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Identification of microsatellites in cattle unigenes |
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| Authors: | Qiuliang Yan Yinghan Zhang Hongbin Li Caihong Wei Lili Niu Shan Guan Shangang Li Lixin Du |
| Institution: | 1. College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China;National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100094, China 2. College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China 3. National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100094, China 4. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China |
| 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%, respec-tively, 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. |
| Keywords: | cattle microsatellite expressed sequence tags EST-SSR |
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