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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (4): 650-659.doi: 10.3724/SP.J.1006.2021.04136


Genome-wide association study of 1000-seed weight in rapeseed (Brassica napus L.)

ZHANG Chun1,2(), ZHAO Xiao-Zhen1,2, PANG Cheng-Ke1,2, PENG Men-Lu1,2, WANG Xiao-Dong2, CHEN Feng2, ZHANG Wei2, CHEN Song2, PENG Qi2, YI Bin3, SUN Cheng-Ming2,3,*(), ZHANG Jie-Fu2,*(), FU Ting-Dong3   

  1. 1Nanjing Agricultural University / State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing 210095, Jiangsu, China
    2Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences / Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210014, Jiangsu, China
    3National Key Laboratory of Crop Genetic Improvement / College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
  • Received:2020-06-22 Accepted:2020-09-13 Online:2021-04-12 Published:2020-09-22
  • Contact: SUN Cheng-Ming,ZHANG Jie-Fu E-mail:15662020807@163.com;suncm8331537@gmail.com;jiefu_z@163.com
  • Supported by:
    National Key Research and Development Program of China(2018YFD0100602);China Agriculture Research System(CARS-12);National Natural Science Foundation of China(32001581);Jiangsu Agriculture Science and Technology Innovation Fund(CX(19)3055);Natural Fund Project of Jiangsu Basic Research Program(BK20190260);Fundamental Research Funds for the Central Universities(2662016PY063)


Thousand-seed weight (TSW) is one of the important component of seed yield. In this study, a collection of 496 representative rapeseed accessions were genotyped by the high-throughput 60K SNP array for TSW in three environments (14NJ, 15TZ, 16TZ). The genome-wide association study (GWAS) of TSW was performed via the MLM (Mixed linear model) and GLM (General linear model). The results showed that the broad sense heritability of TSW was 63.12% in three environments. Six and 61 loci were detected with MLM and GLM, which explained 28.92% and 47.08% of the phenotypic variance, respectively. Combining the common loci between two models, 62 significant loci were obtained and accounted for 47.31% of the phenotypic variance. These loci were distributed on all chromosomes of the genome, with the largest number of 9, 8, and 7 loci detected on Chromosome A07, A03, and C06, respectively. The most significant locus Bn-scaff_17526_1-p1066214 was detected on C09, and accounted for 5.55% and 15.26% of the phenotypic variance in MLM and GLM, respectively. Among them, 21 loci overlapped with previously reported QTLs, of which 8 loci were verified by at least two populations. The remaining 41 loci were newly detected, and many of them had high effects and were detected in multiple environments, such as Bn-A03-p560769, Bn-scaff_15743_1-p599416 and Bn-scaff_15743_1-p590955. Besides, 11 candidates orthologous to documented Arabidopsis seed weight genes, like DGAT, EOD3, AGL61, WRI1, DA2, and RAV1, were found near our GWAS loci. The results are helpful for analyzing the genetic basis of TSW of rapeseed and lay a foundation for studying the regulation mechanism and guiding the genetic improvement of TSW.

Key words: Brassica napus L., 1000-seed weight, yield, GWAS, SNP

Table S1

Information of 496 rapeseed accessions"

Line No.
材料号Line No. 材料名称
1 甘油5号 Ganyou 5 中国湖北Hubei, China 2 农林42 Nonglin 42 日本 Japan
3 科里纳 Kelina 国外Unknown 4 淮油6号 Huaiyou 6 中国江苏 Jiangsu, China
5 炎81-2 Yan 81-2 中国重庆Chongqing, China 6 28887 中国重庆Chongqing, China
7 黔油4号 Qianyou 4 中国贵州Guizhou, China 8 黔油331 Qianyou 331 中国贵州 Guizhou, China
9 恩油73 Enyou 73-1-2 中国湖北 Hubei, China 10 牛耳朵 Niuerduo 中国贵州 Guizhou, China
11 880101 中国重庆Chongqing, China 12 SWU40 中国重庆 Chongqing, China
13 SWU42 中国重庆Chongqing, China 14 SWU43 中国重庆 Chongqing, China
15 SWU44 中国重庆Chongqing, China 16 SWU45 中国重庆 Chongqing, China
17 SWU46 中国重庆Chongqing, China 18 SWU47 中国重庆 Chongqing, China
19 SWU48 中国重庆Chongqing, China 20 SWU52 中国重庆 Chongqing, China
21 SWU53 中国重庆Chongqing, China 22 SWU56 中国重庆 Chongqing, China
23 SWU59 中国重庆Chongqing, China 24 SWU65 中国重庆 Chongqing, China
25 SWU82 中国重庆Chongqing, China 26 SWU83 中国重庆 Chongqing, China
27 SWU92 中国重庆Chongqing, China 28 SWU101 中国重庆 Chongqing, China
29 SWU106 中国重庆Chongqing, China 30 SWU108 中国重庆 Chongqing, China
31 川油20 Chuanyou 20 中国四川 Sichuan, China 32 川油18 Chuanyou 18 中国四川Sichuan, China
33 CY12NY-7 中国四川 Sichuan, China 34 CY12Q95406 中国四川Sichuan, China
35 CY12Q8-7 中国四川 Sichuan, China 36 CY12QSZ06 中国四川Sichuan, China
37 CY12QCWH-1 中国四川 Sichuan, China 38 CY12Q95108 中国四川Sichuan, China
39 CY12Q21535-N3 中国四川 Sichuan, China 40 CY12PXW-4 中国四川Sichuan, China
41 CY12PXW-6 中国四川 Sichuan, China 42 CY12PXW-9 中国四川Sichuan, China
43 CY13PXW-17 中国四川 Sichuan, China 44 CY14PXW-18 中国四川Sichuan, China
45 CY15PXW-31 中国四川 Sichuan, China 46 CY16PXW-35 中国四川 Sichuan, China
47 CY17PXW-58 中国四川 Sichuan, China 48 CY18PXW-62 中国四川 Sichuan, China
49 CY19PXW-65 中国四川 Sichuan, China 50 CY20PXW-66 中国四川 Sichuan, China
51 CY21PXW-84 中国四川 Sichuan, China 52 CY12GJ-1 中国四川 Sichuan, China
53 wx1025 中国湖南 Hunan, China 54 wx10213 中国湖南 Hunan, China
55 wx10296 中国湖南 Hunan, China 56 wx10315 中国湖南 Hunan, China
57 10-1043 中国湖南 Hunan, China 58 10-1047 中国湖南 Hunan, China
59 10-1061 中国湖南 Hunan, China 60 10-1070 中国湖南 Hunan, China
61 10-804 中国湖南 Hunan, China 62 10-1358 中国湖南 Hunan, China
63 1472 中国湖南 Hunan, China 64 湘油13号 Xiangyou 13 中国湖南 Hunan, China
65 湘油15号 Xiangyou 15 中国湖南 Hunan, China 66 湘油11号 Xiangyou 11 中国湖南 Hunan, China
67 740 中国湖南 Hunan, China 68 631 中国湖南 Hunan, China
69 613 中国湖南 Hunan, China 70 783 中国湖南 Hunan, China
71 782 中国湖南 Hunan, China 72 YB3 中国湖南 Hunan, China
73 1360 中国湖南 Hunan, China 74 563 中国湖南 Hunan, China
75 WX10329 中国湖南 Hunan, China 76 santana 德国 German
77 1281 中国湖南 Hunan, China 78 509 中国湖南 Hunan, China
79 1368 中国湖南 Hunan, China 80 1322 中国湖南 Hunan, China
81 1252 中国湖南 Hunan, China 82 1321 中国湖南 Hunan, China
83 07022 中国湖北 Hubei, China 84 07094 中国湖北 Hubei, China
85 07016 中国湖北 Hubei, China 86 9F087 中国湖北 Hubei, China
87 97096 中国湖北 Hubei, China 88 97097 中国湖北 Hubei, China
89 07189 中国湖北 Hubei, China 90 07191 中国湖北 Hubei, China
91 07037 中国湖北 Hubei, China 92 RQ011 中国湖北 Hubei, China
93 RR009 中国湖北 Hubei, China 94 RR002 中国湖北 Hubei, China
95 97177 中国湖北 Hubei, China 96 96021 中国湖北 Hubei, China
97 96063 中国湖北 Hubei, China 98 01111 中国湖北 Hubei, China
99 01570 中国湖北 Hubei, China 100 9保22 9Bao 22 中国湖北 Hubei, China
101 01188 中国湖北 Hubei, China 102 02354 中国湖北 Hubei, China
103 02359 中国湖北 Hubei, China 104 02365 中国湖北 Hubei, China
105 93205 中国湖北 Hubei, China 106 93210 中国湖北 Hubei, China
107 Nca 国外 Unknown 108 中双4号 Zhongshuang 4 中国湖北 Hubei, China
109 中双9号 Zhongshuang 9 中国湖北 Hubei, China 110 中双11号 Zhongshuang 11 中国湖北 Hubei, China
111 2011-6200 中国湖北 Hubei, China 112 2011-6308 中国湖北 Hubei, China
113 2011-7103 中国湖北 Hubei, China 114 2012-11526 中国湖北 Hubei, China
115 2012-3448 中国湖北 Hubei, China 116 2012-3546 中国湖北 Hubei, China
117 2012-4531 中国湖北 Hubei, China 118 2012-5086 中国湖北 Hubei, China
119 2012-5113 中国湖北 Hubei, China 120 2012-8327 中国湖北 Hubei, China
121 2012-8355 中国湖北 Hubei, China 122 2012-8380 中国湖北 Hubei, China
123 2012-8998 中国湖北 Hubei, China 124 2012-9323 中国湖北 Hubei, China
125 2012-9354 中国湖北 Hubei, China 126 2012-9380 中国湖北 Hubei, China
127 2012-9478 中国湖北 Hubei, China 128 2012-9542 中国湖北 Hubei, China
129 2012-K8053 中国湖北 Hubei, China 130 R2 中国湖北 Hubei, China
131 希望106 Xiwang 106 中国湖北 Hubei, China 132 阳光198 Yangguang 198 中国湖北 Hubei, China
133 阳光2009 Yangguang 2009 中国湖北 Hubei, China 134 中双10号 Zhongshuang 10 中国湖北 Hubei, China
135 中双12号 Zhongshuang 12 中国湖北 Hubei, China 136 中双6号 Zhongshuang 6 中国湖北 Hubei, China
137 中双7号 Zhongshuang 7 中国湖北 Hubei, China 138 中油589 Zhongyou 589 中国湖北 Hubei, China
139 华油2号 Huayou 2 中国湖北 Hubei, China 140 Major 法国 France
141 华双2号 Huashuang 2 中国湖北 Hubei, China 142 Aurora 德国 German
143 华油13号 Huayou13 中国湖北 Hubei, China 144 Rucabo 德国 German
145 华油3号 Huayou 3 中国湖北 Hubei, China 146 华油14 Huayou 14 中国湖北 Hubei, China
147 宁油1号 Ningyou 1 中国江苏 Jiangsu, China 148 Ceres 德国 German
149 11-9-700 中国湖北 Hubei, China 150 11-9-701 中国湖北 Hubei, China
151 11-9-702 中国湖北 Hubei, China 152 11-9-703 中国湖北 Hubei, China
153 11-9-704 中国湖北 Hubei, China 154 11-9-705 中国湖北 Hubei, China
155 11-9-706 中国湖北 Hubei, China 156 11-9-707 中国湖北 Hubei, China
157 11-P63-5育7
11-P63-5 yu 7
中国湖北 Hubei, China 158 11-P63-8育32
11-P63-8 yu 32
中国湖北 Hubei, China
159 11-P63-3育3
11-P63-3 yu 3
中国湖北 Hubei, China 160 11-P67东 11-P67 Dong 中国湖北 Hubei, China
161 09-P64-1 中国湖北 Hubei, China 162 10-崇23 10-chong23 中国湖北 Hubei, China
163 10-崇24 10-chong 24 中国湖北 Hubei, China 164 10-崇25 10-chong25 中国湖北 Hubei, China
165 10-崇29 10-chong 29 中国湖北 Hubei, China 166 10-崇32 10-chong 32 中国湖北 Hubei, China
167 10-崇33 10-chong 33 中国湖北 Hubei, China 168 10-崇34 10-chong 34 中国湖北 Hubei, China
169 10-江棚2 10-jiangpeng 2 中国湖北 Hubei, China 170 10-江棚3 10-jiangpeng 3 中国湖北 Hubei, China
171 11-育7-103 11-yu 7-103 中国湖北 Hubei, China 172 11-育7-117 11-yu7-117 中国湖北 Hubei, China
173 11-育7-125 11-yu 7-125 中国湖北 Hubei, China 174 11-P74-8 中国湖北 Hubei, China
175 11-P74-13 中国湖北 Hubei, China 176 7-7766-74 中国湖北 Hubei, China
177 P18 中国湖北 Hubei, China 178 64棚-1064 peng-10 中国湖北 Hubei, China
179 圣光77 Shengguang 77 中国湖北 Hubei, China 180 甲预17棚 Jiayu17peng 中国湖北 Hubei, China
181 甲预25棚 Jiayu25peng 中国湖北 Hubei, China 182 甲预16棚 Jiayu16peng 中国湖北 Hubei, China
183 甲预31棚 Jiayu31peng 中国湖北 Hubei, China 184 华双5号 Huashuang5 中国湖北 Hubei, China
185 华双4号 Huashuang 4 中国湖北 Hubei, China 186 甲972Jia972 中国湖北 Hubei, China
187 华双128 Huashuang 128 中国湖北 Hubei, China 188 甲904 Jia904 中国湖北 Hubei, China
189 甲908 Jia 908 中国湖北 Hubei, China 190 甲PF190棚 Jia PF190peng 中国湖北 Hubei, China
191 甲915 Jia 915 中国湖北 Hubei, China 192 甲922 Jia 922 中国湖北 Hubei, China
193 甲951棚 Jia951peng 中国湖北 Hubei, China 194 甲917 Jia 917 中国湖北 Hubei, China
195 甲923 Jia923 中国湖北 Hubei, China 196 甲931 Jia 931 中国湖北 Hubei, China
197 甲预05棚 Jiayu05peng 中国湖北 Hubei, China 198 甲963棚 Jia963peng 中国湖北 Hubei, China
199 沪油12号 Huyou 12 中国上海 Shanghai, China 200 宁油16号 Ningyou 16 中国江苏 Jiangsu, China
201 史力佳 Shilijia 中国江苏 Jiangsu, China 202 杨油6号 Yangyou 6 中国江苏 Jiangsu, China
203 扬油5号 Yangyou 5 中国江苏 Jiangsu, China 204 镇油3号 Zhenyou 3 中国江苏 Jiangsu, China
205 苏油1号 Suyou 1 中国江苏 Jiangsu, China 206 浙油18 Zheyou18 中国浙江 Zhejiang, China
207 浙双72 Zheshuang 72 中国浙江 Zhejiang, China 208 浙双8号 Zheshuang 8 中国浙江 Zhejiang, China
209 浙油758 Zheyou 758 中国浙江 Zhejiang, China 210 沪油14 Huyou 14 中国上海 Shanghai, China
211 沪油18 Huyou 18-2 中国上海 Shanghai, China 212 沪油19 Huyou 19 中国上海 Shanghai, China
213 浙油19 Zheyou 19 中国浙江 Zhejiang, China 214 浙油21 Zheyou 21 中国浙江 Zhejiang, China
215 浙双6号 Zheshuang 6 中国浙江 Zhejiang, China 216 皖油15号 Wanyou 15 中国安徽 Anhui, China
217 皖油16号 Wanyou 16 中国安徽 Anhui, China 218 皖油29 Wanyou 29 中国安徽 Anhui, China
219 AGREV012 德国 German 220 AGREV019 德国 German
221 AGREV021 德国 German 222 Topas 瑞典 Sweden
223 cyclon 丹麦 Denmark 224 伟杰 Weijie 加拿大 Canada
225 四达 Sida 加拿大 Canada 226 至尊 Zhizun 加拿大 Canada
227 海神 Haishen 加拿大 Canada 228 D2 丹麦 Denmark
229 D3 丹麦 Denmark 230 Qu 美国 America
231 11-985 中国青海 Qinghai, China 232 11-504 中国青海 Qinghai, China
233 11-997 中国青海 Qinghai, China 234 11-540 中国青海 Qinghai, China
235 11-1184 中国青海 Qinghai, China 236 10-758 中国青海 Qinghai, China
237 10-1230 中国青海 Qinghai, China 238 10-847 中国青海 Qinghai, China
239 11-1124 中国青海 Qinghai, China 240 垦C1 KenC1 中国陕西 Shaanxi, China
241 P113 中国陕西 Shaanxi, China 242 P158 中国陕西 Shaanxi, China
243 P310 中国陕西 Shaanxi, China 244 P312 中国陕西 Shaanxi, China
245 P668 中国陕西 Shaanxi, China 246 P685 中国陕西 Shaanxi, China
247 A117 中国陕西 Shaanxi, China 248 A172 中国陕西 Shaanxi, China
249 B250 中国陕西 Shaanxi, China 250 B265 中国陕西 Shaanxi, China
251 A109 中国陕西 Shaanxi, China 252 B285 中国陕西 Shaanxi, China
253 C052 中国陕西 Shaanxi, China 254 GY270 中国陕西 Shaanxi, China
255 GY282 中国陕西 Shaanxi, China 256 GY284 中国陕西 Shaanxi, China
257 B262 中国河南 Henan, China 258 A82 中国江西 Jiangxi, China
259 A98 中国陕西 Shaanxi, China 260 B414 中国新疆 Xinjiang, China
261 B308 瑞典 Sweden 262 A97 中国四川 Sichuan, China
263 A148 瑞典 Sweden 264 B431 丹麦 Denmark
265 08-P35 中国湖北 Hubei, China 266 08-P36 中国湖北 Hubei, China
267 09-P32 中国湖北 Hubei, China 268 09-P36 中国湖北 Hubei, China
269 09-P37 中国湖北 Hubei, China 270 10-P10 中国湖北 Hubei, China
271 10-P29 中国湖北 Hubei, China 272 11-P30 中国湖北 Hubei, China
273 12-P24 中国湖北 Hubei, China 274 12-P25 中国湖北 Hubei, China
275 03ⅡB 中国湖北 Hubei, China 276 03Ⅱ3B 中国湖北 Hubei, China
277 03Ⅰ32B 中国湖北 Hubei, China 278 964 中国湖北 Hubei, China
279 DD1 中国湖北 Hubei, China 280 9L302-1 中国湖北 Hubei, China
281 06T9F 中国湖北 Hubei, China 282 03Ⅱ4B 中国湖北 Hubei, China
283 03LF1 中国湖北 Hubei, China 284 9852 中国湖北 Hubei, China
285 9801C 中国湖北 Hubei, China 286 986 中国湖北 Hubei, China
287 876 中国湖北 Hubei, China 288 武164 Wu164 中国湖北 Hubei, China
289 9889 中国湖北 Hubei, China 290 06H7 中国湖北 Hubei, China
291 湖北白花油菜
中国湖北 Hubei, China 292 南川长角
中国四川 Sichuan, China
293 IMC103 中国重庆 Chongqing, China 294 Oscar 澳大利亚 Australia
295 Sophia 德国 German 296 campina 德国 German
297 Conny 瑞典 Sweden 298 Wesreo 澳大利亚 Australia
299 Wase Chousen 朝鲜 North Korea 300 Gogatsuna 日本 Japan
301 Nakaee Chousen 朝鲜 North Korea 302 Cat.No.117 德国 German
303 90750 中国重庆 Chongqing, China 304 农林43 Nonglin 43 日本
305 西藏油菜 Xizangyoucai 中国西藏 Tibet, China 306 油研2号 Youyan 2 中国贵州
307 矮架早 Aijiazao 中国四川 Sichuan, China 308 SWU41 中国重庆 Chongqing, China
309 SWU49 中国重庆 Chongqing, China 310 SWU54 中国重庆 Chongqing, China
311 SWU57 中国重庆 Chongqing, China 312 SWU60 中国重庆 Chongqing, China
313 SWU61 中国重庆 Chongqing, China 314 SWU62 中国重庆 Chongqing, China
315 SWU63 中国重庆 Chongqing, China 316 SWU64 中国重庆 Chongqing, China
317 SWU66 中国重庆 Chongqing, China 318 SWU67 中国重庆 Chongqing, China
319 SWU68 中国重庆 Chongqing, China 320 SWU69 中国重庆 Chongqing, China
321 SWU70 中国重庆Chongqing, China 322 SWU71 中国重庆 Chongqing, China
323 SWU74 中国重庆 Chongqing, China 324 SWU75 中国重庆 Chongqing, China
325 SWU76 中国重庆 Chongqing, China 326 SWU77 中国重庆 Chongqing, China
327 SWU80 中国重庆 Chongqing, China 328 SWU81 中国重庆 Chongqing, China
329 SWU84 中国重庆 Chongqing, China 330 SWU85 中国重庆 Chongqing, China
331 SWU87 中国重庆 Chongqing, China 332 SWU88 中国重庆 Chongqing, China
333 SWU89 中国重庆 Chongqing, China 334 SWU90 中国重庆 Chongqing, China
335 SWU93 中国重庆 Chongqing, China 336 SWU94 中国重庆 Chongqing, China
337 SWU95 中国重庆 Chongqing, China 338 SWU96 中国重庆 Chongqing, China
339 SWU99 中国重庆 Chongqing, China 340 SWU100 中国重庆 Chongqing, China
341 SWU102 中国重庆 Chongqing, China 342 SWU103 中国重庆 Chongqing, China
343 SWU104 中国重庆 Chongqing, China 344 SWU105 中国重庆 Chongqing, China
345 SWU107 中国重庆 Chongqing, China 346 SWU110 中国重庆 Chongqing, China
347 SWU111 中国重庆 Chongqing, China 348 SWU112 中国重庆 Chongqing, China
349 SWU113 中国重庆 Chongqing, China 350 SWU114 中国重庆 Chongqing, China
351 辐油4号 Fuyou 4 中国重庆 Chongqing, China 352 镇3736 Zhen3736 中国江苏 Jiangsu, China
353 镇2609 Zhen 2609 中国江苏 Jiangsu, China 354 HX0352 中国江苏 Jiangsu, China
355 阳光2009 Yangguang 2009 中国江苏 Jiangsu, China 356 沪油21 Huyou 21 中国上海 Shanghai, China
357 浙双3号 Zheshuang 3 中国浙江 Zhejiang, China 358 浙油21 Zheyou 21 中国浙江 Zhejiang, China
359 皖油20 Wanyou 20 中国安徽 Anhui, China 360 皖油12 Wanyou 12 中国安徽 Anhui, China
361 皖油7号 Wanyou 7 中国安徽 Anhui, China 362 红油3号 Hongyou 3 中国江苏 Jiangsu, China
363 镇油5号 Zhenyou5 中国江苏 Jiangsu, China 364 扬油4号 Yangyou 4 中国上海 Shanghai, China
365 沪油15 Huyou 15 中国上海 Shanghai, China 366 沪油16 Huyou 16 中国上海 Shanghai, China
367 沪油17 Huyou17 中国上海 Shanghai, China 368 浙双72 Zheshuang 72 中国浙江 Zhejiang, China
369 浙双8号 Zheshuang 8 中国浙江 Zhejiang, China 370 浙油50 Zheyou 50 中国浙江 Zhejiang, China
371 中双11 Zhongshuang 11 中国湖北 Hubei, China 372 阳光198 Yangguang198 中国湖北 Hubei, China
373 华航901 Huahang 901 中国湖北 Hubei, China 374 扬J6711 Yang J6711 中国江苏 Jiangsu, China
375 盐6055 Yan 6055 中国江苏 Jiangsu, China 376 杨鉴8号 Yangjian8 中国江苏 Jiangsu, China
377 希望106 Xiwang 106 中国湖北 Hubei, China 378 浙油17号 Zheyou 17 中国浙江 Zhejiang, China
379 中双5号 Zhongshuang 5 中国湖北 Hubei, China 380 中油821 Zhongyou 821 中国湖北 Hubei, China
381 秦油1号 Qinyou 1 中国陕西 Shaanxi, China 382 纬隆88 Weilong 88 中国陕西 Shaanxi, China
383 盐油2号 Yanyou 2 中国江苏 Jiangsu, China 384 秦油5号 Qinyou 5 中国陕西 Shaanxi, China
387 德68-12 De 68-12 中国四川 Sichuan, China 388 Monty 澳大利亚 Australia
389 Oscar 澳大利亚 Australia 390 宁油12 Ningyou 12-1 中国江苏 Jiangsu, China
391 宁油14 Ningyou 14 中国江苏 Jiangsu, China 392 史力丰-1 Shilifeng-1 中国江苏 Jiangsu, China
393 宁油18 Ningyou 18 中国江苏 Jiangsu, China 394 Helios 丹麦 Denmark
395 Hector 加拿大 Canada 396 棉96-203 Mian96-203 中国青海 Qinghai, China
397 青662A Qing662A 中国青海 Qinghai, China 398 699 中国湖北 Hubei, China
399 加拿大2号 Jianada 2 加拿大 Canada 400 中双2号 Zhongshuang 2 中国湖北 Hubei, China
401 WH-12 中国湖北 Hubei, China 402 WH-15 中国湖北 Hubei, China
403 WH-17 中国湖北 Hubei, China 404 WH-19 中国湖北 Hubei, China
405 WH-20 中国湖北 Hubei, China 406 WH-23 中国湖北 Hubei, China
407 WH-24 中国湖北 Hubei, China 408 WH-25 中国湖北 Hubei, China
409 WH-26 中国湖北 Hubei, China 410 WH-27 中国湖北 Hubei, China
411 WH-28 中国湖北 Hubei, China 412 WH-29 中国湖北 Hubei, China
413 WH-30 中国湖北 Hubei, China 414 WH-31 中国湖北 Hubei, China
415 WH-33 中国湖北 Hubei, China 416 WH-37 中国湖北 Hubei, China
417 WH-38 中国湖北 Hubei, China 418 WH-41 中国湖北 Hubei, China
419 WH-42 中国湖北 Hubei, China 420 WH-43 中国湖北 Hubei, China
421 WH-45 中国湖北 Hubei, China 422 WH-49 中国湖北 Hubei, China
423 WH-50 中国湖北 Hubei, China 424 WH-55 中国湖北 Hubei, China
425 WH-56 中国湖北 Hubei, China 426 WH-57 中国湖北 Hubei, China
427 WH-58 中国湖北 Hubei, China 428 WH-59 中国湖北 Hubei, China
429 WH-60 中国湖北 Hubei, China 430 WH-61 中国湖北 Hubei, China
431 WH-62 中国湖北 Hubei, China 432 WH-63 中国湖北 Hubei, China
433 WH-81 中国湖北 Hubei, China 434 WH-83 中国湖北 Hubei, China
435 WH-85 中国湖北 Hubei, China 436 WH-88 中国湖北 Hubei, China
437 WH-93 中国湖北 Hubei, China 438 WH-95 中国湖北 Hubei, China
439 WH-100 中国湖北 Hubei, China 440 WH-127 中国湖北 Hubei, China
441 豫油1号 Yuyou 1 中国河南 Henan, China 442 COBRA 德国 German
443 宁油7号 Ningyou 7 中国江苏 Jiangsu, China 444 Tapidor 法国 France
445 华油6号 Huayou 6 中国湖北 Hubei, China 446 华油12 Huayou 12 中国湖北 Hubei, China
447 Cubs root 朝鲜 North Korea 448 华油10 Huayou 10 中国湖北 Hubei, China
449 Bienvenu 法国 France 450 胜利油菜 Shengliyoucai 中国四川 Sichuan, China
451 ERAKE 波兰 Poland 452 Taisetsu 日本 Japan
453 cresor 加拿大 Canada 454 Daichousen 朝鲜 North Korea
455 comet 瑞典 Sweden 456 Niklas 丹麦 Denmark
457 Askari 德国 German 458 chuosenshu 朝鲜 North Korea
459 WESBROOK 澳大利亚 Australia 460 Suigenshu 朝鲜 North Korea
461 华油4号 Huayou 4 中国湖北 Hubei, China 462 胜利青梗 Shengliqinggeng 中国上海 Shanghai, China
463 密角多头油菜
中国上海 Shanghai, China 464 矮箕胜利 Aijishengli 中国上海 Shanghai, China
465 漕泾胜利 Caojingshengli 中国上海 Shanghai, China 466 沪油三号 Huyou 3 中国上海 Shanghai, China
467 勺叶青 Shaoyeqing 中国上海 Shanghai, China 468 非洲油菜乳黄花
中国上海 Shanghai, China
469 沪激早 Hujizao 中国上海 Shanghai, China 470 漕油2号 Caoyou 2 中国上海 Shanghai, China
471 封顶240 Fengding 240 中国江苏 Jiangsu, China 472 全紫油菜 Quanziyoucai 中国江苏 Jiangsu, China
473 大花球 Dahuaqiu 中国江苏 Jiangsu, China 474 荣选 Rongxuan 中国江苏 Jiangsu, China
475 宁油10号 Ningyou 10 中国江苏 Jiangsu, China 476 宁油8号 Ningyou 8 中国江苏 Jiangsu, China
477 宁油六号 Ningyouliu 中国江苏 Jiangsu, China 478 垛油一号 Duoyou 1 中国江苏 Jiangsu, China
479 淮油12号 Huaiyou 12 中国江苏 Jiangsu, China 480 沛选170 Peixuang 170 中国江苏 Jiangsu, China
481 广德138 Guangde 138 中国安徽 Anhui, China 482 广德8104 Guangde 8104 中国安徽 Anhui, China
483 当油早1号Dangyouzao 1 中国安徽 Anhui, China 484 广德761 Guangde 761 中国安徽 Anhui, China
485 铜陵花叶 Tonglinghuaye 中国安徽 Anhui, China 486 滁610 Chu610 中国安徽 Anhui, China
487 滁107 Chu 107 中国安徽 Anhui, China 488 宿84-6 Su 84-6 中国安徽 Anhui, China
489 皖油早 Wanyouzao 中国安徽 Anhui, China 490 滁油1号 Chuyou 1 中国安徽 Anhui, China
491 滁县白花 Chuxianbaihua 中国安徽 Anhui, China 492 芥65-1 Jie 65-1 中国浙江 Zhejiang, China
493 申黄1号 Shenhuang 1 中国上海 Shanghai, China 494 浙油601 Zheyou 601 中国浙江 Zhejiang, China
495 三高油菜Three high rape 中国浙江 Zhejiang, China 496 早丰一号 Zaofeng 1 中国四川 Sichuan, China

Table 1

Statistical analysis of 1000-seed weight of the association panel"

Average ± SD
Coefficient of variation
2013/2014 南京Nanjing 2.27 7.63 4.27±0.88 0.21
2014/2015 泰州Taizhou 1.64 5.77 3.65±0.58 0.16
2015/2016 泰州Taizhou 1.50 6.13 3.51±0.64 0.18

Fig. 1

1000-seed weight of the association panel in three environments (14NJ, 15TZ, 16TZ)"

Table 2

Significant GWAS loci of 1000-seed weight in MLM (BLUP)"

Position (bp)
-lg (P) 表型变异
R2 (%)
Reported QTL
Bn-A01-p23472380 A01 19,346,196 5.34 6.03 16TZ
Bn-A02-p6300284 A02 3,473,319 4.81 5.41 15TZ
Bn-A02-p6564861 A02 3,784,981 5.38 6.06 14NJ [32]
Bn-A03-p22125583 A03 20,956,967 4.77 5.36 [32,35]
Bn-scaff_16874_1-p411591 C06 31,817,621 4.33 4.86 16TZ [30,36,37]
Bn-scaff_17526_1-p1066214 C09 1,488,283 4.93 5.55 16TZ [32]

Fig. 2

Genome-wide association study of 1000-seed weight in rapeseed (BLUP) A: Manhattan plot of MLM for 1000-seed weight; B: quantile-quantile plot of MLM for 1000-seed weight; C: Manhattan plot of GLM for 1000-seed weight; D: quantile-quantile plot of GLM for 1000-seed weight."

Table 3

Significant GWAS loci of 1000-seed weight in GLM (BLUP)"

Position (bp)
-lg (P) 表型变异
R2 (%)
Reported QTL
Bn-A01-p1156979 A01 760,656 6.37 5.61 15TZ [35]
Bn-A01-p1440009 A01 1,036,032 5.96 5.21
Bn-A01-p9621623 A01 8,234,343 6.43 5.66 [17,30,36]
Bn-A01-p12222806 A01 10,407,989 7.02 7.03 14NJ
Bn-A01-p15496639 A01 12,941,394 6.64 6.67 16TZ
Bn-A02-p6300284 A02 3,473,319 7.22 7.23 14TZ
Bn-A02-p6564861 A02 3,784,981 8.59 8.53 14NJ/16TZ [32,35]
Bn-A03-p560769 A03 445,706 9.16 9.08 14NJ/16TZ
Bn-A03-p4352837 A03 3,885,180 6.18 6.22
Bn-A03-p6586436 A03 5,884,508 8.47 8.43 16TZ
Bn-A03-p8851142 A03 8,156,299 7.88 7.86 14NJ/15TZ/16TZ [32]
Bn-A03-p13758392 A03 12,893,544 6.56 6.60 15TZ
Bn-A03-p14747263 A03 13,916,047 6.57 6.60 14NJ [35]
Bn-A03-p22125583 A03 20,956,967 5.64 5.60 [32,35]
Bn-A03-p24494224 A03 22,999,825 6.05 6.10 [32]
Bn-A04-p13705636 A04 14,344,669 8.84 8.77 15TZ [35]
Bn-A05-p2610006 A05 2,720,763 5.69 5.75
Bn-scaff_27198_1-p445589 A06 15,593,147 8.01 7.99 14NJ/15TZ
Bn-A06-p23759352 A06 22,715,814 5.97 6.01
Bn-Scaffold002856-p361 A07 592,982 5.84 5.89 14NJ/16TZ [14,17,31,36]
Bn-A10-p11601681 A07 2,573,087 6.95 6.15 16TZ [33]
Bn-A07-p5877587 A07 7,824,442 7.24 6.42 14NJ/15TZ [13,32]
Bn-A07-p10557557 A07 11,738,166 5.71 5.77 16TZ
Bn-A02-p305007 A07 12,930,679 5.66 4.93 14NJ/15TZ/16TZ
Bn-A07-p11611255 A07 13,756,170 5.95 6.00 [35]
Bn-A07-p16095589 A07 17,996,553 5.96 6.01
Bn-scaff_15743_1-p590955 A07 18,512,786 8.64 8.58 14NJ/15TZ/16TZ
Bn-A07-p17804261 A07 19,646,053 6.20 5.45 [32,38]
Bn-A08-p2675098 A08 2,098,808 6.81 6.83 16TZ
Bn-A08-p10443959 A08 8,372,628 6.30 6.34 [32]
Bn-A08-p13284369 A08 11,051,828 5.89 5.94
Bn-A08-p20343735 A08 17,811,886 8.82 7.90 15TZ
Bn-A09-p7329993 A09 5,542,361 6.20 6.24 14NJ/15TZ [14,32]
Bn-A10-p15021776 A10 14,967,128 5.78 5.83 15TZ
Bn-A10-p15167470 A10 15,100,392 6.67 6.69 15TZ
Bn-scaff_15803_1-p837307 C01 14,780,320 5.58 5.64 14NJ
Bn-scaff_20942_1-p52095 C02 11,201,048 6.54 6.58 14NJ
Bn-scaff_16002_1-p1803014 C03 12,573,756 6.95 6.97 15TZ
Bn-scaff_26320_1-p269450 C03 30,924,988 5.61 4.89
Bn-scaff_16182_1-p296671 C03 51,992,967 6.41 6.44 14NJ
Bn-scaff_15794_3-p89166 C03 55,716,441 8.28 7.39 14NJ/15TZ
Bn-scaff_17119_1-p148890 C03 56,814,587 9.28 9.19 14NJ/15TZ [35]
Bn-scaff_16217_1-p597569 C04 21,919,412 5.68 4.96 14NJ
Bn-scaff_18062_1-p229981 C04 31,112,520 6.23 5.47 14NJ/16TZ
Position (bp)
-lg (P) 表型变异
R2 (%)
Reported QTL
Bn-scaff_15585_1-p1089867 C04 44,500,243 5.88 5.14 16TZ
Bn-scaff_18903_1-p371596 C04 47,531,676 6.87 6.89 16TZ
Bn-scaff_16414_1-p1774629 C05 279,059 7.33 7.33 14NJ
Bn-scaff_20901_1-p2029631 C05 1,973,973 6.47 6.50 14NJ/16TZ
Bn-scaff_20901_1-p1279675 C05 2,707,564 7.36 7.36 14NJ
Bn-scaff_15763_1-p596396 C05 11,699,136 5.71 4.98 16TZ
Bn-scaff_15763_1-p588874 C06 20,160,298 5.85 5.90 16TZ
Bn-scaff_16064_1-p938130 C06 24,703,441 11.57 11.31 14NJ/15TZ/16TZ [35]
Bn-scaff_15743_1-p599416 C06 27,808,971 9.80 8.80 14NJ/15TZ/16TZ
Bn-scaff_18807_1-p747016 C06 30,110,394 5.69 4.96 [36]
Bn-scaff_16874_1-p411591 C06 31,817,621 6.66 6.69 14NJ/16TZ [30,36,37]
Bn-scaff_17799_1-p2391172 C06 34,110,582 7.71 6.87 14NJ/16TZ
Bn-scaff_17799_1-p853567 C06 35,737,877 7.70 7.69 14NJ [35]
Bn-scaff_15705_1-p2279820 C07 35,285,037 6.12 6.16 16TZ
Bn-A08-p10452462 C08 16,678,522 6.88 6.08 14NJ/15TZ/16TZ
Bn-scaff_17526_1-p1066214 C09 1,488,283 15.98 15.26 14NJ/15TZ/16TZ [32]
Bn-scaff_15576_1-p614226 C09 41,707,720 9.03 8.96 14NJ/16TZ

Table 4

Information of candidate genes of 1000-seed weight GWAS loci"

Rapeseed gene
拟南芥同源基因Arabidopsis homolog gene
基因名称Gene name 基因号Gene ID
Bn-A01-p15496639 BnaA01g20420D A01 12,306,073 NPC6 AT3G48610
Bn-A03-p22125583 BnaA03g41350D A03 20,713,211 DGAT AT3G51520
Bn-A03-p8851142 BnaA03g17130D A03 8,038,181 TTG2 AT2G37260
Bn-A05-p2610006 BnaA05g36830D A05 2,713,236 AGL61 AT5G60440
Bn-A07-p11611255 BnaA07g16350D A07 13,870,810 WRI1 AT3G54320
Bn-A09-p7329993 BnaA09g12210D A09 6,402,925 GW5 AT1G64500
Bn-scaff_20942_1-p52095 BnaA08g15580D C02 12,923,783 CLV3 AT2G27250
Bn-scaff_18903_1-p371596 BnaC04g50960D C04 48,343,005 EOD3 AT2G46660
Bn-scaff_18062_1-p229981 BnaC04g33070D C04 31,436,211 RAV1 AT1G13260
Bn-scaff_17799_1-p853567 BnaC06g38800D C06 36,244,755 GRF2 AT1G78300
Bn-scaff_17799_1-p853567 BnaC06g38900D C06 36,295,477 DA2 AT1G78420
Bn-A08-p10452462 BnaC08g12050D C08 17,299,420 SHB1 AT4G25350
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