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 Yield Distribution in Japonica All Population:

Phenotype Information Table:

Note: -9 means missing value.

Cultivar Name Cultivar ID Subpopulation Yield
Gerdeh C003 Japonica Intermediate 24.54
Li-Jiang-Xin-Tuan-Hei-Gu_ C004 Temperate Japonica 18.82
AZUCENA C005 Tropical Japonica 22.5
CYPRESS C010 Tropical Japonica 21.36
Tainong67 C012 Temperate Japonica 22.97
M202 C014 Japonica Intermediate 22.39
Laoguangtou83 C016 Temperate Japonica 12.43
AnnongwangengB-1 C017 Temperate Japonica 8.94
AnnongwangengB-2 C018 Temperate Japonica 14.89
Funingzipi C023 Temperate Japonica 27.13
Weiguo C026 Temperate Japonica 25.89
Liaogeng287 C028 Temperate Japonica 25.84
Huhui628 C029 Japonica Intermediate 19.0
Longhuamaohu C032 Temperate Japonica 22.01
Zhonglouyihao1 C034 Temperate Japonica 30.28
Yelicanghua C035 Temperate Japonica 15.55
Zaoshunonghu6 C048 Temperate Japonica 25.65
Guihuahuang C052 Temperate Japonica 23.61
Xiushui115 C054 Temperate Japonica 24.28
Jindao1hao C056 Temperate Japonica 16.88
Dandongludao C057 Japonica Intermediate 18.28
Geng87-304 C063 Temperate Japonica 42.22
Sugeng2hao C064 Temperate Japonica 23.28
Muxiqiu C067 Temperate Japonica 25.99
Youmangzaogeng C070 Temperate Japonica 16.79
Laohuzhong C071 Temperate Japonica 26.85
cunsanli C074 Temperate Japonica 17.51
Huangkezaonian C075 Temperate Japonica 28.7
Muguanuo-1 C079 Temperate Japonica 20.06
Gaoyangdiandao C082 Temperate Japonica 29.72
chikenuo C083 Temperate Japonica 20.45
Haobuka C084 Japonica Intermediate 9.1
Shanjiugu C085 Japonica Intermediate 18.64
Lixingeng C087 Temperate Japonica 16.44
Tieganwu C089 Temperate Japonica 15.23
Xiangnuo-2 C093 Temperate Japonica 10.24
Babaili C101 Temperate Japonica 15.45
Yuyannuo-1 C103 Temperate Japonica 17.56
Hongkezhenuo C106 Temperate Japonica 12.18
Ximaxian C111 Temperate Japonica 4.41
LimingB C116 Temperate Japonica 27.4
Ninghui21 C119 Temperate Japonica 17.49
Shuiyuan300li C120 Temperate Japonica 18.72
Taidongludao C123 Tropical Japonica 40.51
Xiangnuo-1 C130 Temperate Japonica 13.15
Muguanuo-2 C133 Temperate Japonica 23.19
Wuzidui C134 Temperate Japonica 11.19
Cungunuo C137 Temperate Japonica 16.62
Lengshuigu C138 Temperate Japonica 13.9
Huangpinuo C144 Temperate Japonica 11.16
Nipponbare C146 Temperate Japonica 20.77
Zhonghua11 C149 Temperate Japonica 27.48
Balilla C150 Temperate Japonica 18.31
02428 C152 Temperate Japonica 18.94
IRAT109 C153 Tropical Japonica 35.52
Heigeng2hao C154 Temperate Japonica 8.95
Xingguo C171 Temperate Japonica 22.73
Zhonghua8hao C172 Temperate Japonica 24.85
Maguzi C177 Temperate Japonica 13.13
Haobayong1 C179 Temperate Japonica 18.55
Feidongtangdao C181 Temperate Japonica 16.84
Haomake(K) C185 Japonica Intermediate 9.56
Sanbangqishiluo C186 Japonica Intermediate 28.61
Niankenuo C187 Temperate Japonica 14.5
Yangkenuo C188 Temperate Japonica 12.13
Putaohuang C189 Temperate Japonica 17.58
Hongmisandan C195 Temperate Japonica 8.72
Yuyannuo-2 C196 Temperate Japonica 16.74
E_B_Gopher W002 Tropical Japonica 11.12
C_5560 W003 Tropical Japonica 23.73
Quinimpol W004 Tropical Japonica 26.55
TAICHU_MOCHI_59 W005 Tropical Japonica 30.8
WC_2811 W006 Tropical Japonica 33.06
Criollo_Chivacoa_2 W007 Tropical Japonica 26.76
Secano_do_Brazil W008 Tropical Japonica 29.29
Sel._No._388 W010 Japonica Intermediate 25.72
SHIMIZU_MOCHI W011 Temperate Japonica 30.85
KRASNODARSKIJ_424 W012 Temperate Japonica 11.32
Pergonil_15 W013 Temperate Japonica 31.51
NORIN_11 W016 Temperate Japonica 6.03
R_75 W017 Tropical Japonica 24.03
UZ_ROSZ_M38 W018 Temperate Japonica 13.23
H57-3-1 W019 Japonica Intermediate 31.73
Khao_Luang W021 Japonica Intermediate 29.0
C_8429 W022 Tropical Japonica 50.38
Padi_Pohon_Batu W024 Tropical Japonica 20.07
Chacareiro_Uruguay W027 Temperate Japonica 15.93
BLUE_STICK W038 Temperate Japonica 43.57
Onu_B W041 Tropical Japonica 22.38
KUBANETS_508 W045 Temperate Japonica 18.94
Jumli_dhan W047 Japonica Intermediate 18.86
HB-6-2 W052 Temperate Japonica 22.37
GPNO_1106 W053 Tropical Japonica 23.21
Tamanishiki W056 Temperate Japonica 32.73
Grassy W057 Tropical Japonica 33.1
Niwahutaw_Mochi W059 Temperate Japonica 28.65
Somewake W060 Temperate Japonica 23.06
Ardito W061 Japonica Intermediate 29.27
NANTON_NO._131 W062 Tropical Japonica 41.03
Vary_Tarva_Osla W063 Japonica Intermediate 25.25
CSORNUJ W064 Temperate Japonica 13.13
R_67 W065 Tropical Japonica 35.81
Mitak W067 Tropical Japonica 33.79
Gazan W068 Temperate Japonica 26.34
Celiaj W082 Temperate Japonica 25.41
CHUNJIANGZAO_NO._1 W088 Temperate Japonica 19.23
Padi_Tarab_Arab W102 Tropical Japonica 12.67
WIR_911 W109 Temperate Japonica 10.06
Lua_Chua_Chan W110 Tropical Japonica 12.99
Simpor W113 Tropical Japonica 31.41
WC_10253 W116 Tropical Japonica 29.11
KRASNODARSKIJ_3352 W117 Temperate Japonica 16.21
EMBRAPA_1200 W118 Tropical Japonica 27.03
WAB462-10-3-1 W119 Tropical Japonica 21.24
Bombilla W120 Temperate Japonica 19.56
BHIM_DHAN W122 Japonica Intermediate 25.77
WC_3532 W123 Tropical Japonica 36.97
Buphopa W127 Japonica Intermediate 29.53
LUSITANO W130 Temperate Japonica 22.98
A_5 W139 Temperate Japonica 20.34
Jyanak W143 Japonica Intermediate 13.77
Shennong265 W160 Temperate Japonica 42.64
Yuanjing7 W162 Temperate Japonica 74.84
Khazar W173 Tropical Japonica 35.23
Dianjing W193 Temperate Japonica 43.01
Yunguang8hao W207 Temperate Japonica 42.97
Zhongchao123 W208 Temperate Japonica 45.72
Gizal159 W209 Temperate Japonica 55.34
Lemont W225 Tropical Japonica 28.37
M401 W226 Temperate Japonica 34.59
Teksichut W249 Temperate Japonica 30.02
Eiko W250 Temperate Japonica 25.87
RUBIO W251 Tropical Japonica 29.24
Sereendan_Kuning W253 Tropical Japonica 43.12
SAI-BUI-BAO W254 Tropical Japonica 33.2
Latisai1 W257 Tropical Japonica 29.57
Uz-Rosz_275 W260 Tropical Japonica 32.8
Anambae_ndanggalasi W273 Tropical Japonica 35.19
Heen_goda_wee W275 Tropical Japonica 28.65
Sholay W281 Temperate Japonica 23.82
Daegujo W283 Temperate Japonica 11.96
Paikasa W284 Tropical Japonica 19.0
Uwi W285 Tropical Japonica 24.48
Dourado_Precoce W288 Tropical Japonica 26.15
Aichi_Asahi W290 Temperate Japonica 39.86
NEW_BONNET W300 Tropical Japonica 29.13
KUNTLAN W302 Tropical Japonica 46.07
British_Honduras_Creole W303 Tropical Japonica 32.36
AKITAKOMACHI W305 Temperate Japonica 22.28
Guangkexiangnuo W319 Temperate Japonica 12.88
Feienuo2 W323 Japonica Intermediate 19.09
Zimangfeie W324 Japonica Intermediate 20.18
Guantuibaihe W325 Temperate Japonica 10.7
Haolvguangnian W326 Japonica Intermediate 24.96
JinghuB W327 Temperate Japonica 35.33
GPNO_5055 W329 Tropical Japonica 34.71

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
vg1012944850 sf1012873665 10 12944850 9.44E-10 NA
vg1011831108 sf1011759923 10 11831108 1.00E-09 6.69E-07
vg0505746038 sf0505745976 5 5746038 3.23E-09 2.87E-07
vg0232914706 sf0232908837 2 32914706 1.02E-08 NA
vg0101824220 sf0101823220 1 1824220 3.98E-08 NA
vg0611497253 sf0611496254 6 11497253 3.52E-07 NA
vg0223186095 sf0223180226 2 23186095 1.69E-06 4.09E-06