Distribution and Molecular Marker of SSR in EST Resource of Casuarinaceae

doi:10.7525/j.issn.1673-5102.2016.01.016

Abstract

Abstract: There are 34 752 ESTs of Casuarinaceae in the database of NCBI, resulting in 12 062 non-redundant sequences(Unigene) with total length of 7 278.578 kb. 367 SSR were discovered to distribution on 353 Unigenes, the frequency and repeat motif types number of these EST-SSRs was 2.93% and 39, and the mean distance was 19.83 kb. Dinucleotide and trinucleotide repeats were the dominant types among the EST-SSRs, accounting for 57.77% and 34.06%, respectively. AG/CT(93.87%) and AAG/CTT(44.09%) were the most abundant motifs for dinucleotide and trinucleotide. There were 97 pairs of primers designed for the obtained EST-SSR, and 32 of all could be effectively amplified. By Blast analysis, 77.3% ESTs sequences containing SSR locus were homologous with functional sequences in non-redundant protein sequences databases. The homology with functions from Vitis vinifera had the greatest proportion(10.4%). By GO functional classification, 47.3% EST sequences containing SSR locus had at least one GO ontology, the sequences relevant to cellular components were most, and the functional items relevant to cytoplasm and nucleus were highest.

Key words: Casuarinaceae, EST, SSR

HU Pan1；ZHONG Chong-Lu1；ZHANG Yong1；JIANG Qing-Bin1；CHEN Yu1；CHEN Zhen1；HAN Qiang1；Khongsak Pinyopusarerk2；Didier Bogusz3. Distribution and Molecular Marker of SSR in EST Resource of Casuarinaceae[J]. Bulletin of Botanical Research, 2016, 36(1): 116-122.

References

1.Chen X,Cho Y G,McCouch S R.Sequence divergence of rice microsatellites in Oryza and other plant species［J］.Mol Gen Genomics,2002,268:331-343.

2.Fahima T,Röder M S,Grama A,et al.Microsatellite DNA polymorphism divergence in Triticum dicoccoides accessions highly resistant to yellow rust［J］.Theor Appl Genet,1998,96:187-195.

3.Huang X,Börner A,Röder M,et al.Assessing genetic diversity of wheat(Triticum aestivum L.)germplasm using microsatellite markers［J］.Theoretical and Applied Genetics,2002,105(5):699-707.

4.Loudet O,Chaillou S,Camilleri C,et al.Bay-0×Shahdara recombinant inbred line population:a powerful tool for the genetic dissection of complex traits in Arabidopsis［J］.Theoretical and Applied Genetics,2002,104(6-7):1173-1184.

5.Röder M S,Korzun V,Wendehake K,et al.A microsatellite map of wheat［J］.Genetics,1998,149(4):2007-2023.

6.Ma X F,Wanous M K,Houchins K,et al.Molecular linkage mapping in rye(Secale cereale L.)［J］.Theoretical and applied genetics,2001,102(4):517-523.

7.Gupta P K,Varshney R K.The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat［J］.Euphytica,2000,113(3):163-185.

8.Korzun V,Röder M,Worland A J,et al.Intra-chromosomal mapping of genes for dwarfing(Rht12) and verbalization response(Vrn1) in wheat by using RFLP and microsatellite markers［J］.Plant Breeding,1997,116(3):227-232.

9.Liu X,Smith C,Gill B.Identification of microsatellite markers linked to Russian wheat aphid resistance genes Dn4 and Dn6［J］.Theoretical and Applied Genetics,2002,104(6-7):1042-1048.

10.Buchanan F C,Adams L J,Littlejohn R P,et al.Determination of evolutionary relationships among sheep breeds using microsatellites［J］.Genomics,1994,22(2):397-403.

11.Li C D,Rossnagel B G,Scoles G J.The development of oat microsatellite markers and their use in identifying relationships among Avena species and oat cultivars［J］.Theoretical and Applied Genetics,2000,101(8):1259-1268.

12.Matsuoka Y,Mitchell S E,Kresovich S,et al.Microsatellites in Zea-variability,patterns of mutations,and use for evolutionary studies［J］.Theoretical and Applied Genetics,2002,104(2-3):436-450.

13.Cardle L,Ramsay L,Milbourne D,et al.Computational and experimental characterization of physically clustered simple sequence repeats in plants［J］.Genetics,2000,156(2):847-854.

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

15.Morgante M,Hanafey M,Powell W.Microsatellites are preferentially associated with non-repetitive DNA in plant genomes［J］.Nature genetics,2002,30(2):194-200.

16.Bundock P C,Potts B M,Vaillancourt R E.Detection and stability of quantitative trait loci(QTL) in Eucalyptus globulus［J］.Tree Genetics & Genomes,2008,4(1):85-95.

17.Freeman J S,Whittock S P,Potts B M,et al.QTL influencing growth and wood properties in Eucalyptus globulus［J］.Tree Genetics & Genomes,2009,5(4):713-722.

18.Byrne M,Murrell J C,Owen J V,et al.Mapping of quantitative trait loci influencing frost tolerance in Eucalyptus nitens［J］.Theoretical and Applied Genetics,1997,95(5-6):975-979.

19.Wilson K L,Johnson L A S.Casuarinaceae.Flora of Australia:Volume 3 Hamamelidales to Casuarinales［M］.Canberra:Australian Government Publishing Service,1989.

20.仲崇禄.木麻黄遗传变异规律的研究［D］.北京:中国林业科学研究院,2000.

21.葛菁萍,林鹏.厦门三种木麻黄属(Casuarina)植物的种内遗传变异和种间亲缘关系分析［J］.黑龙江大学自然科学学报,2002,19(4):110-114.

22.郭启荣,林益明,周涵滔.4种木麻黄亲缘关系的RAPD分析［J］.厦门大学学报:自然科学版,2003,42(3):378-383.

23.何坤益,萧如英,邓书麟.应用RAPD分子指纹研究木贼叶木麻黄国际种源之遗传变异［J］.台湾林业科学,2001,16(4):285-293.

24.黄桂华.短枝木麻黄种质资源遗传多样性的AFLP分析［D］.北京:中国林业科学研究院,2006.

25.Huang G H,Zhong C L,Su X H,et al.Genetic variation and structure of native and introduced Casuarina equisetifolia(L.Johnson) provenances［J］.Silvae Genetica,2009,58(1-2).

26.Ho Kuen-yih,Lee Shih-chieh.ISSR-based genetic diversity of Casuarina spp.in coastal windbreaks of Taiwan［J］.African Journal of Agriculture Research,2011,6(25):5664-5671.

27.Doyle J J.Trees within trees:genes and species,molecules and morphology［J］.Systems Biology,1997,46:537-553.

28.Falgueras J,Lara A J,Fernández-Pozo N,et al.SeqTrim:a high-throughput pipeline for preprocessing any type of sequence read［J］.BMC bioinformatics,2010,11(1):38.

29.Gordon D,Abajian C,Green P.Consed:a graphical toolfor sequence finishing［J］.Genome Res,1998,8:195-202.

30.Gordon D,Desmarais C,Green P.Automated finishingwith auto-finish［J］.Genome Res,2001,11:614-625.

31.Conesa A,Götz S,Carcía-Gómes JM,et al.Blast2go:a universal tool for annotation,visualization and analysis in functional genomics research［J］.Bioinformatics,2005,21(18):3674-3676.

32.Areshchenkova T,Ganal M W.Comparative analysis of polymorphism and chromosomal location of tomato microsatellite markers isolated from different sources［J］.Theoretical and Applied Genetics,2002,104(2-3):229-235.

33.吴春太,陈青,刘锐,等.油棕EST序列中SSR的分布特征分析［J］.中国油料作物学报,2012,34(1):101-105.

34.韩明利,崔娜,于志海,等.番茄果实EST资源SSR信息分析［J］.华北农学报,2011,26(4):213-217.

35.李永强,李宏伟,高丽锋,等.基于表达序列标签的微卫星标记(EST-SSRs)研究进展［J］.植物遗传资源学报,2004(5):91-95.

36.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.

37.詹少华,盛新颖,樊洪泓,等.大豆EST序列长度与SSR特性的关系［J］.大豆科学,2009,28(2):204-209.

38.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.

39.Thibodeau S N,Bren G,Schaid D.Microsatellite instability in cancer of the proximal colon［J］.Science,1993,260(5109):816-819.

40.Aaltonen L A,Lauri A,Leach F S,et al.Clues to the pathogenesis of familial colorectal cancer［J］.Science,1993,260(5109):812-816.

41.张新叶,宋丛文,张亚东,等.杨树EST-SSR 标记的开发［J］.林业科学,2009,45(9):53-59.

42.Ellis J R,Burke J M.EST-SSRs as a resource for population genetic analyses［J］.Heredity,2007,99:125-132.

[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]	Yuanyuan CAI, Jibenben XIA, Wenhan YING, Jieyao WANG, Tao XIE, Kongya XING, Xuanjun FENG, Xuejun HUA. Detailed Phenotypical Analysis on the Mutant ssr1-2 Encoding a Mitochondrial Protein of Arabidopsis thaliana [J]. Bulletin of Botanical Research, 2023, 43(3): 421-431.
[4]	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.
[5]	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.
[6]	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.
[7]	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.
[8]	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.
[9]	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.
[10]	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.
[11]	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.
[12]	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.
[13]	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.
[14]	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.
[15]	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.