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

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS •     Next Articles

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).

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Abstract:

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"

性状
Trait		 基因
Gene		 SNP位点
SNP locus		 染色体
Chr.		 物理位置
Physical location		 纯合等位
基因比例
Homozygous allele ratio (%)		 变异类型
Mutation type		 基因型
Genotype		 遗传多样性指数
Genetic
diversity index
结荚习性
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
茸毛色
Pubescence color		 Glyma06g21920 AR7 6 18540661 87.25 3D A/- 0.382
TT8 6 18540852 57.56 3D C/- 0.701
熟期
Maturity		 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
胞囊线虫
SCN		 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
花叶病毒病
SMV		 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
百粒重
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"

种植区
Planting area		 品种数
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"

品种
Variety		 统一编号
Number		 类别
Category		 品种身份证条形码
Bar code of variety ID		 二维码
QR code
青仁黑豆
Qingrenheidou		 ZDD18049 地方种
Landrace
小粒秣食豆
Xiaolimoshidou		 ZDD17767 地方种
Landrace
花黑虎
Huaheihu		 ZDD18558 地方种
Landrace
滑绿豆
Hualvdou		 ZDD10129 地方种
Landrace
青棵圆豆Qingkeyuandou ZDD08633 地方种
Landrace
铁角黄
Tiejiaohuang		 ZDD20188 选育种
Bred variety
吉林30
Jilin 30		 ZDD23704 地方种
Landrace
锦豆33
Jindou 33		 ZDD00745 选育种
Bred variety
冀豆17
Jidou 17		 ZDD24685 地方种
Landrace
晋豆31
Jindou 31		 ZDD24705 选育种
Bred variety
科新4号
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
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