonica 26.35
LimingB C116 Temperate Japonica 16.61
Ninghui21 C119 Temperate Japonica 20.38
Shuiyuan300li C120 Temperate Japonica 18.65
Taidongludao C123 Tropical Japonica 21.76
Xiangnuo-1 C130 Temperate Japonica 24.43
Muguanuo-2 C133 Temperate Japonica 25.13
Wuzidui C134 Temperate Japonica 22.99
Cungunuo C137 Temperate Japonica 24.76
Lengshuigu C138 Temperate Japonica 33.34
Huangpinuo C144 Temperate Japonica 28.44
Nipponbare C146 Temperate Japonica 17.49
Zhonghua11 C149 Temperate Japonica 21.45
Balilla C150 Temperate Japonica 15.58
02428 C152 Temperate Japonica 23.67
IRAT109 C153 Tropical Japonica 23.21
Heigeng2hao C154 Temperate Japonica 14.16
Xingguo C171 Temperate Japonica 24.03
Zhonghua8hao C172 Temperate Japonica 21.3
Maguzi C177 Temperate Japonica 20.08
Haobayong1 C179 Temperate Japonica 27.39
Feidongtangdao C181 Temperate Japonica 22.43
Haomake(K) C185 Japonica Intermediate 25.02
Sanbangqishiluo C186 Japonica Intermediate 30.33
Niankenuo C187 Temperate Japonica 25.87
Yangkenuo C188 Temperate Japonica 23.11
Putaohuang C189 Temperate Japonica 19.15
Hongmisandan C195 Temperate Japonica 23.07
Yuyannuo-2 C196 Temperate Japonica 25.76
E_B_Gopher W002 Tropical Japonica 25.26
C_5560 W003 Tropical Japonica 24.31
Quinimpol W004 Tropical Japonica 23.04
TAICHU_MOCHI_59 W005 Tropical Japonica 22.65
WC_2811 W006 Tropical Japonica 24.6
Criollo_Chivacoa_2 W007 Tropical Japonica 26.47
Secano_do_Brazil W008 Tropical Japonica 25.83
Sel._No._388 W010 Japonica Intermediate 23.92
SHIMIZU_MOCHI W011 Temperate Japonica 25.74
KRASNODARSKIJ_424 W012 Temperate Japonica 21.89
Pergonil_15 W013 Temperate Japonica 20.24
NORIN_11 W016 Temperate Japonica 13.68
R_75 W017 Tropical Japonica 24.36
UZ_ROSZ_M38 W018 Temperate Japonica 20.02
H57-3-1 W019 Japonica Intermediate 20.68
Khao_Luang W021 Japonica Intermediate 24.5
C_8429 W022 Tropical Japonica 28.84
Padi_Pohon_Batu W024 Tropical Japonica 22.92
Chacareiro_Uruguay W027 Temperate Japonica 23.31
BLUE_STICK W038 Temperate Japonica 21.46
Onu_B W041 Tropical Japonica 27.49
KUBANETS_508 W045 Temperate Japonica 19.5
Jumli_dhan W047 Japonica Intermediate 23.86
HB-6-2 W052 Temperate Japonica 19.74
GPNO_1106 W053 Tropical Japonica 25.81
Tamanishiki W056 Temperate Japonica 22.79
Grassy W057 Tropical Japonica 28.27
Niwahutaw_Mochi W059 Temperate Japonica 21.57
Somewake W060 Temperate Japonica 24.91
Ardito W061 Japonica Intermediate 20.73
NANTON_NO._131 W062 Tropical Japonica 30.45
Vary_Tarva_Osla W063 Japonica Intermediate 21.28
CSORNUJ W064 Temperate Japonica 16.95
R_67 W065 Tropical Japonica 24.33
Mitak W067 Tropical Japonica 29.03
Gazan W068 Temperate Japonica 22.29
Celiaj W082 Temperate Japonica 24.32
CHUNJIANGZAO_NO._1 W088 Temperate Japonica 18.43
Padi_Tarab_Arab W102 Tropical Japonica 25.89
WIR_911 W109 Temperate Japonica 18.03
Lua_Chua_Chan W110 Tropical Japonica 24.37
Simpor W113 Tropical Japonica 25.27
WC_10253 W116 Tropical Japonica 32.1
KRASNODARSKIJ_3352 W117 Temperate Japonica 20.9
EMBRAPA_1200 W118 Tropical Japonica 22.82
WAB462-10-3-1 W119 Tropical Japonica 20.01
Bombilla W120 Temperate Japonica 19.86
BHIM_DHAN W122 Japonica Intermediate 25.56
WC_3532 W123 Tropical Japonica 26.1
Buphopa W127 Japonica Intermediate 25.69
LUSITANO W130 Temperate Japonica 18.79
A_5 W139 Temperate Japonica 16.51
Jyanak W143 Japonica Intermediate 27.59
Shennong265 W160 Temperate Japonica 16.62
Yuanjing7 W162 Temperate Japonica 18.55
Khazar W173 Tropical Japonica 26.55
Dianjing W193 Temperate Japonica 23.73
Yunguang8hao W207 Temperate Japonica 25.54
Zhongchao123 W208 Temperate Japonica 23.01
Gizal159 W209 Temperate Japonica 22.48
Lemont W225 Tropical Japonica 24.5
M401 W226 Temperate Japonica 22.42
Teksichut W249 Temperate Japonica 21.38
Eiko W250 Temperate Japonica 19.81
RUBIO W251 Tropical Japonica 20.7
Sereendan_Kuning W253 Tropical Japonica 23.77
SAI-BUI-BAO W254 Tropical Japonica 24.26
Latisai1 W257 Tropical Japonica 26.58
Uz-Rosz_275 W260 Tropical Japonica 24.17
Anambae_ndanggalasi W273 Tropical Japonica 30.35
Heen_goda_wee W275 Tropical Japonica 26.45
Sholay W281 Temperate Japonica 27.37
Daegujo W283 Temperate Japonica 17.04
Paikasa W284 Tropical Japonica 21.73
Uwi W285 Tropical Japonica 23.2
Dourado_Precoce W288 Tropical Japonica 24.56
Aichi_Asahi W290 Temperate Japonica 23.56
NEW_BONNET W300 Tropical Japonica 24.66
KUNTLAN W302 Tropical Japonica 25.93
British_Honduras_Creole W303 Tropical Japonica 23.45
AKITAKOMACHI W305 Temperate Japonica 18.06
Guangkexiangnuo W319 Temperate Japonica 26.28
Feienuo2 W323 Japonica Intermediate 23.97
Zimangfeie W324 Japonica Intermediate 28.58
Guantuibaihe W325 Temperate Japonica 22.39
Haolvguangnian W326 Japonica Intermediate 30.23
JinghuB W327 Temperate Japonica 20.06
GPNO_5055 W329 Tropical Japonica 26.7

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
vg0113384484 sf0113383458 1 13384484 3.10E-21 3.83E-06
vg0428761895 sf0428576746 4 28761895 2.44E-19 NA
vg0140366212 sf0140365169 1 40366212 1.13E-18 NA
vg1200417909 sf1200416909 12 417909 4.16E-18 NA
vg0919398119 sf0919397709 9 19398119 2.66E-17 NA
vg0224963772 sf0224957903 2 24963772 1.13E-13 3.09E-07
vg0913016357 sf0913015356 9 13016357 2.23E-11 NA
vg0719711141 sf0719710148 7 19711141 NA 1.64E-08
vg0719650559 sf0719649566 7 19650559 NA 1.20E-06