Please wait a minute...
浙江大学学报（农业与生命科学版）
Journal of Zhejiang University (Agriculture and Life Sciences)  2019, Vol. 45 Issue (3): 278-287    DOI: 10.3785/j.issn.1008-9209.2018.10.261
Biological sciences & biotechnology     
Comparison of simple sequence repeat (SSR) and sequence related amplified polymorphism (SRAP) markers for genetic diversity analysis in strawberry
Ya XIN1(),Xianping FANG1,2,Shuzhen WANG1,Jianxin TONG1,Wenguo LAI1,Jianrong WANG1,Hong YU1()
1. Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China
2. Institute of Forestry and Pomology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Download: HTML   HTML ( )    PDF(809KB)
Export: BibTeX | EndNote (RIS)      

Abstract  

Simple sequence repeat (SSR) and sequence related amplified polymorphism (SRAP) markers were applied to analyze genetic diversity among 43 strawberry (Fragaria×ananassa Duch.) cultivars and effectivenesses of these two kinds of molecular markers were also compared. The results showed that there were 6.43 polymorphic sites per primer pair of 30 SSR primers, and the average polymorphism information content (PIC) of each site was 0.628 4. While there were 14.30 polymorphic sites per primer pair of 20 SRAP primers，and the average PIC of each site was 0.911 4. The correlation coefficient between clustering results based on SSR markers and SRAP markers was 0.817, which was significant. The correlation coefficients between SSR markers, SRAP markers and SSR+SRAP joint markers were 0.938 and 0.966, respectively, which reached extremely significant levels. Both SSR and SRAP markers can be used to analyze the genetic diversity of strawberry, but the effect of SRAP marker is better than that of SSR marker. The analysis of SSR+SRAP joint markers can better evaluate the genetic diversity and genetic relationship of strawberry germplasm.

Key words： strawberry      simple sequence repeat (SSR)      sequence related amplified polymorphism (SRAP)      genetic diversity     
Received: 26 October 2018      Published: 25 June 2019
CLC:  S 668.4  
Corresponding Authors: Hong YU     E-mail: xinya0@yeah.net;yhtlzj12345@126.com
Service
E-mail this article
Add to my bookshelf
Add to citation manager
E-mail Alert
RSS
Articles by authors
Ya XIN
Xianping FANG
Shuzhen WANG
Jianxin TONG
Wenguo LAI
Jianrong WANG
Hong YU
Cite this article:

Ya XIN,Xianping FANG,Shuzhen WANG,Jianxin TONG,Wenguo LAI,Jianrong WANG,Hong YU. Comparison of simple sequence repeat (SSR) and sequence related amplified polymorphism (SRAP) markers for genetic diversity analysis in strawberry. Journal of Zhejiang University (Agriculture and Life Sciences), 2019, 45(3): 278-287.

URL:

http://www.zjujournals.com/agr/10.3785/j.issn.1008-9209.2018.10.261     OR     http://www.zjujournals.com/agr/Y2019/V45/I3/278


简单重复序列标记和序列相关扩增多态性标记在草莓遗传多样性分析中的比较

利用简单重复序列（simple sequence repeat, SSR）和序列相关扩增多态性(sequence related amplified polymorphism, SRAP)标记分析了来自国内外43个草莓品种的遗传多样性，并比较了这2种分子标记的效果差异。结果表明：30对SSR引物平均多态性位点数为6.43个，每个位点的平均多态性信息含量（polymorphism information content, PIC）值为0.628 4；20个SRAP引物组合平均多态性位点数为14.30个，PIC值高达0.911 4。基于SSR标记的聚类结果与基于SRAP标记的聚类结果的相关系数为0.817，呈显著水平。而SSR标记、SRAP标记分别与SSR+SRAP联合标记的相关系数为0.938和0.966，都达到极显著水平。SSR和SRAP标记都能较好地分析草莓遗传多样性，其中SRAP标记的效果略优于SSR标记，而SSR+SRAP联合标记分析则能更好地评估种质的遗传多样性和亲缘关系。


关键词： 草莓,  简单重复序列,  序列相关扩增多态性,  遗传多样性 

编号

No.

 品种Cultivar

类型

Type

编号

No.

品种

Cultivar

类型

Type
1 章姬 日本品种 23 阿尔比 美国品种（日中性）
2 幸香 日本品种 24 波拉特 美国品种（日中性）
3 红玉 国内选育品种 25 卡姆罗莎 美国品种
4 宁玉 国内选育品种 26 达赛 法国品种
5 晶瑶 国内选育品种 27 法国1号 法国品种
6 红颊 日本品种 28 法国2号 法国品种
7 丰香 日本品种 29 法国3号 法国品种
8 甜查理 美国品种 30 京藏香 国内选育品种
9 越心 国内选育品种 31 京桃香 国内选育品种
10 越丽 国内选育品种 32 妙香 国内选育品种
11 香野 日本品种 33 黔莓 国内选育品种
12 阿玛奥 日本品种 34 艳丽 国内选育品种
13 弥生姬 日本品种 35 中莓1号 国内选育品种
14 初恋情人 日本品种（白草莓） 36 中莓3号 国内选育品种
15 桃熏 日本品种（十倍体） 37 白雪公主 国内选育品种（白草莓）
16 野生白袍 野生型 38 京郊小白 国内选育品种（白草莓）
17 野生白草莓 野生型 39 华艳 国内选育品种
18 芦根 野生型 40 香蕉草莓 国内选育品种
19 点雪 日本品种 41 粉红公主 国内选育品种
20 甘露 日本品种 42 俏佳人 国内选育品种
21 圣安德瑞斯 美国品种（日中性） 43 圣诞红 韩国品种
22 蒙特瑞 美国品种（日中性）
Table 1 Strawberry cultivars used in this study

标记

Markers

条带数

Number of bands

多态性条带数

Number of polymorphic bands

多态性比率

Polymorphic rate/%

基因型数

Number of genotypes

多态性信息含量

PIC
平均 Average 7.77 6.43 82.83 10.2 0.628 4
SB1 9 8 88.89 12 0.728 0
SB3 6 4 66.67 6 0.698 8
SB4 10 10 100.00 14 0.834 0
SB5 9 7 77.78 10 0.766 9
SB6 9 8 88.89 15 0.799 4
SB9 5 3 60.00 3 0.374 3
SB10 8 4 50.00 9 0.815 6
SB12 6 4 66.67 5 0.253 1
SB13 8 5 62.50 9 0.806 9
SB15 6 6 100.00 7 0.366 7
SB16 8 8 100.00 26 0.936 7
SB18 11 10 90.91 18 0.831 8
SB19 10 5 50.00 9 0.761 5
SB21 8 5 62.50 4 0.252 0
SB22 3 2 66.67 3 0.310 4
SB23 17 16 94.12 29 0.955 1
SB24 6 6 100.00 15 0.825 3
SB25 5 4 80.00 4 0.554 9
SB26 8 5 62.50 8 0.601 4
SB27 7 6 85.71 14 0.850 2
SB28 8 8 100.00 19 0.909 7
SB29 4 4 100.00 5 0.325 6
SB30 13 13 100.00 17 0.890 2
SB31 4 4 100.00 2 0.045 4
SB33 5 4 80.00 6 0.498 6
SB34 11 9 81.82 18 0.889 1
SB35 2 1 50.00 2 0.129 8
SB36 7 6 85.71 2 0.467 3
SB37 7 6 85.71 5 0.660 9
SB38 13 12 92.31 9 0.712 8
Table 2 Polymorphism of different SSR markers

标记

Markers

条带数

Number of bands

多态性条带数

Number of polymorphic bands

多态性比率

Polymorphic rate/%

基因型数

Number of genotypes

多态性信息量

PIC
平均 Average 16.20 14.30 88.27 27.8 0.911 4
F1R1 22 19 86.36 37 0.969 2
F1R3 13 12 92.31 37 0.969 2
F1R4 13 11 84.62 31 0.948 6
F2R1 16 15 93.75 37 0.969 2
F2R4 21 19 90.48 34 0.960 5
F3R2 20 20 100.00 39 0.969 2
F3R3 15 12 80.00 19 0.910 8
F3R4 18 18 100.00 29 0.944 3
F4R1 16 15 93.75 37 0.970 3
F4R2 11 5 45.45 8 0.708 6
F4R3 16 16 100.00 36 0.967 0
F5R1 19 16 84.21 40 0.972 4
F5R2 15 14 93.33 21 0.917 3
F5R4 12 11 91.67 11 0.808 0
F6R2 21 19 90.48 43 0.976 7
F7R2 15 11 73.33 22 0.934 6
F7R3 15 12 80.00 12 0.755 0
F8R2 8 7 87.50 20 0.844 8
F8R3 19 18 94.74 25 0.871 8
F8R4 19 16 84.21 18 0.859 9
Table 3 Polymorphism of different SRAP markers
Fig. 1 Dendrogram of 43 strawberry cultivars based on SSR markers
Fig. 2 Dendrogram of 43 strawberry cultivars based on SRAP markers
Fig. 3 Dendrogram of 43 strawberry cultivars based on SSR+SRAP markers
[1]   孙瑞,王桂霞,常琳琳,等 .草莓分子标记技术发展与应用.农业生物技术学报,2018,26(9):1588-1600.
SUN R , WANG G X , CHANG L L , et al . Development and application of molecular marker technique in strawberry (Fragaria×ananassa). Journal of Agricultural Biotechnology, 2018,26(9):1588-1600. (in Chinese with English abstract)
[2]   常琳琳,董静,钟传飞,等 .中国育成草莓品种的系谱分析.果树学报,2018,35(2):158-167.
CHANG L L , DONG J , ZHONG C F , et al . Pedigree analysis of strawberry cultivars released in China. Journal of Fruit Science, 2018,35(2):158-167. (in Chinese with English abstract)
[3]   马鸿翔,盛炳成,戴子林,等 .草莓品种的遗传距离研究.江苏农业学报,1995,11(3):41-45.
MA H X, SHENG B C , DAI Z L , et al . Studies on genetic distances among strawberry varieties. Jiangsu Journal of Agricultural Sciences, 1995,11(3):41-45. (in Chinese with English abstract)
[4]   陈琼娥,钟凤林,潘东明,等 .草莓分子标记技术研究进展.亚热带农业研究,2011,7(1):64-67.
CHEN Q E , ZHONG F L , PAN D M , et al . Progress of molecular mark on genetic research of strawberry. Subtropical Agriculture Research, 2011,7(1):64-67. (in Chinese with English abstract)
[5]   WHITAKER V M . Applications of molecular markers in strawberry. Journal of Berry Research, 2011,1(3):115-127.
[6]   张运涛,冯志广,李天忠,等 .草莓品种亲缘关系的AFLP分子标记分析.园艺学报,2006,33(6):1199-1202.
ZHANG Y T , FENG Z G , LI T Z , et al . Genetic relationships of strawberry cultivars by AFLP analysis. Acta Horticulturae Sinica, 2006,33(6):1199-1202. (in Chinese with English abstract)
[7]   何淑娟 .利用AFLP分子标记分析草莓的遗传多样性.河北,保定:河北农业大学,2007.
HE S J . Using AFLP molecular markers to analyse genetic diversity in strawberry. Baoding, Hebei: Hebei Agricultural University, 2007. (in Chinese with English abstract)
[8]   王志刚,张志宏,李贺,等 .利用RAPD和SCAR标记鉴定草莓品种.园艺学报,2007,34(3):591-596.
WANG Z G , ZHANG Z H , LI H , et al . Identification of strawberry cultivars by RAPD and SCAR markers. Acta Horticulturae Sinica, 2007,34(3):591-596. (in Chinese with English abstract)
[9]   闫玉华,马鸿翔,雷家军,等 .红花草莓红花基因RAPD标记转化为SCAR标记.分子植物育种,2006,4(5):690-694.
YAN Y H , MA H X, LEI J J , et al . Conversion of RAPD marker linked to red-flowered gene of red-flowered strawberry to SCAR marker. Molecular Plant Breeding, 2006,4(5):690-694. (in Chinese with English abstract)
[10]   董清华,王西成,赵密珍,等 .草莓EST-SSR标记开发及在品种遗传多样性分析中的应用.中国农业科学,2011,44(17):3603-3612.
DONG Q H , WANG X C , ZHAO M Z , et al . Development of EST-derived SSR markers and their application in strawberry genetic diversity analysis. Scientia Agricultura Sinica, 2011,44(17):3603-3612. (in Chinese with English abstract)
[11]   韩柏明,赵密珍,王静,等 .草莓属种质资源亲缘关系的SSR标记分析.园艺学报,2012,39(12):2352-2360.
HAN B M , ZHAO M Z , WANG J , et al . Phylogenetic relationships among Fragaria germplasm by SSR markers. Acta Horticulturae Sinica, 2012,39(12):2352-2360. (in Chinese with English abstract)
[12]   忻雅,阮松林,马华升,等 .基于SSR和SCAR标记的草莓主栽品种指纹图谱构建及亲缘关系分析.江西农业大学学报,2013,35(2):307-312.
XIN Y , RUAN S L , MA H S, et al . Establishment of DNA fingerprinting and analysis of genetic relationship among main strawberry cultivars in southern China. Acta Agriculturae Universitis Jiangxiensis, 2013,35(2):307-312. (in Chinese with English abstract)
[13]   LI G , QUIROS C F . Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica . Theoretical & Applied Genetics, 2001,103(2/3):455-461.
[14]   ANEJA B , YADAV N R , CHAWLA V , et al . Sequence-related amplified polymorphism (SRAP) molecular marker system and its applications in crop improvement. Molecular Breeding, 2012,30(4):1635-1648.
[15]   FERRIOL M , PICO B , NUEZ F . Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP markers. Theoretical and Applied Genetics, 2003,107(2):271-282.
[16]   BUDAK H , SHEARMAN R C , PARMAKSIZ I , et al . Comparative analysis of seeded and vegetative biotype buffalograsses based on phylogenetic relationship using ISSRs, SSRs, RAPDs and SRAPs. Theoretical and Applied Genetics, 2004,109:280-288.
[17]   魏丽丽,朱世东,贾庆美,等 .草莓SRAP反应体系优化及引物筛选.中国农学通报,2014,30(25):159-165.
WEI L L , ZHU S D , JIA Q M , et al . Optimization of SRAP reaction system and selection of primers for strawberry. Chinese Agricultural Science Bulletin, 2014,30(25):159-165. (in Chinese with English abstract)
[18]   黄璐琦,钱丹,邓超 .双分子标记法的构建及在中药研究中的应用.中国中药杂志,2015,40(2):165-168.
HUANG L Q , QIAN D , DENG C . Hypothesis and application of bimolecular marking methods in Chinese materia medica. China Journal of Chinese Materia Medica, 2015,40(2):165-168. (in Chinese with English abstract)
[19]   ISOBE S N , HIDEKI H , SHUSEI S , et al . Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria×ananassa) and its applicability. DNA Research, 2012,20(1):79-92.
[20]   NEI M, LI W H . Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the USA, 1979,76:5269-5273.
[21]   BOTSTEIN D , WHITE R L , SKOLNICK M , et al . Construction of genetic linkage map in man using restriction fragment length polymorphisms. The American Journal of Human Genetics, 1980,32:314-331.
[22]   陈伦林,邹小云,李书宇,等 .SSR和SRAP标记揭示甘蓝型油菜遗传多样性的差异分析.分子植物育种,2008,6(3):511-516.
CHEN L L , ZOU X Y , LI S Y , et al . Analysis of the genetic diversity of rapeseed by SSR and SRAP with emphasis on the difference of this two kinds of markers. Molecular Plant Breeding, 2008,6(3):511-516. (in Chinese with English abstract)
[23]   谭祖猛,李云昌,胡琼,等 .通过分子标记估算遗传距离预测甘蓝型油菜的杂种优势.中国油料作物学报,2007,29(2):126-132.
TAN Z M , LI Y C , HU Q , et al . Heterosis prediction based on genetic distance estimated by molecular markers in rapeseed. Chinese Journal of Oil Crop Sciences, 2007,29(2):126-132. (in Chinese with English abstract)
[24]   甘晓燕,程永芳,巩檑,等 .SRAP和SSR标记对马铃薯遗传多样性的差异分析.中国农学通报,2015,31(30):225-230.
GAN X Y , CHENG Y F , GONG L , et al . Variance analysis of genetic diversity of potato with SRAP and SSR markers. Chinese Agricultural Science Bulletin, 2015,31(30):225-230. (in Chinese with English abstract)
[25]   刘通,邓崇岭,程玉芳,等 .利用SSR和SRAP技术分析广西柑橘种质遗传多样性.华中农业大学学报,2016(2):23-29.
LIU T , DENG C L , CHENG Y F , et al . Analyzing genetic diversity of citrus germplasm in Guangxi Province with SSR and SRAP markers. Journal of Huazhong Agricultural University, 2016(2):23-29. (in Chinese with English abstract)
[26]   班骞,谢彩云,范国华,等 .基于EST-SSR及SRAP标记构建苦荬菜品种(系)DNA指纹图谱.草业学报,2018,27(4):111-122.
BAN Q , XIE C Y , FAN G H , et al . DNA fingerprinting of Ixeris polycephala varieties based on EST-SSR and SRAP markers. Acta Prataculturae Sinica, 2018,27(4):111-122. (in Chinese with English abstract)
[27]   王国莉,徐毓璇,黄梅花 .基于SSR和SRAP标记的苦瓜品种鉴定及亲缘关系分析.分子植物育种,2016(2):501-510.
WANG G L , XU Y X , HUANG M H . Identification and genetic relationship analysis of bitter gourd varieties based on SSR and SPAP. Molecular Plant Breeding, 2016(2):501-510. (in Chinese with English abstract)
[28]   延娜,李巧丽,郭军战 .果桑遗传差异的SRAP和EST-SSR分析.西北农业学报,2015,24(9):91-97.
YAN N , LI Q L , GUO J Z . SRAP and EST-SSR analysis of genetic differences in fruit mulberry (Morus spp.). Acta Agriculturae Boreali-Occidentalis Sinica, 2015,24(9):91-97. (in Chinese with English abstract)
[29]   邹自征,陈建华,栾明宝,等 .应用RSAP、SRAP和SSR分析苎麻种质亲缘关系.作物学报,2012,38(5):840-847.
ZHOU Z Z , CHEN J H , LUAN M B , et al . Genetic relationship of ramie germplasm revealed by RSAP, SRAP and SSR markers. Acta Agronomica Sinica, 2012,38(5):840-847. (in Chinese with English abstract)
[30]   董静,张运涛,王桂霞,等 .五叶草莓与凤梨草莓种间杂交F1代的形态学及SSR标记鉴定.西北农业学报,2010,19(11):145-148.
DONG J , ZHANG Y T , WANG G X , et al . Identification of F1 interspecies hybrids between fragaria pentaphylla and F . ananassa by morphological and SSR markers. Acta Agriculturae Boreali-Occidentalis Sinica, 2010,19(11):145-148. (in Chinese with English abstract)
[31]   史芳芳,汪泉,赵密珍,等 .凤梨草莓与绿色草莓种间杂种一代的形态学观察及SSR分析.果树学报,2017(2):175-185.
SHI F F , WANG Q , ZHAO M Z , et al . Identification of interspecific hybrids derived from Fragaria×ananassa×F . viridis by morphological features and SSR markers. Journal of Fruit Science, 2017(2):175-185. (in Chinese with English abstract)
[32]   王壮伟,赵密珍,袁骥,等 .38个欧美草莓栽培品种SSR指纹图谱的构建.果树学报,2011,28(6):1032-1037.
WANG Z W , ZHAO M Z , YUAN J , et al . Establishment of SSR fingerprinting database for 38 cultivars of strawberry (Fragaria ananassa) native to Europe and America. Journal of Fruit Science, 2011,28(6):1032-1037. (in Chinese with English abstract)
[33]   黄志城,石敬韡,庞夫花,等 .基于SSR标记的草莓品种DNA指纹图谱的构建及应用.分子植物育种,2017,15(8):3097-3116.
HUANG Z C , SHI J W , PANG F H , et al . Construction and application of DNA fingerprinting of strawberry (Fragaria ananassa Duch.) varieties based on SSR markers. Molecular Plant Breeding, 2017,15(8):3097-3116. (in Chinese with English abstract)
[1] CAO Lianfei, GU Peipei, LIN Yuqing. Genetic diversity of Apis cerana cerana based on mitochondrial DNA in Lishui, Zhejiang, China.[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2017, 43(4): 425-430.
[2] Lu Lianming, Cheng Baoping, Du Danchao, Hu Xiurong, Pu Zhanxu, Chen Guoqing. Genetic diversity of Lecanicillium lecanii and its pathogenicity against Diaphorina citri[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2015, 41(1): 34-43.
[3] Zhou Jiaping， Yang Chunyuan， Wu Chun， Wang Rengang， Shi Yuewei， Xie Shengdong， Wang Zhihong， Xu Haiming， Ren Xueliang . Genetic diversity and development of core collection in tobacco （Nicotiana tabacum L.） resources[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2014, 40(4): 440-450.
[4] REN Sanjuan, SUN Chu, TONG Chuan, ZHAO Fei, SHU Qingyao, SHEN Shengquan. Genetic analysis and gene mapping of a rice spikelet degradation mutant (spd-hp73)[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2013, 39(3): 267-273.
[5] GAO Li-ping, WANG Jun*, CUI Shao-qing. Evaluation of fresh juice of strawberries at different degrees of ripeness using electronic nose and electronic tongue[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2012, 38(6): 715-724.
[6] GONG Ya‐ming, XU Sheng‐chun, MAO Wei‐hua, LI Ze‐yun. Transferable analysis of pea EST‐SSRs on faba bean and its application[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2011, 37(5): 479-484.
[7] XU Xiao-dong,CHEN Fei,NI Xi-yuan,ZHANG Xiao-wei,ZHAO Jian-yi. Analysis of relationships between molecular distances and heterosis of F1 performance in Brassica Napus L[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2010, 36(6): 641-649.
[8] ZHOU Guo-Zhi, LI Zhi-Miao, YANG Yue-Jian, XING Juan, WANG Rong-Qing. [J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2009, 35(4): 390-394.
[9] . Phenotypic variation and relationships among sesame (Sesamum indicum L.) sub-core collections[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2004, 30(1): 10-16.