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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (4): 887-896.doi: 10.3724/SP.J.1006.2024.31044

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

Genetic similarity and its detection accuracy analysis of wheat varieties based on SNP markers

XU Nai-Yin1(), JIN Shi-Qiao2,*(), JIN Fang2, LIU Li-Hua3, XU Jian-Wen1, LIU Feng-Ze2, REN Xue-Zhen2, SUN Quan2, XU Xu1, PANG Bin-Shuang3,*()   

  1. 1Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
    2National Agricultural Technical Extension and Service Center, Beijing 100125, China
    3Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
  • Received:2023-07-20 Accepted:2023-10-23 Online:2024-04-12 Published:2023-10-27
  • Contact: * E-mail: jinshiqiao@agri.gov.cn; E-mail: 1492196201@qq.com E-mail:naiyin@126.com;jinshiqiao@agri.gov.cn;1492196201@qq.com
  • Supported by:
    National Scientific and Technological Innovation Major Project(2022ZD04019)

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Abstract:

The accuracy estimation of genetic similarity detection of crop varieties is an indispensable supplement and improvement to the application of SNP marker method in crop variety detection technology system. In this study, based on the cross-laboratory collaborative validation test data using SNP molecular marker method in 2021, the genetic similarity among wheat varieties and the accuracy of SNP molecular marker method in variety similarity detection were analyzed. The results showed as follows: (1) The overall accuracy of marker locus similarity detection among 55 wheat variety combinations by 10 laboratories was approximately 98%. (2) The genetic relationship between varieties view of GGE biplot delineated the genetic relationship between varieties. The genetic similarity between seven combinations of wheat varieties was over 95%, and the genetic similarity of other combinations was relatively lower. (3) The “trueness-precision” view and “accuracy ranking” view of GGE biplot identified that the similarity detection accuracy of the variety combination Jinmai 47/Linkang 11 was on average, Jimai 22/Yingbo 700 was relatively lower, while Luohan 7/Luohan 11 and other variety combinations were relatively high. (4) Significant differences were existed in detection accuracy among the 10 laboratories, and the performances in detection trueness, precision and accuracy of two laboratories were significantly worse than those of other laboratories. (5) The tolerance error of the trueness of each laboratory ranged from 1.3% to 1.9%, with an average of 1.5%. The tolerance error of accuracy was distributed between 1.5% and 2.0%, with an average of 1.7%. Among them, the tolerance errors of the detection trueness and accuracy of Lab2 and Lab3 were significantly worse than those of the other laboratories. In this study, the detection accuracy statistical model of SNP marker method in detecting crop variety similarity was constructed to analyze the detection accuracy and the corresponding tolerance error of variety combination in different laboratories, and the GGE biplot techniques were adopted to visualize the detection trueness, precision, and accuracy, so as to verify the accuracy and reliability of the detection method for variety locus similarity in each laboratory. Therefore, the findings in this study could provide the theoretical support and application examples for the accuracy evaluation of SNP marker detection technique system for genetic similarity among crop varieties.

Key words: wheat (Triticum aestivum L.), GGE biplot, SNP marker, genetic similarity, locus similarity, accuracy

Table 1

Information of sampled wheat varieties and laboratories involved in variety genetic similarity identification based on SNP molecular markers"

实验室信息 Laboratory information 品种信息 Variety information
实验室
Laboratory		 所在省(市)
Province (city)		 检测平台
Detection platform		 品种编号
Variety code		 品种名称
Variety name
Lab1 北京Beijing IMAP W01 济麦22 Jimai 22
Lab2 北京Beijing LGC SNP line W02 婴泊700 Yingbo 700
Lab3 甘肃Gansu Quantitative PCR W03 晋麦47 Jinmai 47
Lab4 河北Hebei LGC SNP line W04 临抗11 Linkang 11
Lab5 河南Henan LGC SNP line W05 洛旱7号Luohan 7
Lab6 山西Shanxi LGC SNP line W06 洛旱11 Luohan 11
Lab7 陕西Shaanxi LGC SNP line W07 扬麦158 Yangmai 158
Lab8 四川Sichuan Array tape W08 扬麦11 Yangmai 11
Lab9 北京Beijing Quantitative PCR W09 扬麦12 Yangmai 12
Lab10 北京Beijing LGC SNP line W10 中科麦138 Zhongkemai 138
REF# 北京Beijing LGC SNP line W11 中科麦36 Zhongkemai 36

Table 2

Matrix of average SNP locus similarity and testing accuracy of wheat sampling varieties (%)"

编号
Code		 品种
Variety		 W01 W02 W03 W04 W05 W06 W07 W08 W09 W10 W11
W01 济麦22 Jimai 22 97.8 97.1 97.4 98.2 97.4 97.2 97.3 97.7 97.7 97.0
W02 婴泊700 Yingbo 700 94.7 97.3 98.1 97.0 96.5 96.4 97.8 97.3 95.6 95.8
W03 晋麦47 Jinmai 47 52.1 55.5 98.6 96.7 96.2 97.2 97.7 96.2 97.2 97.6
W04 临抗11 Linkang 11 50.8 52.4 96.1 98.5 98.0 98.5 98.6 96.8 98.2 98.2
W05 洛旱7号 Luohan 7 60.2 58.2 53.0 54.1 99.1 98.1 98.0 97.0 98.0 98.3
W06 洛旱11 Luohan 11 59.3 57.4 52.8 53.9 96.9 97.0 97.0 97.0 98.2 98.3
W07 扬麦158 Yangmai 158 50.3 49.1 48.2 47.7 48.5 47.7 98.7 98.9 98.3 98.1
W08 扬麦11 Yangmai 11 49.5 48.2 51.0 50.5 49.5 48.7 96.1 98.8 98.6 98.9
W09 扬麦12 Yangmai 12 51.4 50.2 48.7 47.9 48.8 48.0 98.2 94.8 98.0 97.6
W10 中科麦138 Zhongkemai 138 44.9 42.0 49.9 51.1 47.1 46.9 61.3 62.0 61.8 99.2
W11 中科麦36 Zhongkemai 36 43.6 42.8 53.3 52.7 47.8 47.6 60.6 61.3 61.0 96.3

Fig. 1

“variety genetic relationship” view of GGE biplot based on the average SNP locus similarity (a) and the “variety combination relationship + error” view of GGE biplot (b) The uppercase W followed by the numbers represents variety codes and the specific name of the breeding is shown in Table 1. The angle between the cultivar vectors indicates the genetic correlation between the cultivars, and the smaller the angle, the stronger the correlation. The blue dot in Fig. 1-b represents the similarity mark of variety combination tested by each laboratory, and the length of the line from it to the variety combination mark represents the error size, and the longer the line, the larger the error."

Fig. 2

“trueness-precision” view (a) and “accuracy ranking” view (b) of GGE biplot analysis displaying wheat varieties genetic similarity detection accuracy in different laboratories based on the standard reference value The uppercase W followed by numbers represents variety combination codes. For example, W01/02 indicates the wheat variety W01 compared to W02. See Table 1 for detail. PC1 corresponds to the trueness in variety locus similarity detection and the absolute value of PC2 corresponds to the precision. In Fig. 2-a, the single-arrowed horizontal axis points to the direction of higher accuracy, while the double-arrowed vertical axis points to the direction of lower precision. The origin of concentric circles in Figure 2-b is the ideal variety combination mark, and the Euclidean distance from the variety combination mark to the origin represents the detection accuracy. The smaller the distance, the better the accuracy. The plus sign “+” stand for variety comparison combination mark."

Fig. 3

“trueness-precision” view (a) and “accuracy ranking” view (b) of GGE biplot analysis displaying wheat varieties genetic similarity detection accuracy in different laboratories Lab codes prefixed with star sign “*” are the same as those given in Table 1. The plus sign “+” stands for variety comparison combination mark. PC1 corresponds to the trueness in variety locus similarity detection and the absolute value of PC2 corresponds to the precision. The origin of concentric circles in Fig. 3-b is the standard reference mark, and the Euclidean distance from the variety combination mark to the origin represents the detection accuracy. The smaller the distance, the better the accuracy."

Table 3

The detection accuracy parameters and the corresponding tolerance error estimation for different laboratories using SNP markers"

实验室
Laboratory		 所在省(市)
Province (city)		 正确度
Trueness (%)		 精确度
Precision (%)		 准确度
Accuracy (%)		 容许误差 Tolerance error (%)
正确度Trueness 准确度Accuracy
Lab8 四川Sichuan 99.08 a 1.05 e 98.48 a 1.31 e 1.52 e
Lab9 北京Beijing 98.90 ab 1.13 de 98.30 ab 1.37 de 1.58 de
Lab1 北京Beijing 98.70 abc 1.21 cde 98.11 abc 1.43 cde 1.62 cde
Lab7 陕西Shaanxi 98.60 abc 1.28 cd 98.01 abc 1.46 cd 1.64 cd
Lab4 河北Hebei 98.59 abc 1.25 cde 97.99 abc 1.45 cde 1.64 cd
Lab10 北京Beijing 98.41 bcd 1.36 bc 97.82 bcd 1.52 bc 1.69 bcd
Lab5 河南Henan 98.32 cd 1.37 bc 97.72 cd 1.55 bc 1.73 bc
Lab6 山西Shanxi 98.01 d 1.50 b 97.42 d 1.62 b 1.79 b
Lab2 北京Beijing 97.23 e 1.79 a 96.65 e 1.80 a 1.94 a
Lab3 甘肃Gansu 96.81 e 1.90 a 96.23 e 1.91 a 2.04 a
平均Mean 98.27 1.38 97.67 1.54 1.72
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[1] Li Shaoqing, Li Yangsheng, Wu Fushun, Liao Jianglin, Li Damo. Optimum Fertilization and Its Corresponding Mechanism under Complete Submergence at Booting Stage in Rice[J]. Acta Agronomica Sinica, 2002, 28(01): 115 -120 .
[2] Wang Lanzhen;Mi Guohua;Chen Fanjun;Zhang Fusuo. Response to Phosphorus Deficiency of Two Winter Wheat Cultivars with Different Yield Components[J]. Acta Agron Sin, 2003, 29(06): 867 -870 .
[3] YANG Jian-Chang;ZHANG Jian-Hua;WANG Zhi-Qin;ZH0U Qing-Sen. Changes in Contents of Polyamines in the Flag Leaf and Their Relationship with Drought-resistance of Rice Cultivars under Water Deficiency Stress[J]. Acta Agron Sin, 2004, 30(11): 1069 -1075 .
[4] Yan Mei;Yang Guangsheng;Fu Tingdong;Yan Hongyan. Studies on the Ecotypical Male Sterile-fertile Line of Brassica napus L.Ⅲ. Sensitivity to Temperature of 8-8112AB and Its Inheritance[J]. Acta Agron Sin, 2003, 29(03): 330 -335 .
[5] Wang Yongsheng;Wang Jing;Duan Jingya;Wang Jinfa;Liu Liangshi. Isolation and Genetic Research of a Dwarf Tiilering Mutant Rice[J]. Acta Agron Sin, 2002, 28(02): 235 -239 .
[6] WANG Li-Yan;ZHAO Ke-Fu. Some Physiological Response of Zea mays under Salt-stress[J]. Acta Agron Sin, 2005, 31(02): 264 -268 .
[7] TIAN Meng-Liang;HUNAG Yu-Bi;TAN Gong-Xie;LIU Yong-Jian;RONG Ting-Zhao. Sequence Polymorphism of waxy Genes in Landraces of Waxy Maize from Southwest China[J]. Acta Agron Sin, 2008, 34(05): 729 -736 .
[8] HU Xi-Yuan;LI Jian-Ping;SONG Xi-Fang. Efficiency of Spatial Statistical Analysis in Superior Genotype Selection of Plant Breeding[J]. Acta Agron Sin, 2008, 34(03): 412 -417 .
[9] WANG Yan;QIU Li-Ming;XIE Wen-Juan;HUANG Wei;YE Feng;ZHANG Fu-Chun;MA Ji. Cold Tolerance of Transgenic Tobacco Carrying Gene Encoding Insect Antifreeze Protein[J]. Acta Agron Sin, 2008, 34(03): 397 -402 .
[10] ZHENG Xi;WU Jian-Guo;LOU Xiang-Yang;XU Hai-Ming;SHI Chun-Hai. Mapping and Analysis of QTLs on Maternal and Endosperm Genomes for Histidine and Arginine in Rice (Oryza sativa L.) across Environments[J]. Acta Agron Sin, 2008, 34(03): 369 -375 .
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