苹果基因组SSR位点分析与应用

doi:10.3864/j.issn.0578-1752.2011.21.010

Abstract

Abstract: 【Objective】 In order to provide a theoretical and practical foundation for the genetic analysis of Rosaceae fruit trees which based on the SSR markers, the SSR loci from apple (Malus × domestica Borkh. ‘Golden Delicious’) genome was analyzed.【Method】The genome data of apple ‘Golden Delicious’ was downloaded from the NCBI website and the MISA software was used to analyze the distribution of genome SSR loci. We designed sixty-eight primers, which 4 primers from each chromosome according to the searching results of the SSR loci, were designed and the 10 apple cultivars and F1 progeny of pear were utilized to examine the application and transferability of designed primers, respectively.【Result】The perfect repeat sequences were found that it is the main form of the SSR sequences type and the total number of SSR loci is 163 426 in apple genome. There will be one SSR loci from every 3.22 kb on average. The distribution of the mononucleotide, dinucleotide and trinucleotide repeat motifs in the chromosome standard were stable relatively, whereas the picture of tetranucleotide, pentanucleotide and hexanucleotide repeat motifs were not. The largest proportion of the SSR loci is the mononucleotide and the dinucleotide repeat motifs, they possessed 91.67% of the total SSRs in the whole genome. As scanned for the mononucleotide repeat units, base A/T is the mainly proportion, the base pair AT/TA is the domination in the dinucleotide repeat units. There are 62 and 37 primers could amplify the predicted and polymorphic fragments in apple among 68 designed primers, separately. Whereas, in pear, there are only 16 polymorphic primers in the 40 primers which can be amplified the same size fragments as predicted.【Conclusion】Some distribution raws of SSRs in the apple genome were found. The results that SSR loci in the closer genetic relationship among species are highly conserved and can be used in the following research were demonstrated preliminarily. It is meaningful to develop SSR loci from genomic data for the application of relative genetic analysis.

Key words: apple, genome, SSR, application

GUAN Ling, ZHANG Zhen, WANG Xin-Wei, XUE Hua-Bai, LIU Yan-Hong, WANG San-Hong, QIAO Yu-Shan. Evaluation and Application of the SSR Loci in Apple Genome[J].Scientia Agricultura Sinica, 2011, 44(21): 4415-4428.

0
/ / Recommend

Add to citation manager EndNote|Reference Manager|ProCite|BibTeX|RefWorks

URL: https://www.chinaagrisci.com/EN/10.3864/j.issn.0578-1752.2011.21.010

https://www.chinaagrisci.com/EN/Y2011/V44/I21/4415

References

[1]Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A. The genome of the domesticated apple (Malus domestica Borkh.) . Nature Genetics, 2010, 42(10): 833-841.

[2]The French-Italian Public Consortium for Grapevine Genome Characterization. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 2007, 449(27): 463-468.

[3]Shulaev V, Sargent D J, Crowhurst R N, Mockler T C, Folkerts O. The genome of woodland strawberry (Fragaria vesca). Nature Genetics, 2011, 43(2):109-118.

[4]Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas W J, Wang X. The genome of the cucumber, Cucumber sativus L. Nature Genetics, 2009, 41(12): 1275-1283.

[5]Li B, Xia Q, Lu C, Zhou Z. Analysis on frequency and density of microsatellites in coding sequences of eudaryotic genomes. Genomics Proteomics, 2004, 2(1): 24-31.

[6]Ju Z, Wells M C, Martinez A, Hazlewood L, Walter R B. An in silico mining for simple sequence repeats from expressed sequence tags of zebrafish, medaka, Fundulus, and Xiphophorus. In Silico Biology, 2005, 5(5): 439-463.

[7]蔡斌, 李成慧, 姚泉洪, 周军, 陶建敏, 章镇. 葡萄全基因组SSR分析和数据库构建. 南京农业大学学报, 2009, 32(4): 28-32.

Cai B, Li C H, Yao Q H, Zhou J, Tao J M, Zhang Z. Analysis of SSRs in grape genome and development of SSR database. Journal of Nanjing Agricultural University, 2009, 32(4): 28-32. (in Chinese)

[8]Wang Z, Weber J L, Zhong G, Tanksley S D. Survey of plant short tandem DNA repeats. Theoretical and Applied Genetics, 1994, 88: 1-6.

[9]Richards R I, Sutherland G R. Dynamic mutations: a new class of mutation causing human disease. Cell, 1992, 70(5): 709-712.

[10]Levinson G, Gutman G A. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Molecular Biology and Evolution, 1987, 4(3): 203-221.

[11]Weber J L. Informativeness of human (dC-dA)n•(dG-dT)n polymorphisms. Genomics, 1990, 7(4): 524-530.

[12]Goulão L, Oliveira C M. Molecular characterization of cultivars of apple (Malus × domestica Borkh.) using microsatellite (SSR and ISSR) markers. Euphytica, 2001, 122: 81-89.

[13]Gianfranceschi L, Seglias N, Tarchini R, Komjanc M, Gessler C. Simple sequence repeats for the genetic analysis of apple. Theoretical and Applied Genetics, 1998, 96:1069-1076.

[14]王爱德, 李天忠, 许雪峰, 韩振海. 苹果品种的SSR分析. 园艺学报, 2005, 32(5): 875-877.

Wang A D, Li T Z, Xu X F, Han Z H. SSR analysis for apple cultivars. Acta Horticulturae Sinica, 2005, 32(5): 875-877. (in Chinese)

[15]高华, 樊红科, 万怡震, 王雷存, 赵政阳，王西平. 苹果栽培品种的SSR鉴定及遗传多样性分析. 西北农业学报, 2011,20(2): 153-158.

Gao H, Fan H K, Wan Y Z, Wang L C, Zhao Z Y, Wang X P. SSR analysis of genetic diversity of apple cultivar. Acta Agriculturae Boreali- occidentalis Sinica, 2011, 20(2): 153-158. (in Chinese)

[16]Zhang C Y, Chen X S, He T M, Liu X L, Feng T, Yuan Z H. Genetic structure of Malus sieversii population from Xinjiang, China, revealed by SSR markers. Journal of Genetics and Genomics, 2007, 34(10): 947-955.

[17]Patocchi A, Fernández-fernádez F, Evans k, Gobbin D, Rezzonico F, Boudichevskaia A. Development and test of 21 multiplex PCRs composed of SSRs spanning most of the apple genome. Tree Genetics & Genomes, 2009, 5: 211-223.

[18]Silfverberg-Dilworth E, Matasci C L, Van de Weg W E, Van Kaauwen M P W, Walser M, Kodde L P, Sohlio V, Gianfranceschi L, Durel C E, Costa F, Yamamoto T, Koller B, Gessler C, Patocchi A. Microsatellite markers spanning the apple (Malus × domestica Borkh.) genome. Tree Genetics & Genomes, 2006, 2: 202-224.

[19]Liebhard R, Gianfranceschi L, Koller B, Ryder C D, Tarchini R, Van de Weg E, Gessler C. Development and characterisation of 140 new microsatellites in apple (Malus × domestica Borkh.). Molecular Breeding, 2002, 10: 217-241.

[20]王彩虹, 田义柯, 赵静. 来自苹果的SSRs在蔷薇科植物资源上的通用性分析. 园艺学报, 2005, 32(3): 500-502.

Wang C H, Tian Y K, Zhao J. General application analysis of SSRs derived from apple (Malus pumila) on other species in Rosaceae. Acta Horticulturae Sinica, 2005, 32(3): 500-502. (in Chinese)

[21]Patocchi A, Fernández-Fernández F, Evans F, Silfverberg-Dilworth E, Matasci C . Development of a set of apple SSRs markers spanning the apple genome, genotyping of HiDRAS plant material and validation of genotyping data. Eucarpia Symposium on Fruit Breeding and Genetics, 2007,9: 16-20.

[22]Tanksley S D, Young N D, Paterson A H, Bonierbale M W. RFLP mapping in plant breeding: new tools for an old science. Nature Biotechnology, 1989, 7: 257-264.

[23]唐荣华, 张君诚, 吴为人. SSR分子标记的开发技术研究进展. 西南农业学报, 2002, 15(4): 106-109.

Tang R H, Zhang J C, Wu W R. Progress in the way to develop SSR molecular marker. Southwest China Journal of Agricultural Sciences, 2002, 15(4): 106-109. (in Chinese)

[24]Ghosh A K, Lukens L N. European and Asian pears: simple sequence repeat-polyacrylamide gel electrophoresis-based analysis of commercially important north American cultivars. HortScience, 2006, 41(2): 304-309.

[25]Sawamura Y, Saito T, Takada N, Yamamoto T, Kimura T, Hayashi T, Kotobuki K. Identification of parentage of Japanese pears ‘Housui’. Journal of the Japanese Society for Horticultural Science, 2004, 73(6): 511-518.

[26]Yamamoto T, Kimura T, Sawamura Y, Kotobuki K, Ban Y, Hayashi T, Matsuta N. SSRs isolated from apple can identify polymorphism and genetic diversity in pear. Theoretical and Applied Genetics, 2001, 102: 865-870.

[27]Brini W, Mars M, Hormaza J I. Genetic diversity in local Tunisian pears (Pyrus communis L.) studied with SSR markers. Scientia Horticulturae, 2008, 115: 337-341.

[28]Yamamoto T, Kimura T, Shoda M, Imai T, Saito T, Saito T, Sawamura Y, Kotobuki K, Hayashi T. Genetic linkage maps constructed by using an interspecific cross between Japanese and European pears. Theoretical and Applied Genetics, 2002, 106: 9-18.

[29]Dpndini L, Pierantoni L, Gaiotti F, Chiodini R, Tartarini S, Bazzi C, Sansavini S. Identifying QTLs fire-blight resistance via a European pear (Pyrus communis L.) genetic linkage map. Molecular Breeding, 2004, 14: 407-418.

[30]Tóth G, Gáspári Z, Jurka J. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Research, 2000, 10(7): 967-981.

[31]佟兆国, 王富荣, 章镇, 赵剑波, 张开春, 闫国华, 周宇, 姜立杰. 一种从果树成熟叶片提取DNA的方法. 果树学报, 2008, 25(1): 122-125.

Tong Z G, Wang F R, Zhang Z, Zhao J B, Zhang K C, Yan G H, Zhou Y, Jiang L J. A method for DNA extraction from mature leaves of fruit trees. Journal of Fruit Science, 2008, 25(1): 122-125. (in Chinese)

[32]Brant B J, Gustavo C A, Peter M G. Fast and sensitive silver staining of DNA in polycrylamide gels. Analytical Biochemistry, 1991, 196: 80-83.

[33]李成云, 李进斌, 周晓罡, 董爱荣, 许明辉. 稻瘟病菌基因组中微卫星序列的频率和分布. 中国水稻科学, 2004, 18(3): 269-273.

Li C Y, Li J B, Zhou X G, Dong A R, Xu M H. Frequency and distribution of microsatellites in the whole genome of rice blast fungus, Magnaporthe grisea. Chinese Journal of Rice Science, 2004, 18(3): 269-273. (in Chinese)

[34]Haraoglu H, Lee C M Y, Meyer W. Survey of simple sequence repeats in complete fungal genomes. Molecular Biology and Evolution, 2005, 22(3): 639-649.

[35]陆景标, 李杰勤, 卢杰, 詹秋文. 高粱非编码区SSR引物设计以及e-PCR的验证. 种子, 2010, 29(9): 1-6, 12.

Lu J B, Li J Q, Lu J, Zhan Q W. Design of SSR primers and verification of e-PCR in non-coding regions of sorghum genome. Seed, 2010, 29(9): 1-6,12. (in Chinese)

[36]高亚梅, 韩毅强, 汤辉, 孙东梅, 王彦杰, 王伟东. 根瘤菌基因组内简单重复序列的分析. 中国农业科学, 2008, 41(10): 2992-2998.

Gao Y M, Han Y Q, Tang H, Sun D M, Wang Y J, Wang W D. Analysis of simple sequence repeats in rhizobium genome. Scientia Agricultura Sinica, 2008, 41(10): 2992-2998. (in Chinese)

[37]Sia E A, Kokoska R J, Dominska M, Greenwell P, Petes T D. Microsatellite instability in yeast: dependence on repeat unit size and DNA mismatch repair genes. Molecular and Cellular Biology, 1997, 17(5): 2851-2858.

[38]Harry B, Schlötterer C. Long microsatellite alleles in Drosophila melanogaster have a downward mutation bias and short persistence times, which cause their genome-wide underrepresentation. Genetics, 2000, 155: 1213-1220.

[39]Schorderet D F, Gartler S M. Analysis of CpG suppression in methylated and nonmethylated species. Proceedings of the National Academy of Sciences of the USA, 1992, 89: 957-961.

[40]Morgante M, Hanafey M, Powell W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genome. Nature Genetics, 2002, 30: 194-200.

[41]Lee S B, Kaittanis C, Jansen R K, Hosterler J B, Tallon L J, Town C D, Daniell H. The complete chloroplast genome sequence of Gossypium hisutum: organization and phylogenetic relationships to other angiosperms. BMC Genomics, 2006, 7: 61-72.

[42]尚明照, 刘芳, 华金平, 王坤波. 陆地棉叶绿体基因组密码子使用偏性的分析. 中国农业科学, 2011, 44(2): 245-253.

Shang M Z, Liu F, Hua J P, Wang K B. Analysis on codon usage of chloroplast genome of Gossypium hirsutum. Scientia Agricultura Sinica, 2011, 44(2): 245-253. (in Chinese)

[43]Sangwan I, O′brian M R. Identification of a soybean protein that interacts with GAGA element dinucleotide repeat DNA. Plant Physiology, 2002, 129: 1788-1794.

[44]Downey S L, Lezzoni A F. Polymorphic DNA markers in black cherry (Prunus serotina) are identified using sequences from sweet cherry, peach, and sour cherry. Journal of the American Society for Horticulture Science, 2000, 125(1): 76-80.

[45]Yamamoto T, Kimura T, Saito T, Kotobuki K, Matsuta N, Liebhard R, Gessler C, van de Weg W E, Hayashi T. Genetic linkage maps of Japanese and European pears aligned to the apple consensus map. Acta Horticulturae, 2004, 663: 51-56.

[46]Pierantoni L, Cho K H, Shin I S, Chiodini R, Tartarini S, Dondini L, Kang S J, Sansavini S. Characterisation and transferability of apple SSRs to two European pear F1 populations. Theoretical and Applied Genetics, 2004, 109: 1519-1524.

[47]Toshiya Y, kimura T, Terkami S, Nishitani C, Sawamura Y, Saito T, Kotobuki K, Hayashi T. Integrated reference genetic linkage maps of pear based on SSR and AFLP markers. Breeding Science, 2007, 57: 321-329.

[48]Lu M, Tang H, Chen X, Gao J, Chen Q, Lin L. Comparative genome mapping between apple and pear by apple mapped SSR markers. American-Eurasian Journal of Agricultural & Environmental Science, 2010, 9(3): 303-309.

[49]Vezzulli S, Troggio M, Coppola G, Jermakow A, Cartwright D, Zharkikh A, Stefanini M, Grando M S, Viola R, Adam-Blondon A, Thonmas M, This P, Velasco R. A reference integrated map for cultivated grapevine (Vitis vinifera L.) from three crosses, based on 283 SSR and 501 SNP-based makers. Theoretical and Applied Genetics, 2008, 117(4): 499-511.

[50]Decroocq V, Favé M G, Hagen L, Bordenave L, Decroocq S. Development and transferability of apricot and grape EST microsatellite markers across taxa. Theoretical and Applied Genetics, 2003, 106(5): 912-922.

[51]Monfort A, Vilanova S, Davis T M, Arús P. A new set of polymorphic simple sequence repeat (SSR) markers from a wild strawberry (Fragaria veaca) are transferable to other diploid Fragaria species and to Fragaria × ananassa. Molecular Ecology Note, 2006, 6: 197-200.

[52]Chen C, Zhou P, Choi Y A, Choi Y A. Mining and characterizing microsatellites from citrus EST. Theoretical and Applied Genetics, 2006, 112(7): 1248-1257.

[53]Olmstead J W, Sebolt A M, Cabrera A, Sooriyapathirana S S, Hammar S, Iriarte G, Wang D, Chen C Y, van der Knaap E, Iezzoni A F. Construction of an intra-specific sweet cherry (Prunus avium L.) genetic linkage map and synteny analysis with the Prunus reference map. Tree Genetics & Genomes, 2008, 4(4): 897-910.

[54]Ekué M R M, Gailing O, Finkedey R. Transferability of simple sequence repeat (SSR) markers developed in Lichi chinensis to Blighia sapida (Sapindaceae). Plant Molecular Biology Reporter, 2009, 27(4): 570-574.

Related Articles 15

[1]	LI ZhouShuai,DONG Yuan,LI Ting,FENG ZhiQian,DUAN YingXin,YANG MingXian,XU ShuTu,ZHANG XingHua,XUE JiQuan. Genome-Wide Association Analysis of Yield and Combining Ability Based on Maize Hybrid Population [J]. Scientia Agricultura Sinica, 2022, 55(9): 1695-1709.
[2]	DONG YongXin,WEI QiWei,HONG Hao,HUANG Ying,ZHAO YanXiao,FENG MingFeng,DOU DaoLong,XU Yi,TAO XiaoRong. Establishment of ALSV-Induced Gene Silencing in Chinese Soybean Cultivars [J]. Scientia Agricultura Sinica, 2022, 55(9): 1710-1722.
[3]	LI YiLing,PENG XiHong,CHEN Ping,DU Qing,REN JunBo,YANG XueLi,LEI Lu,YONG TaiWen,YANG WenYu. Effects of Reducing Nitrogen Application on Leaf Stay-Green, Photosynthetic Characteristics and System Yield in Maize-Soybean Relay Strip Intercropping [J]. Scientia Agricultura Sinica, 2022, 55(9): 1749-1762.
[4]	JIANG Hui,FENG Yu,QIN YuMing,ZHU LiangQuan,FAN XueZheng,DING JiaBo. Method Improvement and Its Application of Micro Complement Fixation Test for Brucellosis [J]. Scientia Agricultura Sinica, 2022, 55(8): 1676-1684.
[5]	ZHI Lei,ZHE Li,SUN NanNan,YANG Yang,Dauren Serikbay,JIA HanZhong,HU YinGang,CHEN Liang. Genome-Wide Association Analysis of Lead Tolerance in Wheat at Seedling Stage [J]. Scientia Agricultura Sinica, 2022, 55(6): 1064-1081.
[6]	LIU Miao,LIU PengZhao,SHI ZuJiao,WANG XiaoLi,WANG Rui,LI Jun. Critical Nitrogen Dilution Curve and Nitrogen Nutrition Diagnosis of Summer Maize Under Different Nitrogen and Phosphorus Application Rates [J]. Scientia Agricultura Sinica, 2022, 55(5): 932-947.
[7]	CHEN XueSen, YIN HuaLin, WANG Nan, ZHANG Min, JIANG ShengHui, XU Juan, MAO ZhiQuan, ZHANG ZongYing, WANG ZhiGang, JIANG ZhaoTao, XU YueHua, LI JianMing. Interpretation of the Case of Bud Sports Selection to Promote the High-Quality and Efficient Development of the World’s Apple and Citrus Industry [J]. Scientia Agricultura Sinica, 2022, 55(4): 755-768.
[8]	LI YaFei, SHI JiangLan, WU TianQi, WANG ShaoXia, LI YuNuo, QU ChunYan, LIU CongHui, NING Peng, TIAN XiaoHong. Effects of Combined Foliar Application of Zinc with Imidacloprid on Zinc Enrichment and Protein Components Content in Wheat Grain [J]. Scientia Agricultura Sinica, 2022, 55(3): 514-528.
[9]	LU Xiang, GAO Yuan, WANG Kun, SUN SiMiao, LI LianWen, LI HaiFei, LI QingShan, FENG JianRong, WANG DaJiang. Analysis of Aroma Characteristics in Different Cultivated Apple Strains [J]. Scientia Agricultura Sinica, 2022, 55(3): 543-557.
[10]	DU WenTing,LEI XiaoXiao,LU HuiYu,WANG YunFeng,XU JiaXing,LUO CaiXia,ZHANG ShuLan. Effects of Reducing Nitrogen Application Rate on the Yields of Three Major Cereals in China [J]. Scientia Agricultura Sinica, 2022, 55(24): 4863-4878.
[11]	REN ZiQi,KANG YuJie,LI HaiZhen,WANG LianGang,MA HaoYun,LI Hui,WANG LiuYang,MEI XiangDong,NING Jun. Synthesis and Bioactivity of Sex Pheromone Analogues of Trachea atriplicis [J]. Scientia Agricultura Sinica, 2022, 55(23): 4640-4650.
[12]	LI Heng,ZI XiangDong,WANG Hui,XIONG Yan,LÜ MingJie,LIU Yu,JIANG XuDong. Screening of Key Regulatory Genes for Litter Size Trait Based on Whole Genome Re-Sequencing in Goats (Capra hircus) [J]. Scientia Agricultura Sinica, 2022, 55(23): 4753-4768.
[13]	XIE LiXue,ZHANG XiaoYan,ZHANG LiJie,ZHENG Shan,LI Tao. Complete Genome Sequence Characteristics and TC-RT-PCR Detection of East Asian Passiflora Virus Infecting Passiflora edulis [J]. Scientia Agricultura Sinica, 2022, 55(22): 4408-4418.
[14]	ZHU YanSong,ZHANG YaFei,CHENG Li,YANG ShengNan,ZHAO WanTong,JIANG Dong. Identification of 60 Citrus Accessions Using Target SSR-seq Technology [J]. Scientia Agricultura Sinica, 2022, 55(22): 4458-4472.
[15]	XU Ke,FAN ZhiLong,YIN Wen,ZHAO Cai,YU AiZhong,HU FaLong,CHAI Qiang. Coupling Effects of N-fertilizer Postponing Application and Intercropping on Maize Photosynthetic Physiological Characteristics [J]. Scientia Agricultura Sinica, 2022, 55(21): 4131-4143.

Metrics

Viewed

Full text

Abstract

Cited

Shared

Discussed

Comments

Recommended 0

No Suggested Reading articles found!

Evaluation and Application of the SSR Loci in Apple Genome

PDF

Cited

Abstract

Cite this article

share this article

References

Related Articles 15

Metrics

Comments

Recommended 0