Identification of microsatellites in cattle unigenes

Qiuliang Yan; Yinghan Zhang; Hongbin Li; Caihong Wei; Lili Niu; Shan Guan; Shangang Li; Lixin Du

doi:10.1016/S1673-8527(08)60037-5

Volume 35 Issue 5

May 2008

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Article Navigation > Journal of Genetics and Genomics > 2008 > 35(5): 261-266

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Identification of microsatellites in cattle unigenes

doi: 10.1016/S1673-8527(08)60037-5

a
College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China
b
National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100094, China
c
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China

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Corresponding author: E-mail address: lxdu@263.net (Lixin Du)
Received Date: 2007-08-15
Accepted Date: 2008-02-19
Rev Recd Date: 2008-02-18

Available Online: 2008-05-20

Publish Date: 2008-05-20

Abstract

Abstract

To identify EST-SSR molecular markers, 41,986 cattle UniGene sequences from NCBI were mined for analyzing SSRs. A total of 1,831 SSRs were identified from 1,666 ESTs, which represented an average density of 19.88 kb per SSR. The frequency of EST-SSRs was 4.0%. The dinucleotide repeat motif was the most abundant SSR, accounting for 54%, followed by 22%, 13%, 7% and 4%, respectively, for tri-, hexa-, penta- and tetra-nucleotide repeats. Depending upon the length of the repeat unit, the length of microsatellites varied from 14 to 86 bp. Among the di- and tri-nucleotide repeats, AC/TG (57%) and AGC (12%) were the most abundant type. Annotation of EST-SSRs was also carried out. Three hundred primer pairs were randomly designed using Prime Premier 5.0 program and Oligo 5.0 for further experimental validation.
- cattle,
- microsatellite,
- expressed sequence tags,
- EST-SSR

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References(26)

References

[1]	Adams, M.D., Kelley, J.M., Gocayne, J.D. et al. Complementary DNA sequencing, expressed sequence tags and human genome project Science, 252 (1991),pp. 1651-1656
[2]	Andrés-Mateos, E., Cruces, J., Renart, J. et al. Gene, 380 (2006),pp. 54-61
[3]	Cardle, L., Ramsay, L., Milbourne, D. et al. Computational and experimental characterization of physically clustered simple sequence repeats in plants Genetics, 156 (2002),pp. 847-854
[4]	Gao, L., Tang, J., Li, H. et al. Analysis of microsatellites in major crops assessed by computational and experimental approaches J. Mol. Biol., 12 (2003),pp. 245-261
[5]	Gupta, P.K., Balyan, H.S., Sharma, P.C. et al. Microsatellites in plants, a new class of molecular markers Curr. Sci., 70 (1996),pp. 45-54
[6]	Gupta, P.K., Rustgi, S., Sharma, S. et al. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat Mol. Genet. Genomics, 270 (2003),pp. 315-323
[7]	Hackauf, B., Wehling, P. Identification of microsatellite polymorphisms in an expressed portion of the rye genome Plant Breed., 121 (2002),pp. 17-25
[8]	Ju, Z., Wells, M.C., Martinez, A. et al. In Silico Biol., 5 (2005),pp. 439-463
[9]	Kantety, R.V., La, R.M., Matthews, D.E. et al. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat Plant Mol. Biol., 48 (2002),pp. 501-510
[10]	Katti, M.V., Ranjekar, P.K., Gupta, V.S. Differential distribution of simple sequence repeats in eukaryotic genome sequences Mol. Biol. Evol., 18 (2001),pp. 1161-1167
[11]	Kumpatla, S.P., Mukhopadhyay, S. Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species Genome, 48 (2005),pp. 985-998
[12]	Li, Y.C., Korol, A.B., Fahima, T. et al. Microsatellites within genes, structure, function, and evolution Mol. Biol. Evol., 21 (2004),pp. 991-1007
[13]	Morgante, M., Hanafey, M., Powell, W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes Nat. Genet., 30 (2002),pp. 194-200
[14]	Nicot, N., Chiquet, V., Gandon, B. et al. Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs) Theor. Appl. Genet., 109 (2004),pp. 800-805
[15]	Olivero, M., Ruggiero, T., Coltella, N. et al. Amplification of repeat-containing transcribed sequences (ARTS), a transcriptome fingerprinting strategy to detect functionally relevant microsatellite mutations in cancer Nucleic Acids Res., 31 (2003),p. e33
[16]	Peng, J.H., Lapitan, N.L. Characterization of EST-derived microsatellites in the wheat genome and development of eSSR markers Funct. Integr. Genomics, 5 (2005),pp. 80-96
[17]	Perez, F., Ortiz, J., Zhinaula, M. et al. Mar. Biotechnol. (N.Y.), 7 (2005),pp. 554-569
[18]	Pinto, L.R., Oliveira, K.M., Ulian, E.C. et al. Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats Genome, 47 (2004),pp. 795-804
[19]	Powell, W., Machray, G.C., Provan, J. Polymorphism revealed by simple sequence repeats Trends Plant Sci., 1 (1996),pp. 215-222
[20]	Rohrer, G.A., Fahrenkrug, S.C., Nonneman, D. et al. Mapping microsatellite markers Identified in porcine EST sequences Anim. Genet., 33 (2002),pp. 372-376
[21]	Scott, K.D., Eggler, P., Seaton, G. et al. Analysis of SSRs derived from grape ESTs Theor. Appl. Genet., 100 (2000),pp. 723-726
[22]	Serapion, J., Kucuktas, H., Feng, J. et al. J. Mar. Biotechnol., 6 (2004),pp. 364-377
[23]	Thiel, T., Michalek, W., Varshney, R.K. et al. Theor. Appl. Genet., 106 (2003),pp. 411-422
[24]	Toth, G., Gaspari, Z., Jurka, J. Microsatellites in different eukaryotic genome, survey and analysis Genome Res., 10 (2000),pp. 1967-1981
[25]	Varshney, R.K., Thiel, T., Stein, N. et al. Cell Mol. Biol. Lett., 7 (2002),pp. 537-546
[26]	Wierdl, M., Dominska, M., Petes, T.D. Microsatellite instability in yeast, dependence on the length of the microsatellite Genetics, 146 (1997),pp. 769-779