Characterization of EST-SSR Among Six Genera of Rosaceae

doi:10.7525/j.issn.1673-5102.2014.06.016

Abstract

Abstract: EST-SSR is a molecular marker based on functional genomics, had been widely used because of its evenly distributed among the genome, better universality between species or genera and characters associated with the phenotypic traits. We downloaded the EST sequences of six genera in Rosaceae (Rosa, Malus, Pyrus, Prunus, Fragaria and Rubus) to study the distributed characteristic of SSR in Rosaceae by bioinformatics methods. There was significant difference of EST-SSR distribution frequency among genera, from 10.94%(Rubus) to 43.49%(Pyrus). The dinucleotide and trinucleotide repeats were the major types, AG/CT, GA/TC and AT/TA were the preponderant dinucleotide motifs, the trinucleotide repeats showed significant difference among genera, and the dominant type included AGA/TCT, GAA/TTC, AAG/CTT, CAC/GTG and ACA/TGT. Our results provided a research platform for plant molecular phylogeny and evolution, germplasm identification, genetic diversity and genetic mapping of Rosaceae.

Key words: Rosaceae, EST-SSR, EST

CLC Number:

ZHANG De-Fang1；LI Shu-Xian2；XIA Tao2*. Characterization of EST-SSR Among Six Genera of Rosaceae[J]. Bulletin of Botanical Research, 2014, 34(6): 810-815.

References

1.Powell W,Machray G C,Provan J.Polymorphism revealed by simple sequence repeats［J］.Trends Plant Science,1996,1:215-222.

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

3.Varshney R K,Graner A,Sorrells M E.Genic microsatellite markers in plants:features and applications［J］.Trends in Biotechnology,2005,23(1):48-55.

4.Li S X,Yin T M.Map and analysis of microsatellites in genome of Populus:the first sequenced perennial plant［J］.Science in China C:Life Sciences,2006,50(5):690-699.

5.李淑娴,张新叶,王英亚,等.桉树EST序列中微卫星含量及相关特征［J］.植物学报,2010,45(3):363-371.

6.Talia P,Nishinakamasu V,Hopp H E,et al.Genetic mapping of EST-SSR,SSR and InDel to improve saturation of genomic regions in a previously developed sunflower map［J］.Electronic Journal of Biotechnology,2010,13(6):7-8.

7.Celton J M,Tustin D S,Chagne D,et al.Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences［J］.Tree Genetics & Genomes,2009,5(1):93-107.

8.Riju A,Rajesh M K,Sherin P T P F,et al.Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools［J］.Journal of genetics,2009,88(2):217-225.

9.Li X,Shangguan L,Song C,et al.Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers［J］.BMC genetics,2010,11(1):66.

10.俞德浚.中国植物志:第36卷［M］.北京:科学出版社,1974.

11.俞德浚.蔷薇科植物的起源和进化［J］.植物分类学报,1984,22(6):431-444.

12.Watson L,Dallwitz M J.The families of angiosperms:automated descriptions,with interactive identification and information retrieval［J］.Australian Systematic Botany,1991,4(4):681-695.

13.Huang X,Madan A.CAP3:A DNA Sequence Assembly Program［J］.Genome Research,1999,9:868-877.

14.Thiel T.MISA-Microsatellite Identification Tool,Version 1.0.2001,http://pgrc.ipk-gatersleben.de/misa/misa.html

15.黄启星，左娇，孔华，等.11种热带植物EST-SSR标记的开发和多样性分析［J］.热带作物学报,2012,33(7):1208-1214.

16.刘峰,王运生,田雪亮，等.辣椒转录组SSR挖掘及其多态性分析［J］.园艺学报,2012,39(1):168-174.

17.段紫英,胡丽芳,黄长干，等.黄瓜EST中SSR的分布特征分析［J］.广东农业科学,2012,39(22):160-161.

18.Yan M M,Dai X G,Li S X,et al.A Meta-Analysis of EST-SSR Sequences in the Genomes of Pine,Poplar and Eucalyptus［J］.Genomics and Applied Biology,2011,30(1):1-7.

19.安泽伟,赵彦宏,程汉,等.橡胶树EST-SSR标记的开发与应用［J］.遗传,2009,31(3):311-319.

20.Liang X,Chen X,Hong Y,et al.Utility of EST-derived SSR in cultivated peanut（Arachis hypogaea L.）and Arachis wild species［J］.BMC Plant Biology,2009,9:35-48.

21.Gupta P K,Balyan H S,Sharma P C,et al.Microsatellites in plants:A new class of molecular marker［J］.Current sciences,1996,70(1):45-54.

22.Jung S,Abbott A,Jesudurai C,et al.Frequency,type,distribution and annotation of simple sequence repeats in Rosaceae ESTs［J］.Functional & integrative genomics,2005,5(3):136-143.

23.Gao L F,Tang J,Li H,et al.Analysis of microsatellites in major crops assessed by computational and experimental approaches［J］.Molecular Breed,2003,113:163-185.

24.Nicot N,Chiquet V,Gandon B,et al.Study of simple sequence repeat(SSR) markers from wheat expressed sequence tags(ESTs)［J］.Theory of Apply Genets,2004,109:800-805.

25.Aggarwal R K,Hendre P S,Varshney R K,et al.Identification,characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species［J］.Theoretical and Applied Genetics,2007,114:359-372.

26.Schorderet D F,Gartler S M.Analysis of CpG suppression in methylated and nonmethylated species［J］.PNAS,1992,89:957-961.

27.Akkaya M S,Bhagwat A A,Cregan P B.Length polymorphisms of simple sequence repeat DNA in soybean［J］.Genetics,1992,132:1131-1139.

28.Kumpatla S P,Mukhopadhyay S.Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species［J］.Genome,2005,48:985-998.

29.Zhang D X.Lepidopteran microsatellite DNA:redundant but promising［J］.Trends in Ecology and Evolution,2004,19:507-509.

30.Yadav H K,Ranjan A,Asif M H,et al.EST-derived SSR markers in Jatropha curcas L.:development,characterization,polymorphism,and transferability across the species/genera［J］.Tree Genetics & Genomes,2011,7(1):207-219.

31.Clement C R.1492 and the loss of Amazonian crop genetic resources.Ⅰ.The relation between domestication and human population decline［J］.Economic.Botany,1999,53:188-202.

32.Pickersgill B.Domestication of plants in the Americas:insights from Mendelian and molecular genetics［J］.Annual Botany,2007,100:925-940.

33.Potter D,Eriksson T,Evans R C.et al.Phylogeny and classification of Rosaceae［J］.Plant Systematics and Evolution,2007,266(12):5-43.

[1]	Hongxia XIA, Lilan LIU, Xuping ZHOU, Ke CHEN, Ying LI, Peigang KUANG, Geng SUN, Yanbao LEI. Selection of Suitable Mosses for Bare Rock and Steep Slope Greening after Jiuzhaigou Earthquake Based on the Analytic Hierarchy Process [J]. Bulletin of Botanical Research, 2023, 43(4): 540-549.
[2]	Mingyang CONG, Yongkun LI, Wenjing YANG, Puqing CHEN. Bryophyte Diversity of Underground Forests in Craters of Jingpohu Global Geopark [J]. Bulletin of Botanical Research, 2023, 43(3): 361-369.
[3]	Zhenggang XU, Hang XU, Xiutao PENG, Shijun LIANG, Rong LIU, Shanghua LUO, Juan XIAO. Effects of N addition on Root Exudates and Their Mediated Nutrient Rransformation Processes in a Betula albosinensis Burk Forest in Southwest China [J]. Bulletin of Botanical Research, 2023, 43(2): 194-206.
[4]	Shuzhen ZOU, Caijia YIN, Qian YANG, Long MA, Di KANG. Competition Pattern of Standing Trees in Secondary Pinus Forest in the Ziwuling Mountains, China [J]. Bulletin of Botanical Research, 2023, 43(1): 140-149.
[5]	Jinxia DU, Tingting SHEN, Haoran WANG, Yiping LIN, Huiyu LI, Lianfei ZHANG. Construction of Suppression Expression Vector and Genetic Transformation of BpSPL9 gene from Betula platyphylla [J]. Bulletin of Botanical Research, 2023, 43(1): 30-35.
[6]	Na LI, Xiaonan WANG. Screening and Phenotypic Identification of Seed Coat Pigmentation Mutants in Arabidopsis thaliana [J]. Bulletin of Botanical Research, 2023, 43(1): 59-68.
[7]	Xiaolu CAO, Qiaozhu ZHAO, Hua XING, Mengfei LI. Anatomical Structure of Seed and Morphological Character at Different Germination Stages of Sinopodophyllum hexandrum [J]. Bulletin of Botanical Research, 2022, 42(5): 746-752.
[8]	Yujin XU, Xihe WANG, Pingyang LI, Yulei LI, Dexiao LI, Yunyang WU, Quan SUN, Lili GE, Xiyang ZHAO. Effect of Fruit-Expander on Cone Performance of Pinus sylvestris var. mongolica [J]. Bulletin of Botanical Research, 2022, 42(5): 762-771.
[9]	Denggao LI, Rui LIN, Qinghui MU, Na ZHOU, Yanru ZHANG, Wei BAI. Cloning and Functional Analysis of StNPR4 gene in Solanum tuberosum [J]. Bulletin of Botanical Research, 2022, 42(5): 821-829.
[10]	Heming LI, Hongtao QIN, Deqiang WEI, Xu LI, Xingguo LAN. Prokaryotic Expression, Preparation Polyclonal Antibody and Protein Expression of BoMAPK4 of Ornamental Kale(Brassica oleracea var. acephala) [J]. Bulletin of Botanical Research, 2022, 42(4): 584-591.
[11]	Xun Li, Yan Zhang, Simeng Song, Yang Zhou, Jian Zhang. Dynamic Changes of Total Carbon Release During Mixed Decomposition of Leaf Litter of Pinus massoniana and Native Broad-leaved Tree Species [J]. Bulletin of Botanical Research, 2022, 42(2): 309-320.
[12]	Jie ZHANG, Rong-Rong LI, Jing-Xiang MENG, Yong ZHANG, Chong-Lu ZHONG. Phenotypic Variation and Genetic Diversity of Leaves Traits of Tabebuia and Handroanthus(Bignoniaceace) in China [J]. Bulletin of Botanical Research, 2021, 41(6): 851-861.
[13]	Wen-Hai HU, Yi-An XIAO, Xiao-Hong YAN, Zi-Piao YE, Jian-Jun ZENG, Xiao-Hong LI. Photoprotective Mechanisms under Low Temperature and High Light Stress of Photinia × fraseri and Osmanthus fragrans During Overwintering [J]. Bulletin of Botanical Research, 2021, 41(6): 938-946.
[14]	Zhi-Gang WEI, De-An XIA, Rui-Qi Wang, Yang ZHANG, Ying-Ying Liu, Ruo-Lin LI, Chuan-Ping YANG. Provenance Test of Pinus koraiensis in Different Types of Natural Secondary Forests in Xiaoxing’an Mountains [J]. Bulletin of Botanical Research, 2021, 41(5): 807-815.
[15]	Min WANG, Run-Hui ZHOU, Fei-Yan YU, Hong-Jun DONG, Cong-Lin CHEN, Jing YU, Jian-Feng HAO. Dynamic Changes of Undergrowth Species Diversity and Biomass of Eucalyptus robusta Plantations at Different Ages [J]. Bulletin of Botanical Research, 2021, 41(4): 496-505.