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 thickness Distribution in Japonica All Population:

Phenotype Information Table:

Note: -9 means missing value.

Cultivar Name Cultivar ID Subpopulation Grain thickness
Gerdeh C003 Japonica Intermediate 2.12
Li-Jiang-Xin-Tuan-Hei-Gu_ C004 Temperate Japonica 2.08
AZUCENA C005 Tropical Japonica 1.95
CYPRESS C010 Tropical Japonica 1.9
Tainong67 C012 Temperate Japonica 1.99
M202 C014 Japonica Intermediate 2.03
Laoguangtou83 C016 Temperate Japonica 2.24
AnnongwangengB-1 C017 Temperate Japonica 2.27
AnnongwangengB-2 C018 Temperate Japonica 2.27
Funingzipi C023 Temperate Japonica 2.0
Weiguo C026 Temperate Japonica 2.21
Liaogeng287 C028 Temperate Japonica 2.2
Huhui628 C029 Japonica Intermediate 2.0
Longhuamaohu C032 Temperate Japonica 2.15
Zhonglouyihao1 C034 Temperate Japonica 2.01
Yelicanghua C035 Temperate Japonica 2.04
Zaoshunonghu6 C048 Temperate Japonica 2.3
Guihuahuang C052 Temperate Japonica 2.29
Xiushui115 C054 Temperate Japonica 2.17
Jindao1hao C056 Temperate Japonica 2.31
Dandongludao C057 Japonica Intermediate 2.11
Geng87-304 C063 Temperate Japonica 2.11
Sugeng2hao C064 Temperate Japonica 2.2
Muxiqiu C067 Temperate Japonica 1.9
Youmangzaogeng C070 Temperate Japonica 2.22
Laohuzhong C071 Temperate Japonica 2.11
cunsanli C074 Temperate Japonica 2.11
Huangkezaonian C075 Temperate Japonica 2.33
Muguanuo-1 C079 Temperate Japonica 2.13
Gaoyangdiandao C082 Temperate Japonica 2.19
chikenuo C083 Temperate Japonica 2.07
Haobuka C084 Japonica Intermediate 2.43
Shanjiugu C085 Japonica Intermediate 2.22
Lixingeng C087 Temperate Japonica 2.14
Tieganwu C089 Temperate Japonica 2.02
Xiangnuo-2 C093 Temperate Japonica 2.01
Babaili C101 Temperate Japonica 2.09
Yuyannuo-1 C103 Temperate Japonica 2.2
Hongkezhenuo C106 Temperate Japonica 1.97
Ximaxian C111 Temperate Japonica 1.93
LimingB C116 Temperate Japonica 2.15
Ninghui21 C119 Temperate Japonica 1.98
Shuiyuan300li C120 Temperate Japonica 2.28
Taidongludao C123 Tropical Japonica 2.45
Xiangnuo-1 C130 Temperate Japonica 1.96
Muguanuo-2 C133 Temperate Japonica 2.21
Wuzidui C134 Temperate Japonica 2.06
Cungunuo C137 Temperate Japonica 2.24
Lengshuigu C138 Temperate Japonica 2.19
Huangpinuo C144 Temperate Japonica 2.35
Nipponbare C146 Temperate Japonica 2.23
Zhonghua11 C149 Temperate Japonica 2.32
Balilla C150 Temperate Japonica 2.24
02428 C152 Temperate Japonica 1.92
IRAT109 C153 Tropical Japonica 2.28
Heigeng2hao C154 Temperate Japonica 2.16
Xingguo C171 Temperate Japonica 2.09
Zhonghua8hao C172 Temperate Japonica 2.31
Maguzi C177 Temperate Japonica 2.03
Haobayong1 C179 Temperate Japonica 2.18
Feidongtangdao C181 Temperate Japonica 2.13
Haomake(K) C185 Japonica Intermediate 2.07
Sanbangqishiluo C186 Japonica Intermediate 2.22
Niankenuo C187 Temperate Japonica 2.14
Yangkenuo C188 Temperate Japonica 2.05
Putaohuang C189 Temperate Japonica 2.11
Hongmisandan C195 Temperate Japonica 1.91
Yuyannuo-2 C196 Temperate Japonica 2.1
E_B_Gopher W002 Tropical Japonica 1.81
C_5560 W003 Tropical Japonica 2.06
Quinimpol W004 Tropical Japonica 1.98
TAICHU_MOCHI_59 W005 Tropical Japonica 1.73
WC_2811 W006 Tropical Japonica 1.95
Criollo_Chivacoa_2 W007 Tropical Japonica 1.8
Secano_do_Brazil W008 Tropical Japonica 1.91
Sel._No._388 W010 Japonica Intermediate 1.93
SHIMIZU_MOCHI W011 Temperate Japonica 2.2
KRASNODARSKIJ_424 W012 Temperate Japonica 2.38
Pergonil_15 W013 Temperate Japonica 2.45
NORIN_11 W016 Temperate Japonica 2.27
R_75 W017 Tropical Japonica 1.89
UZ_ROSZ_M38 W018 Temperate Japonica 2.1
H57-3-1 W019 Japonica Intermediate 1.92
Khao_Luang W021 Japonica Intermediate 2.31
C_8429 W022 Tropical Japonica 2.11
Padi_Pohon_Batu W024 Tropical Japonica 1.83
Chacareiro_Uruguay W027 Temperate Japonica 1.8
BLUE_STICK W038 Temperate Japonica 2.06
Onu_B W041 Tropical Japonica 1.9
KUBANETS_508 W045 Temperate Japonica 2.23
Jumli_dhan W047 Japonica Intermediate 2.19
HB-6-2 W052 Temperate Japonica 2.12
GPNO_1106 W053 Tropical Japonica 1.87
Tamanishiki W056 Temperate Japonica 2.15
Grassy W057 Tropical Japonica 1.9
Niwahutaw_Mochi W059 Temperate Japonica 2.1
Somewake W060 Temperate Japonica 2.23
Ardito W061 Japonica Intermediate 2.45
NANTON_NO._131 W062 Tropical Japonica 2.05
Vary_Tarva_Osla W063 Japonica Intermediate 2.12
CSORNUJ W064 Temperate Japonica 2.01
R_67 W065 Tropical Japonica 2.03
Mitak W067 Tropical Japonica 2.03
Gazan W068 Temperate Japonica 1.91
Celiaj W082 Temperate Japonica 2.18
CHUNJIANGZAO_NO._1 W088 Temperate Japonica 2.23
Padi_Tarab_Arab W102 Tropical Japonica 1.91
WIR_911 W109 Temperate Japonica 2.04
Lua_Chua_Chan W110 Tropical Japonica 2.0
Simpor W113 Tropical Japonica 1.8
WC_10253 W116 Tropical Japonica 2.1
KRASNODARSKIJ_3352 W117 Temperate Japonica 2.38
EMBRAPA_1200 W118 Tropical Japonica 1.96
WAB462-10-3-1 W119 Tropical Japonica 1.91
Bombilla W120 Temperate Japonica 2.24
BHIM_DHAN W122 Japonica Intermediate 1.78
WC_3532 W123 Tropical Japonica 2.0
Buphopa W127 Japonica Intermediate 2.1
LUSITANO W130 Temperate Japonica 2.17
A_5 W139 Temperate Japonica 2.17
Jyanak W143 Japonica Intermediate 1.75
Shennong265 W160 Temperate Japonica 2.23
Yuanjing7 W162 Temperate Japonica 2.23
Khazar W173 Tropical Japonica 1.92
Dianjing W193 Temperate Japonica 2.04
Yunguang8hao W207 Temperate Japonica 2.26
Zhongchao123 W208 Temperate Japonica 2.36
Gizal159 W209 Temperate Japonica 2.06
Lemont W225 Tropical Japonica 1.92
M401 W226 Temperate Japonica 1.97
Teksichut W249 Temperate Japonica 2.31
Eiko W250 Temperate Japonica 2.24
RUBIO W251 Tropical Japonica 1.94
Sereendan_Kuning W253 Tropical Japonica 1.96
SAI-BUI-BAO W254 Tropical Japonica 1.96
Latisai1 W257 Tropical Japonica 2.04
Uz-Rosz_275 W260 Tropical Japonica 2.09
Anambae_ndanggalasi W273 Tropical Japonica 1.78
Heen_goda_wee W275 Tropical Japonica 1.98
Sholay W281 Temperate Japonica 2.21
Daegujo W283 Temperate Japonica 2.29
Paikasa W284 Tropical Japonica 1.76
Uwi W285 Tropical Japonica 1.94
Dourado_Precoce W288 Tropical Japonica 2.11
Aichi_Asahi W290 Temperate Japonica 2.16
NEW_BONNET W300 Tropical Japonica 1.83
KUNTLAN W302 Tropical Japonica 2.11
British_Honduras_Creole W303 Tropical Japonica 1.91
AKITAKOMACHI W305 Temperate Japonica 2.21
Guangkexiangnuo W319 Temperate Japonica 2.2
Feienuo2 W323 Japonica Intermediate 2.0
Zimangfeie W324 Japonica Intermediate 2.08
Guantuibaihe W325 Temperate Japonica 2.24
Haolvguangnian W326 Japonica Intermediate 2.09
JinghuB W327 Temperate Japonica 2.32
GPNO_5055 W329 Tropical Japonica 2.05

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
vg0505364751 sf0505364729 5 5364751 3.84E-21 6.72E-08
vg0901448401 sf0901447401 9 1448401 4.00E-18 2.20E-06
vg0523498004 sf0523435425 5 23498004 2.75E-17 NA
vg0904554252 sf0904553252 9 4554252 6.19E-17 NA
vg0217670144 sf0217664274 2 17670144 1.84E-16 NA
vg0901473649 sf0901472649 9 1473649 7.74E-16 2.05E-06
vg0507158546 sf0507158488 5 7158546 3.42E-15 NA
vg0311766273 sf0311764991 3 11766273 6.66E-15 NA
vg0505322118 sf0505322096 5 5322118 1.49E-14 2.30E-08
vg0323490253 sf0323488427 3 23490253 2.30E-13 NA
vg0425995589 sf0425810464 4 25995589 9.26E-13 1.26E-06
vg0901150996 sf0901149996 9 1150996 NA 1.74E-06