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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (02): 307-314.doi: 10.3724/SP.J.1006.2020.91039

• RESEARCH NOTES • Previous Articles    

Revealing the genetic diversity of wheat varieties (lines) in China based on SNP markers

LIU Yi-Ke1,ZHU Zhan-Wang1,CHEN Ling1,ZOU Juan1,2,TONG Han-Wen1,ZHU Guang1,HE Wei-Jie1,ZHANG Yu-Qing1,GAO Chun-Bao1,2,*()   

  1. 1 Food Crops Institute, Hubei Academy of Agricultural Sciences / Wheat Disease Biology Research Station on Central China, Ministry of Agriculture, China / Hubei Engineering and Technology Research Center of Wheat, Wuhan 430064, Hubei, China
    2 Hubei Collaborative Innovation Center for Grain Industry / Yangtze University, Jingzhou 434025, Hubei China
  • Received:2019-06-03 Accepted:2019-08-09 Online:2020-02-12 Published:2019-09-11
  • Contact: Chun-Bao GAO E-mail:gcbgybwj@163.com
  • Supported by:
    The work was supported by the National Key Research and Development Program(2017YFD0100802);the Hubei Technical Innovation Project(2018ABA085);the Modern Agro-Industry Technology Research Systems(CARS-03);the Hubei Agricultural Science and Technology Innovation Center Project


In order to understand the genetic diversity of major wheat cultivars (lines) in China and provide a reference for parent selection, we selected 240 domestically dominated wheat cultivars (lines) for SNP genotyping using the Illumina 90K iSelect SNP chip. The SNP loci were the most in the B genome, and were the least in the D genome, especially in 4D. The mean value of the polymorphism information content (PIC) was 0.26. The genetic similarity of the 240 cultivars (lines) ranged from 0.133 to 0.998 with an average value of 0.656. However, genetic similarity of 0.60 to 0.78 was found in 87.05% of the tested cultivars (lines). The genetic similarity was up to 0.718 between Southwest Wheat Region cultivars (lines), 0.712 between Middle and Low Yangtze Valleys Wheat Region, and 0.552 between foreign cultivars (lines). The 240 wheat cultivars (lines) were classified into seven groups by UPGMA analyses, most of them contained varieties (lines) bred from different regions. Principal component analysis (PCA) showed that the cultivars (lines) bred in different regions intersected together. The exchange of germplasm resources among different regions in China was frequent, but the genetic basis of the cultivars (lines) bred by some units was not rich enough and the genetic similarity between some varieties (lines) was higher. It is urgent to introduce new germplasm and broaden the genetic basis in breeding.

Key words: wheat, cultivars, genetic diversity, SNPs

Supplementary table 1

The wheat varieties(lines) for SNP genotyping analysis"

序号 品种 麦区 序号 品种 麦区 序号 品种 麦区
4 川麦42 西南麦区 37 周麦23 黄淮南片 239 淮麦18 黄淮南片
16 内麦8号 西南麦区 42 众麦1号 黄淮南片 25 济麦20 黄淮北片
18 绵阳99-7 西南麦区 44 洛麦21 黄淮南片 32 烟农22 黄淮北片
23 绵麦42 西南麦区 45 豫麦49-168 黄淮南片 33 青丰1号 黄淮北片
38 绵麦1403 西南麦区 47 项麦99 黄淮南片 43 科农9204 黄淮北片
39 西科麦4号 西南麦区 48 皖麦52 黄淮南片 53 山东664 黄淮北片
40 XK0106-1-0806 西南麦区 49 周麦22 黄淮南片 54 山农189 黄淮北片
56 川麦50 西南麦区 51 周麦16 黄淮南片 60 烟农24 黄淮北片
61 川麦52 西南麦区 52 豫农202 黄淮南片 64 泰山21 黄淮北片
62 西科麦2号 西南麦区 55 豫麦52 黄淮南片 67 临汾138 黄淮北片
83 川麦51 西南麦区 57 新麦18 黄淮南片 68 邯3475 黄淮北片
138 西科麦5号 西南麦区 65 西农979 黄淮南片 69 邯6172 黄淮北片
199 川农42 西南麦区 71 荔垦2号 黄淮南片 70 冀麦30 黄淮北片
211 绵麦37 西南麦区 72 徐麦29 黄淮南片 75 烟5158 黄淮北片
212 川麦43 西南麦区 73 温麦6号 黄淮南片 76 临Y867 黄淮北片
215 绵麦185 西南麦区 74 新麦20 黄淮南片 78 济宁16号 黄淮北片
226 绵阳99-3 西南麦区 79 陕715 黄淮南片 85 科农199 黄淮北片
1 鄂麦596 长江中下游麦区 80 皖麦38 黄淮南片 87 良星99 黄淮北片
2 扬05-117 长江中下游麦区 81 温麦7号 黄淮南片 91 烟农19 黄淮北片
6 鄂麦27 长江中下游麦区 82 豫麦48 黄淮南片 92 长6359 黄淮北片
7 扬06-144 长江中下游麦区 84 新麦22 黄淮南片 98 临汾137 黄淮北片
13 荆辐麦1号 长江中下游麦区 86 连麦1号 黄淮南片 103 冀麦38 黄淮北片
14 扬麦12 长江中下游麦区 88 双抗7438 黄淮南片 107 石家庄8号 黄淮北片
21 鄂恩1号 长江中下游麦区 93 西农3517 黄淮南片 110 济麦21 黄淮北片
28 鄂麦580 长江中下游麦区 96 洛早7 黄淮南片 143 邯5316 黄淮北片
29 CJ9306 长江中下游麦区 100 温麦18 黄淮南片 145 潍麦8号 黄淮北片
30 襄麦55 长江中下游麦区 101 温麦19 黄淮南片 149 泰农18 黄淮北片
36 鄂恩6号 长江中下游麦区 106 郑麦9023 黄淮南片 150 山农16 黄淮北片
41 扬06G5 长江中下游麦区 109 西农9871 黄淮南片 152 衡观115 黄淮北片
58 宁7840 长江中下游麦区 112 新麦11 黄淮南片 156 衡观4422 黄淮北片
59 扬麦158 长江中下游麦区 113 淮麦20 黄淮南片 164 荷麦13 黄淮北片
66 扬07-49 长江中下游麦区 115 漯6010 黄淮南片 165 泰农142 黄淮北片
77 鄂麦23 长江中下游麦区 116 新麦9817 黄淮南片 177 临Y7287 黄淮北片
89 镇麦6号 长江中下游麦区 117 新麦13 黄淮南片 179 济麦22 黄淮北片
95 宁麦16 长江中下游麦区 119 陕麦150 黄淮南片 180 山农15 黄淮北片
97 鄂恩5号 长江中下游麦区 120 周麦18 黄淮南片 184 临优2069 黄淮北片
102 镇麦5号 长江中下游麦区 122 豫农035 黄淮南片 191 烟5286 黄淮北片
105 鄂麦12 长江中下游麦区 126 小偃6号 黄淮南片 192 衡观35 黄淮北片
111 扬06G86 长江中下游麦区 128 郑育麦9987 黄淮南片 194 衡观136 黄淮北片
118 扬06-164 长江中下游麦区 130 洛新998 黄淮南片 200 烟农21 黄淮北片
123 扬麦15 长江中下游麦区 132 泛麦5号 黄淮南片 203 济麦17 黄淮北片
124 华2533 长江中下游麦区 136 漯4-168 黄淮南片 209 鲁麦21号 黄淮北片
125 宁麦13 长江中下游麦区 139 新1817 黄淮南片 213 济南17 黄淮北片
127 扬07-129 长江中下游麦区 140 许科1号 黄淮南片 217 济麦19 黄淮北片
131 扬07-44 长江中下游麦区 142 郑麦004 黄淮南片 219 山农8355 黄淮北片
133 苏麦3号 长江中下游麦区 147 陕麦139 黄淮南片 221 烟2415 黄淮北片
134 华2566 长江中下游麦区 148 04中36 黄淮南片 227 鲁农116 黄淮北片
137 宁麦9号 长江中下游麦区 151 西农2000 黄淮南片 232 泰山23 黄淮北片
141 宁麦8号 长江中下游麦区 154 豫麦49-198 黄淮南片 8 兰天13 北部麦区
146 镇麦168 长江中下游麦区 155 豫麦69 黄淮南片 9 兰天17号 北部麦区
157 扬麦13 长江中下游麦区 161 郑麦98 黄淮南片 15 宁春47号 北部麦区
158 襄麦25 长江中下游麦区 162 新9817 黄淮南片 24 宁冬11号 北部麦区
160 扬07-15 长江中下游麦区 163 矮早781-99 黄淮南片 46 兰天23号 北部麦区
167 鄂麦11 长江中下游麦区 168 小偃166 黄淮南片 50 宁冬10号 北部麦区
170 扬麦14 长江中下游麦区 169 连麦2号 黄淮南片 94 兰天18号 北部麦区
171 鄂352 长江中下游麦区 172 郑麦366 黄淮南片 104 兰天15号 北部麦区
174 荆州66 长江中下游麦区 173 西农88 黄淮南片 108 京冬17 北部麦区
175 鄂麦18 长江中下游麦区 176 陕农78 黄淮南片 121 北京0045 北部麦区
181 扬辐麦2号 长江中下游麦区 182 陕农757 黄淮南片 129 中麦12号 北部麦区
183 扬麦16 长江中下游麦区 186 陕159 黄淮南片 144 中农2号 北部麦区
185 扬麦11 长江中下游麦区 188 郑农17 黄淮南片 178 轮选987 北部麦区
198 荆麦103 长江中下游麦区 190 豫麦70 黄淮南片 187 京冬8号 北部麦区
204 鄂07901 长江中下游麦区 193 开麦18 黄淮南片 214 兰天12 北部麦区
207 扬麦17 长江中下游麦区 195 豫麦10号 黄淮南片 216 兰天21号 北部麦区
231 Wuhan 1 长江中下游麦区 196 洛早2 黄淮南片 218 兰天00-30 北部麦区
233 宁麦11 长江中下游麦区 197 平安3号 黄淮南片 225 宁春4号 北部麦区
240 扬07-81 长江中下游麦区 201 百农160 黄淮南片 230 宁春43号 北部麦区
3 偃展4110 黄淮南片 202 陕627 黄淮南片 234 兰天22号 北部麦区
5 陕农138 黄淮南片 205 小偃107 黄淮南片 237 中麦9号 北部麦区
11 洛早6 黄淮南片 206 豫麦38 黄淮南片 10 SYN1 国外
12 小偃22 黄淮南片 208 新麦19 黄淮南片 63 14FHBSN6404 国外
17 新麦16 黄淮南片 210 淮麦17 黄淮南片 90 14FHBSN6418 国外
19 平安6号 黄淮南片 220 中育10号 黄淮南片 99 14FHBSN6405 国外
20 金丰3号 黄淮南片 222 陕253 黄淮南片 114 14FHBSN6402 国外
22 豫麦70-36 黄淮南片 223 陕麦175 黄淮南片 135 GAMENYA 国外
26 郑麦9094 黄淮南片 224 新麦208 黄淮南片 153 14FHBSN6409 国外
27 郑育麦958 黄淮南片 228 皖麦50 黄淮南片 159 Ocoroni 国外
31 科大9612 黄淮南片 229 矮抗58 黄淮南片 166 14FHBSN6411 国外
34 徐麦27 黄淮南片 236 徐麦216 黄淮南片 189 14FHBSN6408 国外
35 周麦17 黄淮南片 238 濮麦10号 黄淮南片 235 Mayoor 国外

Fig. 1

Distribution of polymorphic SNPs on individual chromosome (A) and each homoeologous group (B)"

Fig. 2

Distribution of polymorphic information content in 240 elite wheat lines based on SNP marker"

Table 1

Genetic similarity coefficient of varieties (lines) bred in different areas"

No. of varieties
遗传相似系数 Genetic similarity
变幅 Range 均值 Average
西南麦区 Wheat region of southwest China 17 0.609-0.983 0.718
长江中下游麦区Wheat region of the middle and lower reaches of Yangtze River 50 0.161-0.998 0.712
黄淮南片 Wheat region of South Huang-Huai 94 0.146-0.998 0.686
黄淮北片 Wheat region of North Huang-Huai 47 0.559-0.991 0.680
北部麦区 Wheat region of Northern China 21 0.538-0.989 0.660
国外 Abroad 11 0.262-0.861 0.552
总计Total 240 0.133-0.998 0.656

Fig. 3

Distribution of genetic similarity between 240 varieties (lines)"

Fig. 4

Clustering graph for 240 wheat varieties (lines) based on SNP markers analysis"

Fig. 5

Principle component analysis (PCA) of 240 wheat varieties (lines) based on SNP markers A: wheat varieties (lines) from Southwest China; B: wheat varieties (lines) from the middle and lower reaches of Yangtze River; C: wheat varieties (lines) from South Huang-Huai; D: wheat varieties (lines) from North Huang-Huai, China; E: wheat varieties (lines) from Northern China; E: wheat varieties (lines) from Foreign."

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