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作物学报 ›› 2024, Vol. 50 ›› Issue (4): 887-896.doi: 10.3724/SP.J.1006.2024.31044

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于SNP标记的小麦品种遗传相似度及其检测准确度分析

许乃银1(), 金石桥2,*(), 晋芳2, 刘丽华3, 徐剑文1, 刘丰泽2, 任雪贞2, 孙全2, 许栩1, 庞斌双3,*()   

  1. 1江苏省农业科学院经济作物研究所, 江苏南京 210014
    2全国农业技术推广服务中心, 北京 100125
    3北京市农林科学院杂交小麦研究所, 北京 100097
  • 收稿日期:2023-07-20 接受日期:2023-10-23 出版日期:2024-04-12 网络出版日期:2023-10-27
  • 通讯作者: * 金石桥, E-mail: jinshiqiao@agri.gov.cn;庞斌双, E-mail: 1492196201@qq.com
  • 作者简介:E-mail: naiyin@126.com
  • 基金资助:
    国家科技创新重大项目(2022ZD04019)

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 Published:2024-04-12 Published online:2023-10-27
  • Contact: * E-mail: jinshiqiao@agri.gov.cn; E-mail: 1492196201@qq.com
  • Supported by:
    National Scientific and Technological Innovation Major Project(2022ZD04019)

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摘要：

遗传相似度检测的准确度估计是对SNP标记法在农作物品种检测体系中应用的必要补充和完善。本研究基于2021年小麦品种SNP标记法跨实验室协同验证实验数据, 分析了该方法的检测准确度及在品种间的遗传相似度。分析结果表明: (1) 10个实验室对55组小麦品种组合的标记位点相似度检测的总体准确度约为98%。(2) GGE双标图的品种遗传关系功能图显示, 7组小麦品种的组内遗传相似度在95%以上, 其余组合的遗传相似度较低。(3) 依据GGE双标图的“正确度-精确度”功能图和“准确度排序”功能图, 发现洛旱7号/洛旱11等品种组合的相似度检测准确度较高, 晋麦47/临抗11的检测准确度一般, 而济麦22/婴泊700的检测准确度较差。(4) 10个实验室的检测准确度存在显著差异, 其中2个实验室检测的正确度、精确度和准确度表现显著差于其余实验室。(5) 各实验室检测正确度的容许误差分布于1.3%~1.9%之间, 平均为1.5%; 准确度的容许误差分布于1.5%~2.0%之间, 平均为1.7%。其中, Lab2和Lab3的检测正确度和准确度的容许误差显著差于其余实验室。本研究构建了SNP标记法对品种相似性检测的准确度统计模型, 分析了品种组合和实验室的检测准确度及其容许误差, 采用GGE双标图方法对检测正确度、精确度和准确度进行可视化分析, 验证了各实验室对品种位点相似性检测的准确度和可靠性, 为SNP标记法在农作物品种遗传相似性检测中的准确度评价提供了理论支持和应用范例。

关键词: 小麦(Triticum aestivum L.), GGE双标图, SNP标记, 遗传相似度, 位点相似度, 准确度

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

表1

基于SNP标记鉴定小麦品种遗传相似性的实验室和抽样品种信息表"

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

表2

小麦抽检品种SNP位点相似度与检测准确度平均值矩阵"

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

图1

基于小麦品种SNP位点相似度平均值的GGE双标图“品种遗传关系”功能图(a)和“品种组合关系+误差”功能图(b) 大写字母W后面的数字为品种编号, 具体品种名称详见表1。品种向量间的夹角表示品种间的遗传相关性, 夹角越小则相关性越强。图1-b中的蓝色小点表示各实验室检测的品种组合相似性图标, 其到品种组合图标的连线长短表示误差大小, 连线越长误差越大。"

图2

基于标准参照的小麦品种遗传相似度检测准确度GGE双标图分析的“正确度-精确度”功能图(a)和“准确度排序”功能图(b) 大写字母W后面的数字为品种组合编号, 如W01/02表示品种组合W01和W02, 具体品种名称详见表1。PC1相当于品种位点相似性检测的正确度, PC2的绝对值相当于精确度。图2-a中, 单箭头的横轴指向正确度大的方向, 双箭头的纵轴指向精确度差的方向。图2-b中的同心圆圆心为理想品种组合坐标, 品种组合图标到圆心的欧氏距离表示准确度, 距离越小则准确度越好。“+”为实验室图标。"

图3

实验室对小麦品种遗传相似度检测准确度GGE双标图分析的“正确度-精确度”功能图(a)和“准确度排序”功能图(b) 带“*”的实验室编号同表1, “+”表示品种组合图标。PC1相当于品种位点相似性检测的正确度, PC2的绝对值相当于精确度。图3-b中的同心圆圆心为标准参照坐标, 实验室图标到圆心的欧氏距离表示准确度, 距离越小则准确度越好。"

表3

不同实验室SNP标记法检测准确度及其容许误差估计"

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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