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Acta Agronomica Sinica ›› 2018, Vol. 44 ›› Issue (03): 315-323.doi: 10.3724/SP.J.1006.2018.000315


Accurate Identification of Varieties by Nucleotide Polymorphisms and Establishment of Scannable Variety IDs for Soybean Germplasm

Zhong-Yan WEI1(), Hui-Hui LI1, Jun LI2, A. Gamar Yasir1, Yan-Song MA3, Li-Juan QIU1,*()   

  1. 1 National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Laboratory of Germplasm Utilization, Ministry of Agriculture / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    2 College of Agriculture, Guangxi University, Nanjing 530004, Guangxi China
    3 Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, Heilongjiang, China
  • Received:2017-06-11 Accepted:2017-11-21 Online:2018-03-12 Published:2017-12-11
  • Contact: Li-Juan QIU E-mail:w_zhongyan@163.com;qiulijuan@caas.cn
  • Supported by:
    This study was supported by the project of Quality and Safety Supervision of agriculture food (Seed Management) (2130109) and National Infrastructure for Crop Germplasm Resources (NICGR2016 Soybean).


In order to strengthen the management of soybean germplasm and variety protection, SNP markers were developed to establish the identity of soybean varieties. A set of 23 SNP markers distributed in 13 genes were used to discriminate genotypes of 599 soybean varieties, grown in most of the soybean producing areas in China. Fourteen SNPs with high polymorphism selected from the 23 SNPs (GlySNP14) showed the improved variety identification capability, compared with any combination of 14 random SNPs. A simulated experiment confirmed that GlySNP14 could effectively distinguish of 750 soybean varieties, while the combination of random by selected from the 14 SNPs could distinguish only 361 varieties. The established ID of soybean varieties in this study contained a 38-digit serial code, which can be used for the accurate identification of soybean varieties and meet the requirements of genetic resources protection.

Key words: soybean, SNP, genetic diversity, DNA fingerprint, variety ID

Fig. 1

Planting locations of the three sets of soybean germplasm"

Table 1

Analysis of SNP markers diversity"

SNP locus
Physical location
Homozygous allele ratio (%)
Mutation type
diversity index
Stem growth habit
Glyma19g37890 AR2 19 44981190 89.60 1TV G/T 0.334
AR4 19 44980194 95.14 1TV G/A 0.194
AR5 19 44980087 89.95 2TS A/T 0.351
Pubescence color
Glyma06g21920 AR7 6 18540661 87.25 3D A/- 0.382
TT8 6 18540852 57.56 3D C/- 0.701
Glyma06g23026 TT10 6 20007177 99.16 3D A/- 0.049
Glyma10g36600 TT11 10 44732850 62.39 1TV A/T 0.696
Glyma19g41210 TT12 19 47516339 99.83 2TS G/A 0.012
TT13 19 47513779 99.16 3D -/T 0.048
Glyma20g22160 TT14 20 32089731 100.00 4ND G/- 0
PRO15 20 32091662 99.33 3D A/- 0.040
PRO16 20 32091044 100.00 4ND T/- 0
Glyma18g02681 PRO19 18 1712103 55.54 2TS T/C 0.722
Glyma08g11350 AT21 8 8280937 90.12 2TS T/C 0.360
AT22 8 8281297 88.57 1TV A/T 0.337
AT23 8 8281564 94.59 2TS A/G 0.376
Glyma02g13600 AT26 2 11929770 99.50 2TS A/G 0.210
SER27 2 11930414 65.28 1TV G/T 0.032
Glyma02g13380 SER32 2 11693604 88.01 1TV C/G 0.665
Glyma13g26000 SER36 13 29227216 90.12 1TV G/C 0.439
Glyma14g38500 SER43 14 47631542 57.94 1TV T/A 0.708
SER46 14 47633021 100.00 4ND G/C 0
100-seed weight
Glyma13g22850 SER64 13 27548370 80.57 1TV A/C 0.514

Table 2

Genetic similarity of germplasm resources among three main eco-regions"

Planting area
No. of varieties
遗传相似系数 Genetic similarity coefficient
最大值 Max. 最小值 Min. 平均 Average
北方生态区 North eco-region 208 0.9783 0.0435 0.8295
黄淮海生态区 Huang-Huai-Hai eco-region 245 0.9783 0.3261 0.7941
南方生态区 South eco-region 146 0.9783 0.3478 0.7982

Fig. 2

Analysis of haplotype based on SNP markers A: Analysis of haplotype for 599 soybean varieties; B: Analysis of specific haplotype."

Fig. 3

Analysis of SNP markers combination"

Fig. 4

Dendrogram of 100 soybean varieties based on SNP markers"

Fig. 5

Simulating analysis of variety identification capability of the GlySNP and random sets of 14 SNPs"

Fig. 6

Schematic diagram of “Beifeng14” variety ID A: Composition of “Beifeng 14” variety ID; B: Bar code of “Beifeng 14” variety ID."

Table 3

ID information of some soybean varieties"

Bar code of variety ID
QR code
ZDD18049 地方种
ZDD17767 地方种
ZDD18558 地方种
ZDD10129 地方种
青棵圆豆Qingkeyuandou ZDD08633 地方种
ZDD20188 选育种
Bred variety
Jilin 30
ZDD23704 地方种
Jindou 33
ZDD00745 选育种
Bred variety
Jidou 17
ZDD24685 地方种
Jindou 31
ZDD24705 选育种
Bred variety
Kexin 4
ZDD23866 选育种
Bred variety
L64-1061 WDD00247 选育种
Bred variety
L66-707 WDD00230 选育种
Bred variety
L72-1140 WDD00242 美国春
American Spring
Nattosan WDD01547 美国春
American Spring
Wilkin WDD00504 美国春
American Spring
Mustang WDD01992 美国春
American Spring
Newton WDD01583 美国春
American Spring
Peking WDD00467 美国春
American Spring
[1] Fukuda Y.Cytogenetical studies on the wild and cultivated Manchurian soybeans (Glycine L.). Jpn J Bot, 1933, 6: 489-506
[2] Hymowitz T, Newell C A.Taxonomy of the genus Glycine, domestication and uses of soybeans.Econ Bot, 1981, 35(03): 272-288
[3] 宋喜娥, 李英慧, 常汝镇, 郭平毅, 邱丽娟. 中国栽培大豆(Glycine max (L.) Merr.)微核心种质的群体结构与遗传多样性. 中国农业科学, 2010, 43: 2209-2219
Song X E, Li Y H, Chang R Z, Guo P Y, Qiu L J.Population structure and genetic diversity of mini core collection of cultivated soybean (Glycine max (L.) Merr.) in China. Sci Agric Sin, 2010, 43: 2209-2219 (in Chinese with English abstract)
[4] 赵团结, 盖钧镒. 栽培大豆起源与演化研究进展. 中国农业科学, 2004, 37: 954-962
Zhao T J, Gai J Y.The origin and evolution of cultivated soybean [Glycine max(L.) Merr.]. Sci Agric Sin, 2003, 37: 954-962 (in Chinese with English abstract)
[5] 王彩洁, 孙石, 金素娟, 李伟, 吴存祥, 侯文胜, 韩天富. 中国大豆主产区不同年代大面积种植品种的遗传多样性分析. 作物学报, 2013, 39: 1917-1926
Wang C J, Sun S, Jin S J, Li W, Wu T X, Hou W S, Han T F.Genetic Diversity analysis of widely-planted soybean varieties from different decades and major production regions in China.Acta Agron Sin, 2013, 39: 1917-1926 (in Chinese with Englishabstract)
[6] Yoon M S, Song Q J, Choi I Y, Specht J E, Hyten D, Cregan P.BARCSoySNP23: a panel of 23 selected SNPs for soybean cultivar identification.Theor Appl Genet, 2007, 114: 885-899
[7] 宋婉, 续九如. 果树种质资源鉴定及 DNA 指纹图谱应用研究进展. 北京林业大学学报, 2000, 22(1): 76-80
Song W, Xu J R.Progress in application of germplasm identification and fingerprinting of fruit trees.J Beijing For Univ, 2000, 22(1): 76-80 (in Chinese with English abstract)
[8] 邱福林, 庄杰云, 华泽田, 王彦荣, 程式华. 北方杂交粳稻骨干亲本遗传差异的SSR标记检测. 中国水稻科学, 2005, 19: 101-104
Qiu F L, Zhuang J Y, Hua Z T, Wang Y R, Cheng S H.Inspect of genetic differentiation of main parents of japonica hybrid rice in the Northern China by Simple Sequence Repeats (SSR).J Chin Rice Sci, 2005, 19: 101-104 (in Chinese with English abstract)
[9] 滕海涛, 吕波, 赵久然, 徐岩, 王凤格, 堵苑苑, 杨坤, 唐浩, 李祥羽. 利用DNA 指纹图谱辅助植物新品种保护的可能性. 生物技术通报, 2009, (1): 1-6
Teng H T, Lyu B, Zhao J R, Xu Y, Wang F G, Du Y Y, Yang K, Tang H, Li X Y.DNA fingerprint profile involved in plant variety protection practice.Biotech Bull, 2009, (1): 1-6 (in Chinese with English abstract)
[10] Jung J, Park S, Liu W Y, Kang B.Discovery of single nucleotide polymorphism in Capsicum and SNP markers for cultivar identification.Euphytica, 2010, 175: 91-107
[11] Shirasawa K, Monna L, Kishitani S, Nishio T.Single nucleotide polymorphisms in randomly selected genes among japonica rice (Oryza sativa L.) varieties identified by PCR-RF-SSCP. DNA Res, 2004, 11: 275-283
[12] 王大莉. 香菇栽培品种SNP指纹图谱库的构建. 华中农业大学硕士学位论文, 湖北武汉, 2012
Wang D L.Construction of a SNP Fingerprint Databases for Lentinula edodes Cultivars. MS Thesis of Huazhong Agricultural University, Wuhan,China, 2012 (in Chinese with English abstract)
[13] Liu, K, Muse S V. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics, 2005, 21: 2128-2129
[14] Poole R W.Introduction to quantitative ecology. McGraw-Hill, New York, 1974
[15] Milne I, Shaw P, Stephen G, Bayer M, Cardle L, Thomas W T, Flavell A J, Flavell M D, Marshall D.Flapjack-graphical genotype visualization.Bioinformatics, 2010, 26: 3133-3134
[16] 赵洪锟, 李启云. 吉林省大豆骨干亲本及主推品种 DNA 指纹图谱的构建. 中国油料作物学报, 2000, 22(4): 12-14
Zhao H K, Li Q Y.Jilin province soybean backbone parents and construction of main varieties of DNA fingerprint.J Chin Oil Crop Sci, 2000, 22(4): 12-14 (in Chinese with English abstract)
[17] 匡猛, 杨伟华, 许红霞, 王延琴, 周大云, 冯新爱. 中国棉花主栽品种DNA指纹图谱构建及SSR标记遗传多样性分析. 中国农业科学, 2011, 44: 20-27
Kuang M, Yang W H, Xu H X, Wang Y Q, Zhou D Y, Feng X A.Construction of DNA fingerprinting and analysis of genetic diversity with SSR markers for cotton major cultivars in China. Sci Agric Sin, 2011, 44: 20-27 (in Chinese with English abstract)
[18] 陆徐忠, 倪金龙, 李莉, 汪秀峰, 马卉, 张小娟, 杨剑波. 利用SSR分子指纹和商品信息构建水稻品种身份证. 作物学报, 2014, 40: 823-829
Lu X Z, Ni J L, Li L, Wang X F, Ma H, Zhang X J, Yang J B.Construction of rice variety indentity using SSR fingerprint and commodity information.Acta Agron Sin, 2014, 40: 823-829 (in Chinese with English abstract)
[19] Jones E S, Sullivan H, Bhattramakki D, Smith J.A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize (Zea mays L.). Theor Appl Genet, 2007, 115: 361-371
[20] 张昆鹏. 利用SNP标记构建油菜品种指纹图谱及定位下卷叶性状基因的研究. 南京农业大学博士学位论文, 江苏南京, 2013
Zhang K P.Studies on Rapeseed Variety Fingerprints and Mapping of Gene of the Down-curly Leaf by Use of SNP Markers in Brassica napus L. PhD Dissertation of Nanjing Agricultural University, Nanjing,China, 2013 (in Chinese with English abstract)
[21] Song Q J, Quigley C V, Nelson R L, Carter T, Boerma H, Strachan J, Cregan P.A selected set of trinucleotide simple sequence repeat markers for soybean cultivar identification.Plant Var Seeds, 1999, 12: 207-220
[22] Zhu Y L, Song Q J, Hyten D L, Van Tassell C, Matukumalli L, Grimm D, Hyatt S, Fickus E, Young N, Cregan P.Single- nucleotide polymorphisms in soybean.Genetics, 2003, 163: 1123-1134
[23] Li Y, Zhou G, Ma J, Jiang W, Jin L, Zhang Z, Guo Y, Zhang J, Sui Y, Zheng L, Zhang S, Zuo Q, Shi X, Li Y, Zhang W, Hu Y, Kong G, Hong H, Tan B, Song J, Liu Z, Wang Y, Ruan H, Yeung C K L, Liu J, Wang H, Zhang L, Guan R, Wang K, Li W, Chen S, Chang R, Jiang Z, Jackson S A, Li R, Qiu L. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.Nat Biotechnol, 2014, 32: 1045-1052
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