欢迎访问作物学报，今天是
作物学报

作物学报 ›› 2018, Vol. 44 ›› Issue (03): 315-323.doi: 10.3724/SP.J.1006.2018.000315

• 作物遗传育种·种质资源·分子遗传学 •    下一篇

应用SNP精准鉴定大豆种质及构建可扫描身份证

魏中艳1(), 李慧慧1, 李骏2, YasirA.Gamar1, 马岩松3, 邱丽娟1,*()   

  1. 1国家农作物基因资源与遗传改良重大科学工程 / 农业部种质资源利用重点实验室 / 中国农业科学院作物科学研究所, 北京100081
    2广西大学农学院, 广西南宁 530004
    3 黑龙江省农业科学院大豆研究所, 黑龙江哈尔滨 150086
  • 收稿日期:2017-06-11 接受日期:2017-11-21 出版日期:2018-03-12 网络出版日期:2017-12-11
  • 通讯作者: 邱丽娟
  • 作者简介:

    w_zhongyan@163.com

  • 基金资助:
    本研究由农产品质量安全监管(种子管理)项目(2130109)和国家农作物资源共享平台(NICGR2016大豆)项目资助

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 Published:2018-03-12 Published online:2017-12-11
  • Contact: Li-Juan QIU
  • 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).

RichHTML

35

PDF

1988

摘要：

为加强大豆种质资源管理及品种保护, 本研究构建了一套基于单核苷酸多态性(SNP)标记的快速鉴定体系。选用分布于13个基因的23个SNP标记对599份大豆表型精准鉴定种质进行基因型分析。结果表明, SNP标记的遗传多样性指数范围0~0.722, 其中3个SNP在供试材料中不存在碱基差异, 2个SNP为特异等位变异。从具有多态性的20个SNP中选出14个(GlySNP14)用于种质鉴定, 其中12个为高多态性SNP, 2个为特异性SNP。模拟结果表明, GlySNP14的种质鉴别能力(750份种质)高于任意相同数目标记构成的SNP随机组合(最多361份种质)。GlySNP14在599份种质中共形成了176个单倍型, 其中100份种质具有独特的单倍型。结合这些种质的其他属性, 构建了100份种质由38个数字组成的身份证, 前10位数字为种质属性信息码, 包括品种类别、来源地等; 11~38位数字为品种分子指纹码, 代表品种的特异分子信息, 并最终以一维码和二维码的形式表示, 为种质资源简易管理与保护利用提供了有效途径。

关键词: 大豆, SNP, 遗传多样性, DNA指纹图谱, 品种ID

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

图1

大豆精准鉴定种质的种植分布图"

表1

SNP标记多样性分析"

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

表2

大豆3个主要生态区种质资源的遗传相似性"

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

图2

基于SNP标记的单倍型分析 A: 599份大豆品种的单倍型分析; B: 特异单倍型分析。"

图3

SNP标记组合分析"

图4

基于SNP标记的100份大豆品种聚类分析图"

图5

随机选择的14个SNP与GlySNP鉴别能力的模拟分析"

图6

“北丰14”品种身份证及条形码示意图 A: “北丰14”品种身份证构成; B: “北丰14”品种身份证条形码。"

表3

部分大豆品种的身份证条码信息"

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
[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
[1] 肖颖妮, 于永涛, 谢利华, 祁喜涛, 李春艳, 文天祥, 李高科, 胡建广. 基于SNP标记揭示中国鲜食玉米品种的遗传多样性[J]. 作物学报, 2022, 48(6): 1301-1311.
[2] 陈玲玲, 李战, 刘亭萱, 谷勇哲, 宋健, 王俊, 邱丽娟. 基于783份大豆种质资源的叶柄夹角全基因组关联分析[J]. 作物学报, 2022, 48(6): 1333-1345.
[3] 胡文静, 李东升, 裔新, 张春梅, 张勇. 小麦穗部性状和株高的QTL定位及育种标记开发和验证[J]. 作物学报, 2022, 48(6): 1346-1356.
[4] 杨欢, 周颖, 陈平, 杜青, 郑本川, 蒲甜, 温晶, 杨文钰, 雍太文. 玉米-豆科作物带状间套作对养分吸收利用及产量优势的影响[J]. 作物学报, 2022, 48(6): 1476-1487.
[5] 王炫栋, 杨孙玉悦, 高润杰, 余俊杰, 郑丹沛, 倪峰, 蒋冬花. 拮抗大豆斑疹病菌放线菌菌株的筛选和促生作用及防效研究[J]. 作物学报, 2022, 48(6): 1546-1557.
[6] 于春淼, 张勇, 王好让, 杨兴勇, 董全中, 薛红, 张明明, 李微微, 王磊, 胡凯凤, 谷勇哲, 邱丽娟. 栽培大豆×半野生大豆高密度遗传图谱构建及株高QTL定位[J]. 作物学报, 2022, 48(5): 1091-1102.
[7] 李阿立, 冯雅楠, 李萍, 张东升, 宗毓铮, 林文, 郝兴宇. 大豆叶片响应CO2浓度升高、干旱及其交互作用的转录组分析[J]. 作物学报, 2022, 48(5): 1103-1118.
[8] 彭西红, 陈平, 杜青, 杨雪丽, 任俊波, 郑本川, 罗凯, 谢琛, 雷鹿, 雍太文, 杨文钰. 减量施氮对带状套作大豆土壤通气环境及结瘤固氮的影响[J]. 作物学报, 2022, 48(5): 1199-1209.
[9] 王好让, 张勇, 于春淼, 董全中, 李微微, 胡凯凤, 张明明, 薛红, 杨梦平, 宋继玲, 王磊, 杨兴勇, 邱丽娟. 大豆突变体ygl2黄绿叶基因的精细定位[J]. 作物学报, 2022, 48(4): 791-800.
[10] 李瑞东, 尹阳阳, 宋雯雯, 武婷婷, 孙石, 韩天富, 徐彩龙, 吴存祥, 胡水秀. 增密对不同分枝类型大豆品种同化物积累和产量的影响[J]. 作物学报, 2022, 48(4): 942-951.
[11] 刘丹, 周彩娥, 王晓婷, 吴启蒙, 张旭, 王琪琳, 曾庆东, 康振生, 韩德俊, 吴建辉. 利用集群分离分析结合高密度芯片快速定位小麦成株期抗条锈病基因YrC271[J]. 作物学报, 2022, 48(3): 553-564.
[12] 杜浩, 程玉汉, 李泰, 侯智红, 黎永力, 南海洋, 董利东, 刘宝辉, 程群. 利用Ln位点进行分子设计提高大豆单荚粒数[J]. 作物学报, 2022, 48(3): 565-571.
[13] 周悦, 赵志华, 张宏宁, 孔佑宾. 大豆紫色酸性磷酸酶基因GmPAP14启动子克隆与功能分析[J]. 作物学报, 2022, 48(3): 590-596.
[14] 王娟, 张彦威, 焦铸锦, 刘盼盼, 常玮. 利用PyBSASeq算法挖掘大豆百粒重相关位点与候选基因[J]. 作物学报, 2022, 48(3): 635-643.
[15] 郑向华, 叶俊华, 程朝平, 魏兴华, 叶新福, 杨窑龙. 利用SNP标记进行水稻品种籼粳鉴定[J]. 作物学报, 2022, 48(2): 342-352.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备15008789号-2